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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Aging Neurosci.</journal-id>
<journal-title>Frontiers in Aging Neuroscience</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Aging Neurosci.</abbrev-journal-title>
<issn pub-type="epub">1663-4365</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fnagi.2017.00403</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Neuroscience</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Prebiotic Effect of Fructooligosaccharides from <italic>Morinda officinalis</italic> on Alzheimer&#x2019;s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name><surname>Chen</surname> <given-names>Diling</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/377525/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Yang</surname> <given-names>Xin</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Yang</surname> <given-names>Jian</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/431207/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Lai</surname> <given-names>Guoxiao</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Yong</surname> <given-names>Tianqiao</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Tang</surname> <given-names>Xiaocui</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Shuai</surname> <given-names>Ou</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Zhou</surname> <given-names>Gailian</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Xie</surname> <given-names>Yizhen</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>&#x002A;</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Wu</surname> <given-names>Qingping</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/254423/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Chinese Academy of Sciences</institution>, <addr-line>Guangzhou</addr-line>, <country>China</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Pharmacy, The Fifth Affiliated Hospital of Guangzhou Medical University</institution>, <addr-line>Guangzhou</addr-line>, <country>China</country></aff>
<aff id="aff3"><sup>3</sup><institution>Guangxi University of Chinese Medicine</institution>, <addr-line>Nanning</addr-line>, <country>China</country></aff>
<aff id="aff4"><sup>4</sup><institution>Guangdong Yuewei Edible Fungi Technology Co., Ltd.</institution>, <addr-line>Guangzhou</addr-line>, <country>China</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: <italic>Ghulam Md Ashraf, King Abdulaziz University, Saudi Arabia</italic></p></fn>
<fn fn-type="edited-by"><p>Reviewed by: <italic>Rongqiao He, Institute of Biophysics (CAS), China; Tarique Khan, Buck Institute for Research on Aging, United States</italic></p></fn>
<fn fn-type="corresp" id="fn001"><p>&#x002A;Correspondence: <italic>Diling Chen, <email>diling1983@163.com</email> Yizhen Xie, <email>xieyizhen@126.com</email></italic></p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>08</day>
<month>12</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection">
<year>2017</year>
</pub-date>
<volume>09</volume>
<elocation-id>403</elocation-id>
<history>
<date date-type="received">
<day>08</day>
<month>09</month>
<year>2017</year>
</date>
<date date-type="accepted">
<day>22</day>
<month>11</month>
<year>2017</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2017 Chen, Yang, Yang, Lai, Yong, Tang, Shuai, Zhou, Xie and Wu.</copyright-statement>
<copyright-year>2017</copyright-year>
<copyright-holder>Chen, Yang, Yang, Lai, Yong, Tang, Shuai, Zhou, Xie and Wu</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>Gut microbiota influences the central nervous system disorders such as Alzheimer&#x2019;s disease (AD). The prebiotics and probiotics can improve the host cognition. A previous study demonstrated that fructooligosaccharides from <italic>Morinda officinalis</italic> (OMO) exert effective memory improvements in AD-like animals, thereby considered as potential prebiotics; however, the underlying mechanism still remains enigma. Thus, the present study investigated whether OMO is effective in alleviating AD by targeting the microbiota-gut-brain axis. OMO was administered in rats with AD-like symptoms (<sc>D</sc>-galactose- and A&#x03B2;<sub>1-42</sub>-induced deficient rats). Significant and systematic deterioration in AD-like animals were identified, including learning and memory abilities, histological changes, production of cytokines, and microbial community shifts. Behavioral experiments demonstrated that OMO administration can ameliorate the learning and memory abilities in both AD-like animals significantly. AD parameters showed that OMO administration cannot only improve oxidative stress and inflammation disorder, but also regulate the synthesis and secretion of neurotransmitter. Histological changes indicated that OMO administration ameliorates the swelling of brain tissues, neuronal apoptosis, and down-regulation of the expression of AD intracellular markers (Tau and A&#x03B2;<sub>1-42</sub>). 16S rRNA sequencing of gut microbiota indicated that OMO administration maintains the diversity and stability of the microbial community. In addition, OMO regulated the composition and metabolism of gut microbiota in inflammatory bowel disease (IBD) mice model treated by overdosed antibiotics and thus showed the prebiotic potential. Moreover, gut microbiota plays a major role in neurodevelopment, leading to alterations in gene expression in critical brain and intestinal regions, thereby resulting in perturbation to the programming of normal cognitive behaviors. Taken together, our findings suggest that the therapeutic effect of the traditional medicine, <italic>M. officinalis</italic>, on various neurological diseases such as AD, is at least partially contributed by its naturally occurring chemical constituent, OMO, via modulating the interaction between gut ecology and brain physiology.</p>
</abstract>
<kwd-group>
<kwd>fructooligosaccharides</kwd>
<kwd>prebiotics</kwd>
<kwd>Alzheimer&#x2019;s disease</kwd>
<kwd>behavior</kwd>
<kwd>microbiota-gut-brain axis</kwd>
</kwd-group>
<counts>
<fig-count count="15"/>
<table-count count="2"/>
<equation-count count="0"/>
<ref-count count="74"/>
<page-count count="28"/>
<word-count count="0"/>
</counts>
</article-meta>
</front>
<body>
<sec><title>Introduction</title>
<p>Gut microbiota is associated with several diseases, including neurodegenerative diseases such as Parkinson&#x2019;s disease (PD) and Alzheimer&#x2019;s disease (AD) (<xref ref-type="bibr" rid="B46">Petra et al., 2015</xref>; <xref ref-type="bibr" rid="B32">Jiang et al., 2017</xref>). Notably, the microbiota-gut-brain axis is a bi-directional communication system that is not fully understood; however, it is known to include neural, immune, endocrine, and metabolic pathways. Studies in germ-free animals and those exposed to pathogenic microbial infections, antibiotics, probiotics, or fecal microbiota transplantation suggest the link of gut microbiota with host cognition or AD-related pathogenesis (<xref ref-type="bibr" rid="B47">Pistollato et al., 2016</xref>; <xref ref-type="bibr" rid="B26">Harach et al., 2017</xref>; <xref ref-type="bibr" rid="B41">Liu et al., 2017</xref>; <xref ref-type="bibr" rid="B50">Rieder et al., 2017</xref>; <xref ref-type="bibr" rid="B52">Russo et al., 2017</xref>).</p>
<p>Several studies have supported the theory of the occurrence of a pathway of communication between the gut and the brain, modulated by gut microbiota (<xref ref-type="bibr" rid="B23">Gareau, 2014</xref>; <xref ref-type="bibr" rid="B43">Mayer et al., 2014</xref>). It has been speculated that targeting the microbiota can affect the behavior and modulate brain plasticity and cognitive functions while aging (<xref ref-type="bibr" rid="B35">Leung and Thuret, 2015</xref>). Some studies demonstrated that gut-targeted intervention by consuming <italic>lactic acid bacteria</italic> such as those in yogurt, could improve or delay the onset of cognitive decline associated with aging (<xref ref-type="bibr" rid="B33">Jung et al., 2012</xref>; <xref ref-type="bibr" rid="B16">Choi et al., 2015</xref>; <xref ref-type="bibr" rid="B54">Scott et al., 2017</xref>). Therefore, using probiotics for ameliorating the cognitive and behavioral disorders could be a potential treatment.</p>
<p>The hypothesis that the microbiota-gut-brain axis (<xref ref-type="bibr" rid="B49">Rhee et al., 2009</xref>) plays a critical role in health and disease, including neuropsychiatric disorders (<xref ref-type="bibr" rid="B41">Liu et al., 2017</xref>), is rapidly progressing. Nurturing a beneficial gut microbiome with prebiotics, such as fructooligosaccharides and inulin, is an appealing but under-investigated microbiota-induced manipulation. A previous study showed that the prebiotic treatment could modify the behavior across domains relevant to anxiety, depression, cognition, stress response, and social behavior (<xref ref-type="bibr" rid="B9">Burokas et al., 2017</xref>). Previous findings strengthened the evidence supporting the therapeutic targeting of gut microbiota in brain-gut axis disorders, thereby opening new prospects in the field of nutritional neuropsychopharmacology. Thus, it is imperative to develop novel and effective drugs or foods with prebiotic effects from natural resources.</p>
<p><italic>Morinda officinalis</italic> How. (<italic>M. officinalis</italic>), as a Chinese traditional natural herbal medicine, contains a number of active components. Reportedly, the content of saccharides in <italic>M. officinalis</italic> radix is 49.79&#x2013;58.25%, which is highly composed of oligosaccharides, such as inulin-type hexasaccharide exerting antidepressant effects in the model systems (<xref ref-type="bibr" rid="B11">Cai et al., 1996</xref>; <xref ref-type="bibr" rid="B38">Li et al., 2001</xref>). This phenomenon can be effectuated by up-regulating the expression of neurotrophic factors and/or down-regulating the [Ca<sup>2+</sup>]<sub>i</sub> overloading (<xref ref-type="bibr" rid="B37">Li et al., 2004</xref>). Bajijiasu, another oligosaccharide, protects PC12 cells from A&#x03B2;<sub>25-35</sub>-induced neurotoxicity (<xref ref-type="bibr" rid="B14">Chen et al., 2013</xref>), ameliorates the cognitive deficits induced by <sc>D</sc>-galactose in mice, and protects against ischemia-induced neuronal damage or death (<xref ref-type="bibr" rid="B57">Tan et al., 2000a</xref>,<xref ref-type="bibr" rid="B58">b</xref>). Our previous study suggested that oligosaccharide extracted from <italic>M. officinalis</italic> (OMO) might inhibit the oxidative stress and neuronal apoptosis, restore normal energy metabolism, as well as, increase the cell viability and mitochondrial membrane potential in AD animal models significantly (<xref ref-type="bibr" rid="B12">Chen et al., 2014a</xref>). However, the underlying mechanism is yet to be elucidated.</p>
<p>Alzheimer&#x2019;s disease is the most common neurodegenerative disorder, affecting approximately >5% of the worldwide population aged >65 years, annually. AD is a chronic neurodegenerative disease that frequently exhibits a slow progression accompanied by a greater recession of the disease over a period. Although the cause of AD is poorly understood, among various biochemical and morphological events, the presence of neurofibrillary tangles, senile plaques, and neuronal and synaptic loss are considerably noted (<xref ref-type="bibr" rid="B13">Chen et al., 2017</xref>). Several pieces of evidence have confirmed that the accumulation of intracellular &#x03B2;-amyloid (A&#x03B2;) may be an early event in the development of AD. A&#x03B2; is a peptide comprised of 36&#x2013;43 amino acids formed by a large transmembrane glycoprotein, such as amyloid precursor protein (APP), expressed on the cell. A&#x03B2; may activate the inflammatory and neurotoxic processes, including the excessive generation of free radicals and oxidative damage among intracellular proteins and other macromolecules (<xref ref-type="bibr" rid="B1">Abbott, 2011</xref>). <sc>D</sc>-galactose can form advanced glycation end products (AGEs). The administration of <sc>D</sc>-galactose to human populations can induce cognitive deficits and disruptions in the synaptic communication. Thus, <sc>D</sc>-galactose-treated rats with synaptic disruption and memory impairment have been extensively used as model rodents (<xref ref-type="bibr" rid="B73">Zhan et al., 2014</xref>; <xref ref-type="bibr" rid="B21">Gao et al., 2016</xref>; <xref ref-type="bibr" rid="B30">Huang et al., 2016</xref>; <xref ref-type="bibr" rid="B36">Li et al., 2016</xref>). In our previous, we have used these two models to screen the effective compounds for curing the AD (<xref ref-type="bibr" rid="B15">Chen et al., 2014b</xref>, <xref ref-type="bibr" rid="B13">2017</xref>). Thus, in this study, the two AD-like models were induced by <sc>D</sc>-galactose and A&#x03B2;, respectively.</p>
<p>Herein, we investigated whether OMO is effective in alleviating AD by targeting the microbiota-gut-brain axis. OMO was administered in rats exhibiting AD-like symptoms induced by <sc>D</sc>-galactose and A&#x03B2;<sub>1-42</sub>, respectively. Some indexes and histological deterioration, including learning and memory abilities, histological alterations, production of cytokines, microbial communities, and transcriptome in small intestine and brain, were identified in AD-like animals. And the prebiotics were directly evaluated in an overdose antibiotics-treated trinitro-benzene-sulfonic acid (TNBS)-induced mice model.</p>
</sec>
<sec id="s1" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec><title>Animal Models and Treatments</title>
<p>Adult male Sprague&#x2013;Dawley rats (180&#x2013;220 g) and C57 mice (18&#x2013;22 g, 10-moth-old) obtained from the Center of Laboratory Animal of Guangdong Province, SCXK [Yue] 2008-0020, SYXK [Yue] 2008-0085) were pair-housed in plastic cages in a temperature-controlled (25&#x00B0;C) colony room at a 12/12 h light/dark cycle. Food and water were available <italic>ad libitum</italic>. All experimental protocols were approved by the Center of Laboratory Animals of the Guangdong Institute of Microbiology (GT-IACUC20160426). All efforts were made to minimize the number of animals used.</p>
<sec><title><sc>D</sc>-Galactose-Induced Deficient Rats and Treatment</title>
<p>The rats were randomly divided into four groups as follows: control group received distilled water orally, model group received intraperitoneal injection (i.p.) of 100 mg/kg/d <sc>D</sc>-galactose (<xref ref-type="bibr" rid="B74">Zhong et al., 2016</xref>; <xref ref-type="bibr" rid="B13">Chen et al., 2017</xref>; <xref ref-type="bibr" rid="B39">Liang et al., 2017</xref>), low-dose group was administered <sc>D</sc>-galactose (100 mg/kg/d) by i.p. and gavage at a dosage of 50 mg/[kg&#x22C5;d] OMO, and high-dose group received <sc>D</sc>-galactose (100 mg/kg/d) by i.p. and gavage at a dosage of 100 mg/[kg&#x22C5;d] OMO daily in the morning. Every group consisted of eight animals, and the duration of the procedure was 8 weeks.</p>
</sec>
<sec><title>A&#x03B2;<sub>1-42</sub>-Induced Deficient Rats and Treatment</title>
<p>The procedures were similar to those described previously (<xref ref-type="bibr" rid="B15">Chen et al., 2014b</xref>). Rats were anesthetized using 30 g/L pentobarbital sodium (40 mg/kg, i.p.; Sigma&#x2013;Aldrich) and placed in a stereotaxic frame (RWD Life Science Co., Ltd., Shenzhen, China). The hair was shaved, scalp opened, and holes drilled with an electric dental drill (brushless motor, 30,000 rpm) according to the mouse brain atlas (AP-3.6 mm, ML &#x00B1; 2.5 mm, DV3.0 mm). Then, 5 &#x03BC;L (10 &#x03BC;g) A&#x03B2;<sub>1-42</sub> in a fibrillar state (<xref ref-type="bibr" rid="B14">Chen et al., 2013</xref>) was slowly injected into the CA1 region of the hippocampus over a 5-min period in one hole, and the needle was retained inside for an additional 5 min. Subsequently, the wound was sutured, and penicillin (30 U/kg) was injected intramuscularly to protect against infection. Finally, the rats were isolated in a warm box until consciousness was recovered.</p>
<p>After 15 days, the rats were screened with water maze tests to identify the animals that were appropriate models, followed by random categorization into four groups as follows: control group (received saline and distilled water orally), model group (received A&#x03B2;<sub>1-42</sub> and distilled water orally), low-dose group (received A&#x03B2;<sub>1-42</sub> and OMO 50 mg/[kg&#x22C5;d] orally), high-dose group (received A&#x03B2;<sub>1-42</sub> and OMO 100 mg/[kg&#x22C5;d] orally). Every group consisted of seven animals, and the duration of the experiments was 28 days.</p>
</sec>
</sec>
<sec><title>Water Maze Tests</title>
<p>The spatial learning and memory abilities of the rats were tested using the Morris water maze (MWM, DMS-2, Chinese Academy of Medical Sciences Institute of Medicine). The MWM consisted of a circular opaque fiberglass pool (200 cm diameter) filled with water (25 &#x00B1; 1&#x00B0;C). The pool was surrounded by light blue curtains, and three distal visual cues were fixed on the curtains. A total of four floor light sources of equal power provided uniform illumination to the pool and testing room. A CCD camera was placed above the center of the pool in order to record the swim paths of the animals. The video output was digitized by an EthoVision tracking system (Noldus, Leesburg, VA, United States). The tests included three periods: initial spatial training, spatial reversal training, and the probe test; the procedures were same as those described previously (<xref ref-type="bibr" rid="B15">Chen et al., 2014b</xref>).</p>
</sec>
<sec><title>Evaluation of AD Parameters</title>
<p>The appearance, behavior, and fur color of the animals were observed and documented daily. The weights of the animals were measured every 3 days during the period of drug administration. Following the MWM, the blood and serum were acquired, and the brains of the animals were dissected. Routine index and cytokines (<xref ref-type="bibr" rid="B68">Wang et al., 2016</xref>), including the production of cytokines interleukins [(1L)-1&#x03B1;, 1L-2, 1L-8, 1L-10, 1L-11, IL-12], tumor necrosis factor (TNF)-&#x03B3;, TNF-&#x03B1;, vascular endothelial growth factor (VGEF), human macrophage inflammatory protein-1&#x03B1; (MIP-&#x03B1;), and macrophage colony-stimulating factor (M-CSF), activities of malondialdehyde (MDA), total superoxide dismutase (T-SOD), catalase (CAT), glutathione reductase (GSH-Px), and levels of acetylcholine (ACh), acetylcholinesterase (AChE), and Na<sup>+</sup>/K<sup>+</sup>-ATPase, and some monoamine neurotransmitters, were measured.</p>
<p>A total of three brains, small intestine, and other tissues from each group were fixed in 4% paraformaldehyde and prepared as paraffin sections that were stained with hematoxylin-eosin (H&#x0026;E) and immunohistochemistry (IHC) before examining under light microscopy (<xref ref-type="bibr" rid="B72">Zeng et al., 2013</xref>; <xref ref-type="bibr" rid="B15">Chen et al., 2014b</xref>).</p>
</sec>
<sec><title>Evaluation of Prebiotic Effects of OMO in TNBS-Induced Mice</title>
<p>After 24 h fasting, the mice were anesthetized by intraperitoneal injection of 2% sodium pentobarbital (0.2 ml/100 g), followed by intubation (latex tubing of 2 mm diameter, lubricated with edible oil before usage) from the anus, gently inserted into the lumen about 4.0 cm. Subsequently, 150 mg/kg of TNBS (Sigma&#x2013;Aldrich, St. Louis, MO, United States, solubilized in 50% ethanol) solution was injected through the latex tubing, the rats were hanged upside down for 30 s to ensure complete seepage of the mixture into the lumen without leakage (<xref ref-type="bibr" rid="B69">Wei et al., 2017</xref>). Then, the animals were randomly divided into nine groups (<italic>n</italic> = 9): control, model, model and high-dose antibiotics, OMO (100 mg/kg/d), <italic>Bifidobacterium</italic>, OMO and high-dose antibiotics, OMO and <italic>Bifidobacterium</italic>, <italic>Bifidobacterium</italic> and high-dose antibiotics, OMO and <italic>Bifidobacterium</italic> and high-dose antibiotics. All the antibiotics were administered for 4 days, then inflammatory bowel disease (IBD) was induced with TNBS, followed 7-day drug treatments and TNBS induction, followed by an additional 4-day drug treatments.</p>
<p>Consequently, the mice were anesthetized by intraperitoneal injection of 2% sodium pentobarbital (0.25 ml/100 g). The blood plasma was collected by abdominal aortic method and serum by centrifugation (1500 r/min, 10 min). Then, the serum was assessed for the production of cytokines GM-CSF (granulocyte-macrophage colony-stimulating factor), TNF-&#x03B3;, 1L-10, IL-12, 1L-17&#x03B1;, 1L-4, TNF-&#x03B1;, and VGEF. The colon and spleen obtained from the rats were fixed in 4% paraformaldehyde at pH 7.4 for further pathological observations, and the cecum contents were collected for 16S rRNA gene-based analysis.</p>
</sec>
<sec><title>Microbiome Analysis</title>
<p>Fresh fecal samples were collected before fasting of the rats and stored at -80&#x00B0;C. Frozen microbial DNA was isolated from mice cecal sample with total mass ranging from 1.2 to 20.0 ng and preserved at -20&#x00B0;C. The microbial 16S rRNA genes were amplified using the forward primer 5&#x2032;-CCTAYGGGRBGCASCAG-3&#x2032; and reverse primer 5&#x2032;-GGACTACNNGGGTATCTAAT-3&#x2032; for rats. Each amplified product was concentrated via solid-phase reversible immobilization and quantified by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent, United States). After quantification of DNA concentration by NanoDrop, each sample was diluted to 1 &#x00D7; 10<sup>9</sup> molecules/&#x03BC;L in TE buffer and pooled. Subsequently, 20 &#x03BC;L of the pooled mixture was used for sequencing on Illumina MiSeq sequencing platform according to the manufacturer&#x2019;s instructions. The resulting reads were analyzed as described previously (<xref ref-type="bibr" rid="B40">Ling et al., 2014</xref>).</p>
</sec>
<sec><title>Transcriptome Analysis</title>
<p>The RNA-seq transcriptome library was prepared using the TruSeq<sup>TM</sup> RNA Sample Preparation Kit (Illumina, San Diego, CA, United States). <italic>De novo</italic> assembly and annotation identified the differentially expressed genes (DEGs) between different treatments; the expression level of each transcript was measured according to the fragments/kb of exon per million mapped reads method. RSEM<sup><xref ref-type="fn" rid="fn01">1</xref></sup> was used to quantify the abundance of genes and isoforms. The R statistical package software EdgeR<sup><xref ref-type="fn" rid="fn02">2</xref></sup> was used for the analysis of differential expression. Functional enrichment analysis was performed to identify the DEGs enriched significantly in Gene Ontology (GO) and metabolic pathways at Bonferroni-corrected <italic>p</italic>-value &#x2264; 0.05 as compared to the whole- transcriptome background. GO functional enrichment and KEGG pathway analyses were performed using Goatools<sup><xref ref-type="fn" rid="fn03">3</xref></sup> and KOBAS<sup><xref ref-type="fn" rid="fn04">4</xref></sup>, respectively (<xref ref-type="bibr" rid="B67">Wang et al., 2010</xref>; <xref ref-type="bibr" rid="B10">Cabili et al., 2011</xref>; <xref ref-type="bibr" rid="B56">Sun et al., 2013</xref>; <xref ref-type="bibr" rid="B60">Trapnell et al., 2013</xref>).</p>
</sec>
<sec><title>Statistical Analysis</title>
<p>All data are described as the means &#x00B1; standard deviations (SD) of at least three independent experiments. The significant differences between treatments were analyzed by one-way analysis of variance (ANOVA) test at <italic>p</italic> &#x003C; 0.05 using statistical package for the social sciences (SPSS, Abacus Concepts, Berkeley, CA, United States) and Prism5 (GraphPad, San Diego, CA, United States) software.</p>
</sec>
</sec>
<sec><title>Results</title>
<sec><title>Effects of OMO in <sc>D</sc>-Galactose-Induced Deficient Rats</title>
<sec><title>Antioxidative and Neuroprotective Effects, Activation of Energy Metabolism and Regulation of Acetylcholine Esterase by OMO in <sc>D</sc>-Galactose-Induced Deficient Rats</title>
<p>The fur of the treated animals was much smoother than that of the model group. The average weight between the treated and the model groups did not differ significantly (<italic>p</italic> > 0.05); the animals weighed approximately 320 g at the beginning and 500 g at the end of the experiment (<bold>Figure <xref ref-type="fig" rid="F1">1A</xref></bold>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>Effect of OMO in <sc>D</sc>-galactose-induced deficient rats. <bold>(A)</bold> Body weight changes during the treatments time. <bold>(B)</bold> Escape latency in the MWM. <bold>(C)</bold> Swimming time in the platform quadrant during the spatial probe test. <bold>(D)</bold> Effect on SOD, MDA, CAT, GSH-Px TchE, Ach, and Na<sup>+</sup>/K<sup>+</sup>-ATPase levels. <bold>(E)</bold> Histopathological changes in the intestine and brain. The graph Control, control group; Model, model group; OMO-50 mg, low-dose group that received <sc>D</sc>-galactose (100 mg/kg/d) by i.p. and gavage at a dosage of 50 mg/[kg&#x22C5;d] in OMO; OMO-100 mg, high-dose group that received <sc>D</sc>-galactose (100 mg/kg/d) i.p. and gavage at a dosage of 100 mg/[kg&#x22C5;d] in OMO. Values are represented as mean &#x00B1; SD (<italic>n</italic> = 6) and expressed as the percentage of the control group, <sup>#</sup><italic>p</italic> &#x003C; 0.01 vs. control group, <sup>&#x2217;</sup><italic>p</italic> &#x003C; 0.05 vs. model group, <sup>&#x2217;&#x2217;</sup><italic>p</italic> &#x003C; 0.01 vs. model group.</p></caption>
<graphic xlink:href="fnagi-09-00403-g001.tif"/>
</fig>
<p>Compared to the model group, the incubation period for each OMO-treated group was significantly shorter. The incubation period for the low-dose OMO group was (86.37 &#x00B1; 11.46 s) and that for the high-dose group was (82.00 &#x00B1; 19.44 s) on the 1st day. Compared to the model group, the differences were significant (<italic>p</italic> &#x003C; 0.01). On the 4th day, the incubation period for the low-dose OMO group was (39.30 &#x00B1; 5.63 s) and that for the high-dose group was 30.74 &#x00B1; 3.69 s; the differences were significant as compared to the model group (<italic>p</italic> &#x003C; 0.01; <bold>Figure <xref ref-type="fig" rid="F1">1B</xref></bold>). These results demonstrated that OMO administration could ameliorate <sc>D</sc>-galactose-induced learning and memory dysfunction in rats.</p>
<p>Probe test results did not reveal any significant differences (<italic>p</italic> > 0.05) among the groups with respect to total swimming distance or speed. The swimming time of the control group in the NW quadrant (28.00 &#x00B1; 0.81 s) was significantly longer than that in the other three quadrants (24.36 &#x00B1; 0.40, 24.21 &#x00B1; 1.33, and 25.43 &#x00B1; 1.465 s; <italic>p</italic> &#x003C; 0.01). The swimming time in the NW quadrant of the model group was 25.23 &#x00B1; 1.04 s, which was significantly shorter than the control group (<italic>p</italic> &#x003C; 0.01), suggesting that the rats remembered the location of the placement of the platform. The swimming durations of the low- and high-dose OMO groups were 27.13 &#x00B1; 0.85 and 29.00 &#x00B1; 1.08 s, respectively, which were significantly longer than the model group. Compared to the model group, the differences were significant (<italic>p</italic> &#x003C; 0.01; <bold>Figure <xref ref-type="fig" rid="F1">1C</xref></bold>).</p>
<p>As shown in <bold>Figure <xref ref-type="fig" rid="F1">1D</xref></bold>, the SOD levels in the low- and high-dose OMO groups were 95.05 &#x00B1; 1.21, and 97.70 &#x00B1; 1.43 (% of control), respectively, as compared to 90.45 &#x00B1; 2.17 in the model groups. The differences were significant as compared to the model group (<italic>p</italic> &#x003C; 0.05). In addition, the levels of GSH-Px and CAT showed similar trends, while that of the MDA showed opposite trends, suggesting that OMO encouraged SOD, MDA, CAT, and inhibited MDA production, thereby indicating that OMO administration can enhance the antioxidative activities in the <sc>D</sc>-galactose-induced deficient rats.</p>
<p>To evaluate the protective efficacy of OMO on the energy metabolism in <sc>D</sc>-galactose-treated rats, we measured the Na<sup>+</sup>/K<sup>+</sup>-ATPase levels in brain tissue. As shown in <bold>Figure <xref ref-type="fig" rid="F1">1D</xref></bold>, the levels of Na<sup>+</sup>/K<sup>+</sup>-ATPase were significantly lower in the model group (73.53 &#x00B1; 5.17% of control) as compared to the control group (<italic>p</italic> &#x003C; 0.05). The levels of all the OMO-treated groups (90.15 &#x00B1; 2.08 for low-dose, 90.83 &#x00B1; 1.64 for high-dose) were increased significantly, and the differences were significantly different as compared to the model group (<italic>p</italic> &#x003C; 0.05). These levels were based on the concentration-dependent activities; however, the specific underlying mechanism necessitates further studies.</p>
<p>Cholinergic system damage and abnormal ACh levels are observed in AD patients. The results are illustrated in <bold>Figure <xref ref-type="fig" rid="F1">1D</xref></bold>. As compared to the model group (89.85 &#x00B1; 1.93% of control), after treatment with different concentrations (50 and 100mg/[kg&#x22C5;d]) of OMO, the ACh levels of the model rats increased significantly to 99.22 &#x00B1; 1.49 and 99.98 &#x00B1; 1.52, respectively, (<italic>p</italic> &#x003C; 0.05). The AchE decreased to 118.39 &#x00B1; 1.93 and 116.70 &#x00B1; 5.47, respectively. These differences were significant (<italic>p</italic> &#x003C; 0.05) as compared to the model group (159.37 &#x00B1; 4.15).</p>
<p>The HE staining of the small intestinal tissues revealed crypt atrophy, distortion, and surface irregularity in the model group <sc>D</sc>-galactose-induced deficient rats, while those changes in the OMO-treated groups were improved (<bold>Figure <xref ref-type="fig" rid="F1">1E</xref></bold>, intestine). Moreover, the staining did not demonstrate any remarkable neuronal abnormalities in the hippocampus of the rats in the control group. The pyramidal cells in the CA1 region were arranged precisely and tightly, and no cell loss was observed. Additionally, in the control group, the cells were round and intact with stained clear, dark blue nuclei (<bold>Figure <xref ref-type="fig" rid="F1">1E</xref></bold>). However, noticeable damage in the hippocampus was observed in the model groups by histopathology. The pyramidal layered structure was disintegrated, and the neuronal loss was found in the CA1 region. Neurons with pyknotic nuclei and shrunken or irregular shape were also observed. These abnormalities were attenuated by the treatment with OMO. The cells in the OMO-treated groups exhibited superior cell morphology and were more in number than those in the untreated groups, especially those in the OMO-100 treated group were superior to the control group. Together, these results demonstrated that the OMO administration could ameliorate the <sc>D</sc>-galactose-induced deficient rats.</p>
</sec>
<sec><title>Changes in Gut Microbiota after OMO Administration</title>
<p>Operational taxonomic unit (OTU) abundance and taxonomic profiles were analyzed as shown in <bold>Figure <xref ref-type="fig" rid="F2">2</xref></bold>. The values of Chao1, ACE, Shannon, and npShannon were reduced, and that of Simpson was increased significantly in the <sc>D</sc>-galactose-induced group than the normal group (<italic>p</italic> &#x003C; 0.05, <bold>Figure <xref ref-type="fig" rid="F2">2A</xref></bold>). After treatment with 100 mg/kg/d OMO, the values of Chao1, ACE, Shannon, npShannon, and Simpson were improved to resemble the normal (<bold>Figure <xref ref-type="fig" rid="F2">2A</xref></bold>). All the treated groups could be clustered using the principal component analysis (PCA) (<bold>Figure <xref ref-type="fig" rid="F2">2B</xref></bold>); Bray&#x2013;Curtis distance was shown at the phylum level in <bold>Figure <xref ref-type="fig" rid="F2">2C</xref></bold> (<italic>Verrucomicrotia</italic>, <italic>Proteobacteria</italic>, <italic>Firmicutes</italic>, and <italic>Bacteroidetes</italic>), genus level in <bold>Figure <xref ref-type="fig" rid="F2">2D</xref></bold> (left) (<italic>Prevotella</italic>, <italic>Oscillospira</italic>, <italic>Lactobacillus</italic>, <italic>Bacteroides</italic>, <italic>Parabacteroides</italic>, <italic>Sutterella</italic>, <italic>Akkermansia</italic>), and beta diversity at the genus level in <bold>Figure <xref ref-type="fig" rid="F2">2D</xref></bold> (right). Our results indicated that OMO administration could maintain the abundance of gut microbiota in <sc>D</sc>-galactose-induced deficient rats, although additional studies are warranted.</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Effects of OMO on gut microbiota in <sc>D</sc>-galactose-induced deficient rats. <bold>(A)</bold> Sequencing data summary at 97% similarity. <bold>(B)</bold> Results of PCA. <bold>(C)</bold> Classification and abundance of cecal contents at the phylum level. <bold>(D)</bold> Classification and abundance of cecal contents at the genus level, and the beta diversity. The graph N is normal group; M is model group; O is OMO-100 mg, high-dose group that received <sc>D</sc>-galactose (100 mg/kg/d) i.p., and gavage at a dosage of 100 mg/[kg&#x22C5;d] in OMO. Values are the means of six independent experiments (<italic>n</italic> &#x2265; 5).</p></caption>
<graphic xlink:href="fnagi-09-00403-g002.tif"/>
</fig>
</sec>
</sec>
<sec><title>Effects of OMO on A&#x03B2;<sub>1-42</sub>-Induced Deficient Rats</title>
<sec><title>Indexes Improvements by OMO Administration</title>
<p>The fur of the treated animals was much smoother than that of the model group. The average weight of model groups was found to be higher than that of the control group (<italic>p</italic> &#x003C; 0.05), and we found that the rats in the model group present constipation and swollen belly. Moreover, the weight records of OMO-treated groups did not alter significantly (<italic>p</italic> > 0.05) as compared to the control group (<bold>Figure <xref ref-type="fig" rid="F3">3A</xref></bold>).</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>Effect of OMO in A&#x03B2;<sub>1-42</sub>-induced deficient rats. <bold>(A)</bold> Body weight changes during the treatments time. <bold>(B-a)</bold> Escape latency in the MWM. <bold>(B-b)</bold> Swimming distance. <bold>(B-c)</bold> Swimming time in the platform quadrant during the spatial probe test. <bold>(C)</bold> Level of cytokines GM-CSF, TNF-&#x03B3;, 1L-10, IL-12, 1L-17&#x03B1;, 1L-4, TNF-&#x03B1;, and VGEF-&#x03B1; in the serum. <bold>(D)</bold> Levels of monoamine neurotransmitters (NE, DA, 5-HT, and 5-HIAA) in the brain tissue. <bold>(E)</bold> Histopathological changes in the intestine, heart, and brain, and the expressions of A&#x03B2;<sub>1-42</sub> and Tau proteins in brain tissues by immunohistochemistry. The graph Control, control group; Model, model group; OMO-50 mg, low-dose group that received <sc>D</sc>-galactose (100 mg/kg/d) i.p. and gavage at a dosage of 50 mg/[kg&#x22C5;d] in OMO; OMO-100 mg, high-dose group that received <sc>D</sc>-galactose (100 mg/kg/d) i.p. and gavage at a dosage of 100 mg/[kg&#x22C5;d] in OMO. Values are represented as mean &#x00B1; SD (<italic>n</italic> = 6) and expressed as the percentage of the control group, <sup>#</sup><italic>p</italic> &#x003C; 0.01 vs. control group, <sup>&#x2217;</sup><italic>p</italic> &#x003C; 0.05 vs. model group, <sup>&#x2217;&#x2217;</sup><italic>p</italic> &#x003C; 0.01 vs. model group.</p></caption>
<graphic xlink:href="fnagi-09-00403-g003.tif"/>
</fig>
<p>Compared to the model group, the incubation period for each OMO-treated group was significantly shorter. The incubation period for the low-dose OMO group was 86.49 &#x00B1; 11.64 s, while that for the high-dose group was 82.06 &#x00B1; 19.44 s on the 1st day. Compared to the model group (113.75 &#x00B1; 16.11 s), the differences were significant (<italic>p</italic> &#x003C; 0.01). On the 4th day, the incubation period of the low-dose OMO group was 37.19 &#x00B1; 5.36 s, and that for the high-dose group was 28.27 &#x00B1; 3.96 s; the differences were significant as compared to the model group (56.29 &#x00B1; 9.69 s, <italic>p</italic> &#x003C; 0.01; <bold>Figure <xref ref-type="fig" rid="F3">3Ba</xref></bold>). These results showed that OMO administration could ameliorate the A&#x03B2;<sub>1-42</sub>-induced learning and memory dysfunction in rats.</p>
<p>Probe test results showed no significant differences (<italic>p</italic> > 0.05) among the groups with respect to the total swimming distance or speed. The swimming time of the control group in the NW quadrant (26.63 &#x00B1; 3.83 s) was significantly longer than that in the other three quadrants (<italic>p</italic> &#x003C; 0.01). The swimming time in the NW quadrant of the model group was 20.77 &#x00B1; 2.36 s, which was significantly shorter than the control group (<italic>p</italic> &#x003C; 0.01), suggesting that the rats remembered the location of the platform. The swimming time of the low- and high-dose OMO groups were 26.50 &#x00B1; 3.59 and 27.36 &#x00B1; 2.51 s, which were significantly longer than the model group. Compared to the model group, the differences were significant (<italic>p</italic> &#x003C; 0.01), as shown in <bold>Figure <xref ref-type="fig" rid="F3">3Bc</xref></bold>. The swimming distances did not differ among all groups (<bold>Figure <xref ref-type="fig" rid="F3">3Bb</xref></bold>).</p>
<p>All the cytokines&#x2019; levels in the serum of A&#x03B2;<sub>1-42</sub>-induced group deviated from the normal; GM-CSF, TNF-&#x03B3;, 1L-10, IL-12, 1L-17&#x03B1;, 1L-4, TNF-&#x03B1;, and VGEF were secreted significantly different (<italic>p</italic> &#x003C; 0.05 or <italic>p</italic> &#x003C; 0.01; <bold>Figure <xref ref-type="fig" rid="F3">3C</xref></bold>). When treated with OMO, all these cytokines were strikingly recovered close to the baseline level (<bold>Figure <xref ref-type="fig" rid="F3">3C</xref></bold>), thereby indicating that OMO administration can improve the inflammatory environment.</p>
<p>The monoamine neurotransmitter levels in right brain tissue were dissected from 4 rats in each group, according to the methods described previously (<xref ref-type="bibr" rid="B15">Chen et al., 2014b</xref>). <bold>Figure <xref ref-type="fig" rid="F3">3D</xref></bold> showed that the levels of norepinephrine (NE), dopamine (DA), 5-hydroxytryptamine (5-HT), and 5-hydroxyindole acetic acid (5-HIAA) were reduced in A&#x03B2;<sub>1-42</sub>-induced groups as compared to the control group, and the OMO administration can promote the secretion of some monoamine neurotransmitters (NE, DA, 5-HT, and 5-HIAA) in a concentration-dependent manner (<bold>Figure <xref ref-type="fig" rid="F3">3D</xref></bold>).</p>
<p>The HE staining of small intestinal tissues revealed crypt branching, atrophy, distortion, and surface irregularity in the model group A&#x03B2;<sub>1-42</sub>-induced deficient rats, while those changes in the OMO-treated groups were improved (<bold>Figure <xref ref-type="fig" rid="F3">3E</xref></bold>, intestine). The injury to the atrial tissues in the A&#x03B2;<sub>1-42</sub>-induced group was more severe than that in the normal and OMO-treated groups. Furthermore, the HE staining did not reveal any remarkable neuronal abnormalities in the hippocampus of rats in the control group (<bold>Figure <xref ref-type="fig" rid="F3">3E</xref></bold>). However, the obvious hippocampal histopathological damage was observed in the model groups. The pyramidal layered structure was disintegrated, and neuronal loss was found in the CA1 region. These abnormalities were attenuated by OMO treatment. The cells in OMO-treated groups exhibited better cell morphology and were more in number than those in the untreated groups, especially those in the OMO-100 treated group were superior to the control group. Compared to the normal group, the proportion of A&#x03B2;<sub>1-42</sub> and Tau-positive cells in rats in the model group was significantly higher than that in the normal group (<italic>p</italic> &#x003C; 0.05), while the OMO administration down-regulated the expression of A&#x03B2;<sub>1-42</sub> and Tau proteins (<bold>Figure <xref ref-type="fig" rid="F3">3E</xref></bold>).</p>
</sec>
<sec><title>The Gut Structure of the Microbiota Was Altered Significantly by OMO</title>
<p>OTU abundance and taxonomic profiles were analyzed as shown in <bold>Figure <xref ref-type="fig" rid="F4">4</xref></bold>. Compared to the normal group, the diversity of the microbial communities in A&#x03B2;<sub>1-42</sub>-induced (injected 10 or 20 &#x03BC;g fibrillar state of A&#x03B2;<sub>1-42</sub> into the CA1 region, <bold>Figure <xref ref-type="fig" rid="F4">4D</xref></bold>) group was reduced and negatively related with the doses of A&#x03B2;<sub>1-42</sub> (<bold>Figure <xref ref-type="fig" rid="F4">4A</xref></bold>); All the A&#x03B2;<sub>1-42</sub>-induced groups were clustered as expected using PCA (<bold>Figure <xref ref-type="fig" rid="F4">4B</xref></bold>), which indicated that the A&#x03B2; not only influences the brain but also changes the gut microbiota. After treatment with 50 mg/(kg&#x22C5;d) or 100 mg/(kg&#x22C5;d) OMO, the diversity of the microbial communities was improved similarly as that of the normal (<bold>Figure <xref ref-type="fig" rid="F4">4C</xref></bold>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>Effects of OMO on gut microbiota in A&#x03B2;<sub>1-42</sub>-induced deficient rats. <bold>(A)</bold> Rarefaction curve and <bold>(B)</bold> PCA results of different concentrations of A&#x03B2;<sub>1-42</sub>-induced groups, H (20 &#x03BC;g of A&#x03B2;<sub>1-42</sub>), L (20 &#x03BC;g of A&#x03B2;<sub>1-42</sub>), Z (normal rats with vehicle). <bold>(C)</bold> Rarefaction curve. <bold>(D)</bold> Operation schematic diagram. <bold>(E)</bold> Classification and abundance of cecal contents at the phylum level. <bold>(F)</bold> Classification and abundance of cecal contents at the genus level. <bold>(G)</bold> The dominant species classification tree. <bold>(H)</bold> The relative abundance of the dominant microorganism. Values are the means of six independent experiments.</p></caption>
<graphic xlink:href="fnagi-09-00403-g004.tif"/>
</fig>
<p>Analysis revealed the difference of taxonomic abundance between different groups (<bold>Figure <xref ref-type="fig" rid="F4">4E</xref></bold>). Some bacteria in the fecal samples changed considerably at the phylum level: for instance, <italic>Verrucomicrotia</italic>, <italic>Proteobacteria</italic>, <italic>Firmicutes</italic>, and <italic>Bacteroidetes</italic>. Moreover, at the genus level, the A&#x03B2;<sub>1-42</sub>-induced rats exhibited the enrichment of potentially proinflammatory microbes, such as <italic>Corynebacterium, Staphylococcus, Ruminococcus, Roseburia, Dorea</italic>, and <italic>Sutterella</italic>, and the reduction of potentially anti-inflammatory microbes, such as <italic>Bacteroides, Bifidobacterium, Prevotella, Parabacteroides, Coprococcus, Desulfovibrio</italic>, and <italic>Lactobacillus</italic>, in comparison with the normal group (<bold>Figure <xref ref-type="fig" rid="F4">4F</xref></bold>). However, the treatment with the OMO exhibited a reduction in proinflammatory microbes and enrichment of anti-inflammatory microbes. Thus, our results indicated that the OMO administration had the potential to regulate the structure of the gut microbiota.</p>
<p>We also constructed and visualized a taxonomic tree of the predominant taxa (<bold>Figure <xref ref-type="fig" rid="F4">4G</xref></bold>), which showed that <italic>Firmicutes</italic>, <italic>Bacteroidetes</italic>, <italic>Clostridia</italic>, <italic>Bacteroidia</italic>, <italic>Bacilli</italic>, <italic>Clostridiales</italic>, <italic>Lactobacillales</italic>, <italic>Bacteroidales</italic>, <italic>Lactobacillaceae</italic>, and <italic>Lactobacillus</italic> were the predominant taxa. The altered details of the predominant taxa (<bold>Figure <xref ref-type="fig" rid="F4">4H</xref></bold>) showed that the abundance of <italic>Clostridia</italic> and <italic>Clostridiales</italic> in A&#x03B2;<sub>1-42</sub>-induced groups was increased sharply, while the aforementioned taxa as <italic>Firmicutes</italic>, <italic>Bacteroidetes</italic>, <italic>Bacteroidia</italic>, <italic>Bacilli</italic>, <italic>Lactobacillales</italic>, <italic>Bacteroidales</italic>, <italic>Lactobacillaceae</italic>, and <italic>Lactobacillus</italic> were reduced (<italic>p</italic> &#x003C; 0.05 vs. normal group). On the other hand, the OMO-treated groups can reverse those changes, especially the probiotic <italic>Lactobacillus</italic> increased obviously, which indicated that OMO administration might have a prebiotic role in intestinal dysbacteriosis in AD animals as induced by A&#x03B2;<sub>1-42</sub>.</p>
</sec>
</sec>
<sec><title>Prebiotic Effect of OMO on TNBS-Induced Mice</title>
<sec><title>The Tissue Damages and Inflammation Induced by TNBS Combined Antibiotics Were Relieved</title>
<p>In order to ensure the prebiotic role of OMO, we established an IBD mice model after a broad spectrum antibiotics treatment. Compared to the control group, post treatment with TNBS by enema, a majority of the mice presented diarrhea and the weight gain declined relatively (<bold>Figure <xref ref-type="fig" rid="F5">5A</xref></bold>). All the cytokines&#x2019; levels were deviated from the normal, as some anti-inflammatory cytokines of GM-CSF, TNF-&#x03B3;, 1L-10, IL-12, 1L-17&#x03B1;, 1L-4, TNF-&#x03B1;, and VGEF were secreted differently (<italic>p</italic> &#x003C; 0.05 or <italic>p</italic> &#x003C; 0.01; <bold>Figure <xref ref-type="fig" rid="F5">5C</xref></bold>). Simultaneously, we found that the content of lipopolysaccharide (LPS) (<bold>Figure <xref ref-type="fig" rid="F5">5B</xref></bold>) was higher than that in the control group; the colon tissues (<bold>Figure <xref ref-type="fig" rid="F5">5D</xref></bold>) and splenic tissues (<bold>Figure <xref ref-type="fig" rid="F5">5E</xref></bold>) were severely damaged. Also, immunohistochemistry staining showed that the expressions of Foxp3 (<bold>Figure <xref ref-type="fig" rid="F6">6A</xref></bold>), IL-17 (<bold>Figure <xref ref-type="fig" rid="F6">6B</xref></bold>), NF-&#x03BA;B (<bold>Figure <xref ref-type="fig" rid="F6">6C</xref></bold>), and TNF-&#x03B1; (<bold>Figure <xref ref-type="fig" rid="F6">6D</xref></bold>) deviated from the control, especially the additional broad spectrum and overdose antibiotics groups. After treatment with OMO, all the deviated parameters returned to the baselines, especially the OMO + <italic>Bifidobacterium</italic>-treated group (<bold>Figures <xref ref-type="fig" rid="F5">5</xref></bold>, <bold><xref ref-type="fig" rid="F6">6</xref></bold>). Cumulatively, our results suggested that OMO and <italic>Bifidobacterium</italic> exert anti-inflammatory effects in IBD, synergistically; however, the underlying mechanism needs further studies.</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>OMO improves the pathological parameters of the high-dose broad spectrum antibiotics and TNBS-induced inflammatory bowel disease (IBD) mice. <bold>(A)</bold> Body weight changes. <bold>(B)</bold> Levels of LPS in serum. <bold>(C)</bold> The levels of cytokines (GM-CSF, TNF-&#x03B3;, 1L-10, IL-12, 1L-17&#x03B1;, 1L-4, TNF-&#x03B1;, and VGEF-&#x03B1;) in serum. <bold>(D)</bold> The histopathological changes in colon. <bold>(E)</bold> The histopathological changes in spleen. Control is the normal group; model is the TNBS-induced group; model and high-dose antibiotics, HEP3 (100 mg/kg/d), <italic>Bifidobacterium</italic>, HEP3 and high-dose antibiotics, HEP3 and <italic>Bifidobacterium</italic>, <italic>Bifidobacterium</italic> and high-dose antibiotics, HEP3, <italic>Bifidobacterium</italic>, and high-dose antibiotics.</p></caption>
<graphic xlink:href="fnagi-09-00403-g005.tif"/>
</fig>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Immunohistochemistry staining of Foxp3 <bold>(A)</bold>, IL-17 <bold>(B)</bold>, NF-&#x03BA;B p65 <bold>(C)</bold>, and TNF-&#x03B1; <bold>(D)</bold> in the colons of different experimental groups in high-dose broad spectrum antibiotics and TNBS-induced IBD mice after treatment with OMO.</p></caption>
<graphic xlink:href="fnagi-09-00403-g006.tif"/>
</fig>
</sec>
<sec><title>Promotion of the Engraftment Ability of <italic>Bifidobacterium</italic></title>
<p>To clarify the synergistical action between OMO and <italic>Bifidobacterium</italic>, OTU abundance and taxonomic profiles were analyzed as shown in <bold>Figure <xref ref-type="fig" rid="F7">7</xref></bold>. Compared to the normal group, the diversity of the microbial community in TNBS and TNBS and antibiotics-induced groups was reduced (<bold>Figure <xref ref-type="fig" rid="F7">7A</xref></bold>). OMO can ameliorate this dysbacteriosis; the bacterial compositions at the phylum (<bold>Figure <xref ref-type="fig" rid="F7">7C</xref></bold>) and family level (<bold>Figure <xref ref-type="fig" rid="F7">7D</xref></bold>) encompassed <italic>Verrucomicrotia</italic>, <italic>Proteobacteria</italic>, <italic>Firmicutes</italic>, <italic>Bacteroidetes</italic>, <italic>Lactobacillaceae</italic>, and <italic>Lachnospiraceae</italic>. Our results showed that the relative abundance of <italic>Bifidobacterium</italic> was increased remarkably (<italic>p</italic> &#x003C; 0.05, <bold>Figure <xref ref-type="fig" rid="F5">5</xref></bold>), and the other probiotics <italic>Lactobacillaceae</italic> were also abundant in the microbial community with stable structures. We also constructed and visualized a taxonomic tree of the predominant taxa (<bold>Figure <xref ref-type="fig" rid="F7">7B</xref></bold>), which showed that the <italic>Firmicutes</italic>, <italic>Bacteroidetes</italic>, <italic>Clostridia</italic>, <italic>Bacteroidia</italic>, <italic>Bacilli</italic>, <italic>Clostridiales</italic>, <italic>Lactobacillales</italic>, <italic>Bacteroidales</italic>, <italic>Lactobacillaceae</italic>, and <italic>Lactobacillus</italic> were the predominant taxa.</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption><p>Effects of OMO on the microbiota of cecal contents in high-dose broad spectrum antibiotics and TNBS-induced IBD mice. <bold>(A)</bold> The graph represents the rarefaction curve. <bold>(B)</bold> The dominant species classification tree. <bold>(C)</bold> The classification and abundance of cecal contents at the phylum level. <bold>(D)</bold> The classification and abundance of cecal contents at the family level. Values are the means of six independent experiments.</p></caption>
<graphic xlink:href="fnagi-09-00403-g007.tif"/>
</fig>
</sec>
</sec>
<sec><title>Influence of A&#x03B2; Levels on Microbiota-Gut-Brain Axis</title>
<p>In order to explore whether A&#x03B2; can influence the gut microbiota by targeting the microbiota-gut-brain axis, we injected 10 and 20 &#x03BC;g A&#x03B2;<sub>1-42</sub> into the CA1 region, respectively. Then, the fecal samples were collected once a week and the last 4 weeks, followed by microbiome analysis using the 16S rRNA genes. We also monitored the transcriptome of the small intestine and brain tissues at the 5th week after injection of A&#x03B2;<sub>1-42</sub>.</p>
<sec><title>Dynamic Variations of Gut Microbiota and KEGG Pathway Analysis in the A&#x03B2;<sub>1-42</sub>-Induced Deficient Rats</title>
<p>The dynamic variations of gut microbiota showed that the diversity in the A&#x03B2;<sub>1-42</sub>-induced microbial community (injected 10 or 20 &#x03BC;g fibrillar state of A&#x03B2;<sub>1-42</sub> into the CA1 region) group was reduced in the 4th week (L3, H3) than that in the 2nd and 3rd week (L1, L2 and H1, H2), as shown in <bold>Figures <xref ref-type="fig" rid="F8">8B,C</xref></bold>, thereby indicating that such a diversity was reduced with the progression of the disease. <bold>Figures <xref ref-type="fig" rid="F8">8D</xref>&#x2013;<xref ref-type="fig" rid="F8">F</xref></bold> showed that the diversity of the microbial community changed with the levels of A&#x03B2;<sub>1-42</sub>, which revealed that the levels of A&#x03B2;<sub>1-42</sub> in the brain influenced the composition of the gut microbiota significantly. We also constructed and visualized a taxonomic tree of the predominant taxa (<bold>Figure <xref ref-type="fig" rid="F8">8G</xref></bold>), which displayed that the <italic>Firmicutes</italic>, <italic>Bacteroidetes</italic>, <italic>Clostridia</italic>, <italic>Bacteroidia</italic>, <italic>Bacilli</italic>, <italic>Clostridiales</italic>, <italic>Lactobacillales</italic>, <italic>Bacteroidales</italic>, <italic>Lactobacillaceae</italic>, and <italic>Lactobacillus</italic> were the predominant taxa. The changes in the details of predominant taxa (<bold>Figure <xref ref-type="fig" rid="F8">8H</xref></bold>), along with the abundance of <italic>Lactobacillaceae</italic>, were negatively correlated with the dose of A&#x03B2;<sub>1-42</sub>.</p>
<fig id="F8" position="float">
<label>FIGURE 8</label>
<caption><p>Effects of A&#x03B2;<sub>1-42</sub> on gut microbiota in rats. <bold>(A&#x2013;F)</bold> The rarefaction curve of different concentrations and durations in A&#x03B2;<sub>1-42</sub>-induced groups, H (20 &#x03BC;g of A&#x03B2;<sub>1-42</sub>), L (20 &#x03BC;g of A&#x03B2;<sub>1-42</sub>), Z (normal rats with vehicle); H1, H2, and H3 (or L1, L2, L3) is the treatment time after injection of A&#x03B2;<sub>1-42</sub> at 2nd, 3rd, and 4th weeks; <bold>(G)</bold> is the dominant species classification tree; <bold>(H)</bold> is the relative abundance of the dominant microorganism. Values represent the means of six independent experiments.</p></caption>
<graphic xlink:href="fnagi-09-00403-g008.tif"/>
</fig>
<p>The KEGG pathway analysis showed that the metabolism of xenobiotics biodegradation, nucleotide metabolism, metabolism of terpenoids and polyketides, metabolism of other amino acids, metabolism of cofactors and vitamins, lipid metabolism, glycan biosynthesis and metabolism, enzyme families, energy metabolism, carbohydrate metabolism, biosynthesis of other secondary metabolites, and amino acid metabolism were altered according to the gut microbiota in the two AD-like rodent models. Additionally, many of these metabolisms were improved by the administration of OMO (<bold>Figure <xref ref-type="fig" rid="F9">9A</xref></bold>) showed the dynamic variations in the 2nd, 3rd, and 4th week after injection of A&#x03B2;<sub>1-42</sub>. <bold>Figure <xref ref-type="fig" rid="F9">9B</xref></bold> represents the 5th week after injection of A&#x03B2;<sub>1-42</sub>, all of which showed that the metabolism of gut microbiota was influenced by the levels of A&#x03B2;<sub>1-42</sub> in hippocampus.</p>
<fig id="F9" position="float">
<label>FIGURE 9</label>
<caption><p>The KEGG pathway enrichment of gut microbiota in the metabolism system. <bold>(A)</bold> The dynamic variations in the 2nd, 3rd, and 4th week after injection of A&#x03B2;<sub>1-42</sub> in rats. <bold>(B)</bold> The 4th week after injection of A&#x03B2;<sub>1-42</sub> in rats. <bold>(C)</bold> The high dose broad spectrum antibiotics and TNBS-induced IBD mice.</p></caption>
<graphic xlink:href="fnagi-09-00403-g009.tif"/>
</fig>
</sec>
<sec><title>Transcriptome Analysis in Small Intestine and Brain in Deficient Rats Post A&#x03B2;<sub>1-42</sub> Injection</title>
<sec>
<title>Small intestine transcriptome analysis</title>
<p>After injection of A&#x03B2;<sub>1-42</sub> for 4 weeks, the rats were sacrificed, and the intestinal tissues were dissected and frozen in liquid nitrogen for RNA extraction and high-throughput RNA-sequencing. To obtain an overview of the gene expression profile of the intestine in AD model rats, three cDNA samples were generated from each group, mixed, and subjected to sequencing by the Illumina NextSeq 500 platform. Approximately 45,323,472, 55,358,634, and 45,134,740 raw reads with a length of 2 &#x00D7; 150 bp were generated for the A&#x03B2;<sub>1-42</sub>-20, A&#x03B2;<sub>1-42</sub>-10, and control group samples, respectively. After stringent quality assessment and data filtering, 44,973,944, 54,933,060, and 44,770,698 clean paired-end sequence reads with a Q20 percentage (those with a base quality >20) over 99% were obtained from the differently treated samples, respectively. Of all the reads, approximately 86.0% were mapped to the rat genome. Based on the normalized data, the expression of 21933 genes was detected (<bold>Figure <xref ref-type="fig" rid="F10">10A</xref></bold>), and the relative expressions of DEGs in all the three treated groups (A&#x03B2;<sub>1-42</sub>-10, A&#x03B2;<sub>1-42</sub>-20, and control) were shown in <bold>Table <xref ref-type="table" rid="T1">1</xref></bold>.</p>
<fig id="F10" position="float">
<label>FIGURE 10</label>
<caption><p>Small intestine transcriptome analysis in the deficit rats by injected A&#x03B2;<sub>1-42</sub>. <bold>(A)</bold> The statistics of transcriptome sequences. <bold>(B)</bold> DEGs in the small intestine at different concentrations of A&#x03B2;<sub>1-42</sub>. <bold>(C)</bold> Venn diagram of DEGs. <bold>(D)</bold> The heat map of the relative expressions of DEGs in all three groups.</p></caption>
<graphic xlink:href="fnagi-09-00403-g010.tif"/>
</fig>
<table-wrap position="float" id="T1">
<label>Table 1</label>
<caption><p>Differentially expressed genes (DEGs) in the small intestine of deficient rat injected at different concentration of A&#x03B2;<sub>1-42</sub>.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<th valign="top" align="left">Genes</th>
<th valign="top" align="center" colspan="2">FoldChange<hr/></th>
<th valign="top" align="center" colspan="2">log2FoldChange<hr/></th>
<th valign="top" align="center">Up&#x2013;down</th>
<th valign="top" align="center" colspan="2"><italic>p</italic>-value<hr/></th>
</tr>
<tr>
<td valign="top" align="left"></td>
<th valign="top" align="center">Normal/A&#x03B2;-10</th>
<th valign="top" align="center">Normal/A&#x03B2;-20</th>
<th valign="top" align="center">Normal/A&#x03B2;-10</th>
<th valign="top" align="center">Normal/A&#x03B2;-20</th>
<td valign="top" align="center"></td>
<th valign="top" align="center">Normal/A&#x03B2;-10</th>
<th valign="top" align="center">Normal/A&#x03B2;-20</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Slc5a4b</td>
<td valign="top" align="center">0.09</td>
<td valign="top" align="center">0.27</td>
<td valign="top" align="center">-3.47</td>
<td valign="top" align="center">-1.86</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.000494</td>
</tr>
<tr>
<td valign="top" align="left">Nts</td>
<td valign="top" align="center">0.41</td>
<td valign="top" align="center">4.57</td>
<td valign="top" align="center">-1.27</td>
<td valign="top" align="center">2.19</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.002207</td>
<td valign="top" align="center">0.000056</td>
</tr>
<tr>
<td valign="top" align="left">Fkbp5</td>
<td valign="top" align="center">0.27</td>
<td valign="top" align="center">2.81</td>
<td valign="top" align="center">-1.90</td>
<td valign="top" align="center">1.49</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000004</td>
<td valign="top" align="center">0.000132</td>
</tr>
<tr>
<td valign="top" align="left">Cubn</td>
<td valign="top" align="center">0.40</td>
<td valign="top" align="center">2.81</td>
<td valign="top" align="center">-1.33</td>
<td valign="top" align="center">1.49</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000323</td>
<td valign="top" align="center">0.000132</td>
</tr>
<tr>
<td valign="top" align="left">Defa8</td>
<td valign="top" align="center">0.03</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">-5.11</td>
<td valign="top" align="center">-3.66</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">AABR07000398.1</td>
<td valign="top" align="center">0.45</td>
<td valign="top" align="center">3.21</td>
<td valign="top" align="center">-1.17</td>
<td valign="top" align="center">1.68</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000995</td>
<td valign="top" align="center">0.000002</td>
</tr>
<tr>
<td valign="top" align="left">LOC257642</td>
<td valign="top" align="center">0.45</td>
<td valign="top" align="center">4.12</td>
<td valign="top" align="center">-1.15</td>
<td valign="top" align="center">2.04</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.032226</td>
<td valign="top" align="center">0.012780</td>
</tr>
<tr>
<td valign="top" align="left">Hpse</td>
<td valign="top" align="center">5.37</td>
<td valign="top" align="center">0.39</td>
<td valign="top" align="center">2.43</td>
<td valign="top" align="center">-1.36</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.000050</td>
<td valign="top" align="center">0.002196</td>
</tr>
<tr>
<td valign="top" align="left">Nop10</td>
<td valign="top" align="center">2.12</td>
<td valign="top" align="center">10.70</td>
<td valign="top" align="center">1.09</td>
<td valign="top" align="center">3.42</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.032836</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Arhgdib</td>
<td valign="top" align="center">2.22</td>
<td valign="top" align="center">0.49</td>
<td valign="top" align="center">1.15</td>
<td valign="top" align="center">-1.03</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.006915</td>
<td valign="top" align="center">0.007868</td>
</tr>
<tr>
<td valign="top" align="left">AABR07065789.1</td>
<td valign="top" align="center">2.13</td>
<td valign="top" align="center">7.85</td>
<td valign="top" align="center">1.09</td>
<td valign="top" align="center">2.97</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.026618</td>
<td valign="top" align="center">0.000001</td></tr>
<tr>
<td valign="top" align="left">Reg3g</td>
<td valign="top" align="center">2.72</td>
<td valign="top" align="center">0.35</td>
<td valign="top" align="center">1.44</td>
<td valign="top" align="center">-1.52</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.000232</td>
<td valign="top" align="center">0.000032</td>
</tr>
<tr>
<td valign="top" align="left">Rps24</td>
<td valign="top" align="center">4.88</td>
<td valign="top" align="center">66.16</td>
<td valign="top" align="center">2.29</td>
<td valign="top" align="center">6.05</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Pou2af1</td>
<td valign="top" align="center">2.14</td>
<td valign="top" align="center">0.36</td>
<td valign="top" align="center">1.10</td>
<td valign="top" align="center">-1.47</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.048293</td>
<td valign="top" align="center">0.001217</td>
</tr>
<tr>
<td valign="top" align="left">Adh6</td>
<td valign="top" align="center">2.32</td>
<td valign="top" align="center">0.14</td>
<td valign="top" align="center">1.21</td>
<td valign="top" align="center">-2.88</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.004548</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">RGD1311933</td>
<td valign="top" align="center">2.24</td>
<td valign="top" align="center">5.12</td>
<td valign="top" align="center">1.16</td>
<td valign="top" align="center">2.36</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.006467</td>
<td valign="top" align="center">0.000000</td></tr>
<tr>
<td valign="top" align="left">Rps27</td>
<td valign="top" align="center">2.08</td>
<td valign="top" align="center">19.07</td>
<td valign="top" align="center">1.05</td>
<td valign="top" align="center">4.25</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.003563</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Wfdc21</td>
<td valign="top" align="center">2.46</td>
<td valign="top" align="center">0.45</td>
<td valign="top" align="center">1.30</td>
<td valign="top" align="center">-1.15</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.002445</td>
<td valign="top" align="center">0.002823</td>
</tr>
<tr>
<td valign="top" align="left">Rps27a-ps1</td>
<td valign="top" align="center">3.22</td>
<td valign="top" align="center">6.84</td>
<td valign="top" align="center">1.69</td>
<td valign="top" align="center">2.77</td>
<td valign="top" align="center">Down</td>
<td valign="top" align="center">0.000020</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Ccl21</td>
<td valign="top" align="center">3.20</td>
<td valign="top" align="center">0.30</td>
<td valign="top" align="center">1.68</td>
<td valign="top" align="center">-1.73</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.001820</td>
<td valign="top" align="center">0.000047</td>
</tr>
<tr>
<td valign="top" align="left">Pdx1</td>
<td valign="top" align="center">3.20</td>
<td valign="top" align="center">0.49</td>
<td valign="top" align="center">1.68</td>
<td valign="top" align="center">-1.03</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.007298</td>
<td valign="top" align="center">0.037669</td>
</tr>
<tr>
<td valign="top" align="left">AABR07051670.1</td>
<td valign="top" align="center">7.56</td>
<td valign="top" align="center">0.36</td>
<td valign="top" align="center">2.92</td>
<td valign="top" align="center">-1.49</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.000008</td>
<td valign="top" align="center">0.000992</td>
</tr>
<tr>
<td valign="top" align="left">Igkv5-48</td>
<td valign="top" align="center">30.08</td>
<td valign="top" align="center">0.32</td>
<td valign="top" align="center">4.91</td>
<td valign="top" align="center">-1.65</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.000302</td>
</tr>
<tr>
<td valign="top" align="left">AABR07051684.1</td>
<td valign="top" align="center">23.10</td>
<td valign="top" align="center">0.27</td>
<td valign="top" align="center">4.53</td>
<td valign="top" align="center">-1.91</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.001867</td>
<td valign="top" align="center">0.003488</td>
</tr>
<tr>
<td valign="top" align="left">AABR07065768.3</td>
<td valign="top" align="center">23.64</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">4.56</td>
<td valign="top" align="center">-3.25</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.032367</td>
<td valign="top" align="center">0.000002</td>
</tr>
<tr>
<td valign="top" align="left">Akp3</td>
<td valign="top" align="center">13.94</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">3.80</td>
<td valign="top" align="center">-2.93</td>
<td valign="top" align="center">Up</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.000000</td></tr>
</tbody>
</table>
</table-wrap>
<p>The general chi-squared test was used for the selection of significant DEGs. Based on the criteria of twofold or greater change and <italic>Q</italic> of <italic>p</italic> &#x003C; 0.05, 349 unigenes were identified as significant DEGs between A&#x03B2;<sub>1-42</sub>-10 and control group samples and 420 unigenes between A&#x03B2;<sub>1-42</sub>-20 and control group samples (<bold>Figure <xref ref-type="fig" rid="F10">10B</xref></bold>). To elucidate the DEGs in different contents of A&#x03B2;<sub>1-42</sub>-induced groups, we used the gene expression profiling. As illustrated in the Venn diagram (<bold>Figure <xref ref-type="fig" rid="F10">10C</xref></bold>), the number of genes, as well as the relationships among the overlap between the different groups, were shown in <bold>Figures <xref ref-type="fig" rid="F10">10B,D</xref></bold>, indicating that A&#x03B2;<sub>1-42</sub> level in the brain can influence the transcriptome of the intestine.</p>
<p>To gain insights into the physiological processes regulated by the different A&#x03B2;<sub>1-42</sub> levels and identify the processes enriched in significant DEGs, we subjected significant DEGs to GO term enrichment analysis and KEGG pathway enrichment, a tool developed to represent the common and basic biological information in the annotation. The GO term enrichment results showed that the immune system, extracellular environment, and antigen reaction (Supplementary Tables <xref ref-type="supplementary-material" rid="SM1">S1</xref>-1&#x2013;<xref ref-type="supplementary-material" rid="SM1">S1-3</xref>) altered in different A&#x03B2;<sub>1-42</sub> levels treated groups, which indicated that the inflammatory response of the gut is activated, the variations in the gut microbiota induced by A&#x03B2;<sub>1-42</sub> primarily influences the immune or inflammatory response in the gut.</p>
<p>The KEGG pathway results showed that the DEGs were mainly enriched in phagosome, antigen processing, and presentation, cell adhesion molecules (CAMs), PI3K-Akt signaling pathway, cytokine-cytokine receptor interaction, PPAR signaling pathway, ECM-receptor interaction, B cell receptor signaling pathway, and chemokine signaling pathway (<bold>Figure <xref ref-type="fig" rid="F11">11</xref></bold>, and more details were showed in Supplementary Tables <xref ref-type="supplementary-material" rid="SM1">S2</xref>-1&#x2013;<xref ref-type="supplementary-material" rid="SM1">S2-3</xref>), thereby indicating that A&#x03B2;<sub>1-42</sub> levels in the brain can influence the intestinal functions.</p>
<fig id="F11" position="float">
<label>FIGURE 11</label>
<caption><p>The KEGG pathway enrichment of DEGs in the small intestine transcriptome in deficient rats induced by A&#x03B2;<sub>1-42</sub>. <bold>(A)</bold> The group of A&#x03B2;-10 vs. the Normal; <bold>(B)</bold> the group of A&#x03B2;-20 vs. the Normal; <bold>(C)</bold> the group of A&#x03B2;-20 vs. the A&#x03B2;-10.</p></caption>
<graphic xlink:href="fnagi-09-00403-g011.tif"/>
</fig>
</sec>
<sec>
<title>Brain transcriptome analysis</title>
<p>After injection of A&#x03B2;<sub>1-42</sub> for 4 weeks, the rats were sacrificed, and the brain tissues dissected and frozen in liquid nitrogen for RNA extraction and high-throughput RNA-sequencing. The overview of the brain gene expression profile in AD model rats was shown in <bold>Figure <xref ref-type="fig" rid="F12">12</xref></bold>. The profiling analysis revealed the number of genes (<bold>Figures <xref ref-type="fig" rid="F12">12A-a,b</xref></bold>), the DEGs in <bold>Figure <xref ref-type="fig" rid="F12">12B</xref></bold>, Venn diagram (<bold>Figure <xref ref-type="fig" rid="F12">12C</xref></bold>), as well as, the relationships among the overlap between the different groups in <bold>Figure <xref ref-type="fig" rid="F12">12D</xref></bold>; the relative expressions of DEGs in all the three treated groups (A&#x03B2;<sub>1-42</sub>-10, A&#x03B2;<sub>1-42</sub>-20, and control) were shown in <bold>Table <xref ref-type="table" rid="T2">2</xref></bold>, which indicated that the A&#x03B2;<sub>1-42</sub> levels could significantly influence the brain transcriptome.</p>
<fig id="F12" position="float">
<label>FIGURE 12</label>
<caption><p>Brain transcriptome analysis in the deficit rats by injected A&#x03B2;<sub>1-42</sub>. <bold>(A)</bold> Statistics of the transcriptome sequences. <bold>(B)</bold> The differentially expressed genes in the brain at different concentration of A&#x03B2;<sub>1-42</sub>. <bold>(C)</bold> Venn diagram of DEGs. <bold>(D)</bold> The heat map of the relative expressions of DEGs in all the three groups.</p></caption>
<graphic xlink:href="fnagi-09-00403-g012.tif"/>
</fig>
<table-wrap position="float" id="T2">
<label>Table 2</label>
<caption><p>Differentially expressed genes in the brain of the deficient rats injected at different concentrations of A&#x03B2;<sub>1-42.</sub></p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<th valign="top" align="left">Genes</th>
<th valign="top" align="center" colspan="2">A&#x03B2;-10<hr/></th>
<th valign="top" align="center" colspan="2">A&#x03B2;-20<hr/></th>
</tr>
<tr>
<td valign="top" align="left"></td>
<th valign="top" align="center">Foldchange</th>
<th valign="top" align="center"><italic>p</italic>-value</th>
<th valign="top" align="center">Foldchange</th>
<th valign="top" align="center"><italic>p</italic>-value</th>
</tr>
<tr>
<td valign="top" align="left"></td>
<th valign="top" align="center">(Normal/A&#x03B2;-10)</th>
<td valign="top" align="center"></td>
<th valign="top" align="center">(Normal/A&#x03B2;-20)</th>
<td valign="top" align="center"></td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Cbln1</td>
<td valign="top" align="center">10.94</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000105</td></tr>
<tr>
<td valign="top" align="left">Grm4</td>
<td valign="top" align="center">2.39</td>
<td valign="top" align="center">0.000030</td>
<td valign="top" align="center">0.21</td>
<td valign="top" align="center">0.002146</td>
</tr>
<tr>
<td valign="top" align="left">Pcp2</td>
<td valign="top" align="center">60.50</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.09</td>
<td valign="top" align="center">0.000007</td>
</tr>
<tr>
<td valign="top" align="left">Uncx</td>
<td valign="top" align="center">36.00</td>
<td valign="top" align="center">0.000034</td>
<td valign="top" align="center">0.09</td>
<td valign="top" align="center">0.000041</td></tr>
<tr>
<td valign="top" align="left">Adora2a</td>
<td valign="top" align="center">2.31</td>
<td valign="top" align="center">0.000004</td>
<td valign="top" align="center">15.53</td>
<td valign="top" align="center">0.000001</td>
</tr>
<tr>
<td valign="top" align="left">Wdr66</td>
<td valign="top" align="center">3.13</td>
<td valign="top" align="center">0.000018</td>
<td valign="top" align="center">0.19</td>
<td valign="top" align="center">0.001367</td></tr>
<tr>
<td valign="top" align="left">Lhx5</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.000034</td>
<td valign="top" align="center">0.20</td>
<td valign="top" align="center">0.007717</td>
</tr>
<tr>
<td valign="top" align="left">Barhl2</td>
<td valign="top" align="center">3.13</td>
<td valign="top" align="center">0.036893</td>
<td valign="top" align="center">0.09</td>
<td valign="top" align="center">0.000025</td></tr>
<tr>
<td valign="top" align="left">Lhx1</td>
<td valign="top" align="center">30.79</td>
<td valign="top" align="center">0.000182</td>
<td valign="top" align="center">0.10</td>
<td valign="top" align="center">0.000055</td>
</tr>
<tr>
<td valign="top" align="left">Slc6a4</td>
<td valign="top" align="center">10.61</td>
<td valign="top" align="center">0.004566</td>
<td valign="top" align="center">0.23</td>
<td valign="top" align="center">0.015495</td></tr>
<tr>
<td valign="top" align="left">Gabra6</td>
<td valign="top" align="center">107.05</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.06</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Rgs9</td>
<td valign="top" align="center">2.88</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">10.66</td>
<td valign="top" align="center">0.000012</td>
</tr>
<tr>
<td valign="top" align="left">Tph2</td>
<td valign="top" align="center">4.79</td>
<td valign="top" align="center">0.007662</td>
<td valign="top" align="center">0.21</td>
<td valign="top" align="center">0.006924</td>
</tr>
<tr>
<td valign="top" align="left">Arhgap6</td>
<td valign="top" align="center">2.00</td>
<td valign="top" align="center">0.001638</td>
<td valign="top" align="center">8.30</td>
<td valign="top" align="center">0.000186</td>
</tr>
<tr>
<td valign="top" align="left">Btg1</td>
<td valign="top" align="center">2.16</td>
<td valign="top" align="center">0.000475</td>
<td valign="top" align="center">0.34</td>
<td valign="top" align="center">0.034729</td>
</tr>
<tr>
<td valign="top" align="left">Rxrg</td>
<td valign="top" align="center">2.33</td>
<td valign="top" align="center">0.000179</td>
<td valign="top" align="center">15.69</td>
<td valign="top" align="center">0.000004</td>
</tr>
<tr>
<td valign="top" align="left">Neurod1</td>
<td valign="top" align="center">3.51</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000025</td></tr>
<tr>
<td valign="top" align="left">Car8</td>
<td valign="top" align="center">3.90</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.12</td>
<td valign="top" align="center">0.000060</td>
</tr>
<tr>
<td valign="top" align="left">St14</td>
<td valign="top" align="center">2.78</td>
<td valign="top" align="center">0.017265</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000206</td></tr>
<tr>
<td valign="top" align="left">Trim54</td>
<td valign="top" align="center">0.36</td>
<td valign="top" align="center">0.000003</td>
<td valign="top" align="center">11.11</td>
<td valign="top" align="center">0.000192</td>
</tr>
<tr>
<td valign="top" align="left">Grid2</td>
<td valign="top" align="center">2.34</td>
<td valign="top" align="center">0.000518</td>
<td valign="top" align="center">0.21</td>
<td valign="top" align="center">0.002420</td></tr>
<tr>
<td valign="top" align="left">Slc30a3</td>
<td valign="top" align="center">0.46</td>
<td valign="top" align="center">0.000006</td>
<td valign="top" align="center">5.77</td>
<td valign="top" align="center">0.000880</td>
</tr>
<tr>
<td valign="top" align="left">En2</td>
<td valign="top" align="center">191.37</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.10</td>
<td valign="top" align="center">0.000026</td></tr>
<tr>
<td valign="top" align="left">Arhgef33</td>
<td valign="top" align="center">9.12</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000050</td>
</tr>
<tr>
<td valign="top" align="left">Tac1</td>
<td valign="top" align="center">4.23</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">31.52</td>
<td valign="top" align="center">0.000000</td></tr>
<tr>
<td valign="top" align="left">Slc1a6</td>
<td valign="top" align="center">2.00</td>
<td valign="top" align="center">0.016579</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000032</td>
</tr>
<tr>
<td valign="top" align="left">Crtam</td>
<td valign="top" align="center">2.24</td>
<td valign="top" align="center">0.000013</td>
<td valign="top" align="center">0.28</td>
<td valign="top" align="center">0.010983</td></tr>
<tr>
<td valign="top" align="left">Crtam</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.000115</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">0.000020</td>
</tr>
<tr>
<td valign="top" align="left">Drd2</td>
<td valign="top" align="center">2.73</td>
<td valign="top" align="center">0.000002</td>
<td valign="top" align="center">10.76</td>
<td valign="top" align="center">0.000026</td></tr>
<tr>
<td valign="top" align="left">Cga</td>
<td valign="top" align="center">22.26</td>
<td valign="top" align="center">0.002718</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">0.000031</td>
</tr>
<tr>
<td valign="top" align="left">Kcnh5</td>
<td valign="top" align="center">0.37</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">4.25</td>
<td valign="top" align="center">0.007422</td></tr>
<tr>
<td valign="top" align="left">Nyx</td>
<td valign="top" align="center">3.68</td>
<td valign="top" align="center">0.036361</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000541</td>
</tr>
<tr>
<td valign="top" align="left">Fibcd1</td>
<td valign="top" align="center">2.76</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">24.48</td>
<td valign="top" align="center">0.000000</td></tr>
<tr>
<td valign="top" align="left">Satb2</td>
<td valign="top" align="center">0.47</td>
<td valign="top" align="center">0.000200</td>
<td valign="top" align="center">43.65</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Hes3</td>
<td valign="top" align="center">7.22</td>
<td valign="top" align="center">0.008186</td>
<td valign="top" align="center">0.07</td>
<td valign="top" align="center">0.000006</td></tr>
<tr>
<td valign="top" align="left">Irx3</td>
<td valign="top" align="center">15.47</td>
<td valign="top" align="center">0.004015</td>
<td valign="top" align="center">0.14</td>
<td valign="top" align="center">0.001121</td>
</tr>
<tr>
<td valign="top" align="left">Adamts18</td>
<td valign="top" align="center">3.02</td>
<td valign="top" align="center">0.045565</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000091</td></tr>
<tr>
<td valign="top" align="left">Il16</td>
<td valign="top" align="center">3.40</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.10</td>
<td valign="top" align="center">0.000019</td>
</tr>
<tr>
<td valign="top" align="left">Tfap2b</td>
<td valign="top" align="center">3.39</td>
<td valign="top" align="center">0.022277</td>
<td valign="top" align="center">0.19</td>
<td valign="top" align="center">0.003907</td>
</tr>
<tr>
<td valign="top" align="left">Ppp1r17</td>
<td valign="top" align="center">17.05</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.12</td>
<td valign="top" align="center">0.000083</td>
</tr>
<tr>
<td valign="top" align="left">Impg1</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.009945</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">0.000060</td>
</tr>
<tr>
<td valign="top" align="left">Fat2</td>
<td valign="top" align="center">33.50</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.10</td>
<td valign="top" align="center">0.000009</td></tr>
<tr>
<td valign="top" align="left">Irx2</td>
<td valign="top" align="center">9.63</td>
<td valign="top" align="center">0.003845</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000157</td>
</tr>
<tr>
<td valign="top" align="left">Rgl3</td>
<td valign="top" align="center">3.76</td>
<td valign="top" align="center">0.000002</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000045</td>
</tr>
<tr>
<td valign="top" align="left">Barhl1</td>
<td valign="top" align="center">21.79</td>
<td valign="top" align="center">0.003154</td>
<td valign="top" align="center">0.20</td>
<td valign="top" align="center">0.011641</td></tr>
<tr>
<td valign="top" align="left">Cdhr1</td>
<td valign="top" align="center">2.16</td>
<td valign="top" align="center">0.001501</td>
<td valign="top" align="center">18.13</td>
<td valign="top" align="center">0.000003</td>
</tr>
<tr>
<td valign="top" align="left">Glra1</td>
<td valign="top" align="center">3.33</td>
<td valign="top" align="center">0.005627</td>
<td valign="top" align="center">0.22</td>
<td valign="top" align="center">0.005136</td></tr>
<tr>
<td valign="top" align="left">Cbln2</td>
<td valign="top" align="center">0.43</td>
<td valign="top" align="center">0.000035</td>
<td valign="top" align="center">0.21</td>
<td valign="top" align="center">0.042611</td>
</tr>
<tr>
<td valign="top" align="left">Pax3</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.035388</td>
<td valign="top" align="center">6.15</td>
<td valign="top" align="center">0.008361</td></tr>
<tr>
<td valign="top" align="left">Kcns1</td>
<td valign="top" align="center">0.12</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.10</td>
<td valign="top" align="center">0.000187</td></tr>
<tr>
<td valign="top" align="left">Skor1</td>
<td valign="top" align="center">35.05</td>
<td valign="top" align="center">0.005526</td>
<td valign="top" align="center">0.16</td>
<td valign="top" align="center">0.000376</td>
</tr>
<tr>
<td valign="top" align="left">Zic1</td>
<td valign="top" align="center">3.08</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.35</td>
<td valign="top" align="center">0.049800</td></tr>
<tr>
<td valign="top" align="left">Zic4</td>
<td valign="top" align="center">2.01</td>
<td valign="top" align="center">0.047534</td>
<td valign="top" align="center">14.65</td>
<td valign="top" align="center">0.000001</td>
</tr>
<tr>
<td valign="top" align="left">Cpne7</td>
<td valign="top" align="center">2.09</td>
<td valign="top" align="center">0.000020</td>
<td valign="top" align="center">77.78</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Emx1</td>
<td valign="top" align="center">0.46</td>
<td valign="top" align="center">0.001804</td>
<td valign="top" align="center">0.35</td>
<td valign="top" align="center">0.038103</td></tr>
<tr>
<td valign="top" align="left">Kcng4</td>
<td valign="top" align="center">2.18</td>
<td valign="top" align="center">0.000235</td>
<td valign="top" align="center">0.30</td>
<td valign="top" align="center">0.023002</td>
</tr>
<tr>
<td valign="top" align="left">Zfp521</td>
<td valign="top" align="center">3.24</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.20</td>
<td valign="top" align="center">0.001811</td>
</tr>
<tr>
<td valign="top" align="left">Calb2</td>
<td valign="top" align="center">3.89</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.17</td>
<td valign="top" align="center">0.000482</td></tr>
<tr>
<td valign="top" align="left">LOC688778</td>
<td valign="top" align="center">0.46</td>
<td valign="top" align="center">0.000054</td>
<td valign="top" align="center">51.87</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Atp2a3</td>
<td valign="top" align="center">4.19</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000074</td>
</tr>
<tr>
<td valign="top" align="left">Ptpn22</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.035388</td>
<td valign="top" align="center">0.07</td>
<td valign="top" align="center">0.000080</td>
</tr>
<tr>
<td valign="top" align="left">Gng7</td>
<td valign="top" align="center">2.88</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">24.88</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Asic4</td>
<td valign="top" align="center">2.15</td>
<td valign="top" align="center">0.000048</td>
<td valign="top" align="center">11.89</td>
<td valign="top" align="center">0.000008</td></tr>
<tr>
<td valign="top" align="left">Npas4</td>
<td valign="top" align="center">2.04</td>
<td valign="top" align="center">0.000529</td>
<td valign="top" align="center">13.37</td>
<td valign="top" align="center">0.000006</td>
</tr>
<tr>
<td valign="top" align="left">Cbln3</td>
<td valign="top" align="center">108.68</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">0.000002</td></tr>
<tr>
<td valign="top" align="left">Adra1d</td>
<td valign="top" align="center">0.49</td>
<td valign="top" align="center">0.000370</td>
<td valign="top" align="center">4.54</td>
<td valign="top" align="center">0.006404</td>
</tr>
<tr>
<td valign="top" align="left">Ctxn3</td>
<td valign="top" align="center">3.24</td>
<td valign="top" align="center">0.006074</td>
<td valign="top" align="center">0.16</td>
<td valign="top" align="center">0.000811</td></tr>
<tr>
<td valign="top" align="left">Drd1</td>
<td valign="top" align="center">2.50</td>
<td valign="top" align="center">0.000005</td>
<td valign="top" align="center">35.19</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Syndig1l</td>
<td valign="top" align="center">3.07</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">17.72</td>
<td valign="top" align="center">0.000001</td>
</tr>
<tr>
<td valign="top" align="left">Cdh15</td>
<td valign="top" align="center">2.20</td>
<td valign="top" align="center">0.000772</td>
<td valign="top" align="center">0.20</td>
<td valign="top" align="center">0.001638</td></tr>
<tr>
<td valign="top" align="left">Cnpy1</td>
<td valign="top" align="center">36.47</td>
<td valign="top" align="center">0.000030</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000160</td>
</tr>
<tr>
<td valign="top" align="left">Robo3</td>
<td valign="top" align="center">0.22</td>
<td valign="top" align="center">0.000001</td>
<td valign="top" align="center">26.35</td>
<td valign="top" align="center">0.001324</td></tr>
<tr>
<td valign="top" align="left">Cyp11b2</td>
<td valign="top" align="center">0.23</td>
<td valign="top" align="center">0.000000</td>
<td valign="top" align="center">6.98</td>
<td valign="top" align="center">0.004899</td>
</tr>
<tr>
<td valign="top" align="left">Lrrc10b</td>
<td valign="top" align="center">2.40</td>
<td valign="top" align="center">0.000035</td>
<td valign="top" align="center">34.15</td>
<td valign="top" align="center">0.000000</td></tr>
<tr>
<td valign="top" align="left">Mab21l2</td>
<td valign="top" align="center">4.00</td>
<td valign="top" align="center">0.000280</td>
<td valign="top" align="center">0.17</td>
<td valign="top" align="center">0.000872</td>
</tr>
<tr>
<td valign="top" align="left">Slc6a5</td>
<td valign="top" align="center">4.53</td>
<td valign="top" align="center">0.003476</td>
<td valign="top" align="center">0.08</td>
<td valign="top" align="center">0.000009</td></tr>
<tr>
<td valign="top" align="left">Myom3</td>
<td valign="top" align="center">6.95</td>
<td valign="top" align="center">0.000135</td>
<td valign="top" align="center">0.33</td>
<td valign="top" align="center">0.049080</td>
</tr>
<tr>
<td valign="top" align="left">Svep1</td>
<td valign="top" align="center">2.27</td>
<td valign="top" align="center">0.000253</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000107</td>
</tr>
<tr>
<td valign="top" align="left">Tll1</td>
<td valign="top" align="center">2.15</td>
<td valign="top" align="center">0.034882</td>
<td valign="top" align="center">0.20</td>
<td valign="top" align="center">0.003254</td></tr>
<tr>
<td valign="top" align="left">Irx1</td>
<td valign="top" align="center">5.63</td>
<td valign="top" align="center">0.001444</td>
<td valign="top" align="center">0.23</td>
<td valign="top" align="center">0.009492</td>
</tr>
<tr>
<td valign="top" align="left">Eomes</td>
<td valign="top" align="center">10.74</td>
<td valign="top" align="center">0.030867</td>
<td valign="top" align="center">0.07</td>
<td valign="top" align="center">0.000011</td></tr>
<tr>
<td valign="top" align="left">Tmem215</td>
<td valign="top" align="center">0.34</td>
<td valign="top" align="center">0.000002</td>
<td valign="top" align="center">10.90</td>
<td valign="top" align="center">0.000267</td>
</tr>
<tr>
<td valign="top" align="left">Spp1</td>
<td valign="top" align="center">3.32</td>
<td valign="top" align="center">0.000003</td>
<td valign="top" align="center">0.15</td>
<td valign="top" align="center">0.000348</td>
</tr>
<tr>
<td valign="top" align="left">Comp</td>
<td valign="top" align="center">6.67</td>
<td valign="top" align="center">0.000051</td>
<td valign="top" align="center">0.29</td>
<td valign="top" align="center">0.024367</td>
</tr>
<tr>
<td valign="top" align="left">Shisa8</td>
<td valign="top" align="center">3.49</td>
<td valign="top" align="center">0.000142</td>
<td valign="top" align="center">0.13</td>
<td valign="top" align="center">0.000128</td></tr>
<tr>
<td valign="top" align="left">Gpr6</td>
<td valign="top" align="center">2.45</td>
<td valign="top" align="center">0.000035</td>
<td valign="top" align="center">72.86</td>
<td valign="top" align="center">0.000000</td>
</tr>
<tr>
<td valign="top" align="left">Gdf10</td>
<td valign="top" align="center">4.42</td>
<td valign="top" align="center">0.001245</td>
<td valign="top" align="center">0.16</td>
<td valign="top" align="center">0.000964</td></tr>
<tr>
<td valign="top" align="left">Zic2</td>
<td valign="top" align="center">2.20</td>
<td valign="top" align="center">0.001201</td>
<td valign="top" align="center">0.21</td>
<td valign="top" align="center">0.002489</td>
</tr>
<tr>
<td valign="top" align="left">Dao</td>
<td valign="top" align="center">11.94</td>
<td valign="top" align="center">0.000011</td>
<td valign="top" align="center">0.12</td>
<td valign="top" align="center">0.000114</td></tr>
<tr>
<td valign="top" align="left">Lrp2</td>
<td valign="top" align="center">3.58</td>
<td valign="top" align="center">0.000003</td>
<td valign="top" align="center">0.28</td>
<td valign="top" align="center">0.013024</td>
</tr>
<tr>
<td valign="top" align="left">AABR07010944.1</td>
<td valign="top" align="center">Infinity</td>
<td valign="top" align="center">0.006930</td>
<td valign="top" align="center">0.12</td>
<td valign="top" align="center">0.001066</td>
</tr>
<tr>
<td valign="top" align="left">Sdc1</td>
<td valign="top" align="center">4.80</td>
<td valign="top" align="center">0.000003</td>
<td valign="top" align="center">0.11</td>
<td valign="top" align="center">0.000046</td></tr>
</tbody>
</table>
</table-wrap>
<p>The GO term enrichment results revealed that the single-multicellular organism process (GO:0044707), nervous system development (GO:0007399), system development (GO:0048731), single-organism developmental process (GO:0044767), multicellular organism development (GO:0007275), developmental process (GO:0032502), generation of neurons (GO:0048699), neurogenesis (GO:0022008), neuron differentiation (GO:0030182), and cell differentiation (GO:0030154) (Supplementary Tables <xref ref-type="supplementary-material" rid="SM1">S3-1</xref>&#x2013;<xref ref-type="supplementary-material" rid="SM1">S3-3</xref>) were influenced after treatment with A&#x03B2;<sub>1-42</sub>. In the A&#x03B2;<sub>1-42</sub>-20 group, the synapse (GO:0045202), synaptic signaling (GO:0099536), synaptic transmission (GO:0007268), trans-synaptic signaling (GO:0099537), synapse part (GO:0044456), central nervous system development (GO:0007417), and behavior (GO:0007610) were changed more than that in the A&#x03B2;<sub>1-42</sub>-10 group, which indicated that the occurrence of AD is dependent on the cumulative amount of A&#x03B2;<sub>1-42</sub>. The KEGG pathway results showed that the DEGs were enriched mainly in neuroactive ligand-receptor interaction, cAMP signaling pathway, calcium signaling pathway, serotonergic synapse, PI3K-Akt signaling pathway, dopaminergic synapse, and ECM-receptor interaction (<bold>Figure <xref ref-type="fig" rid="F13">13</xref></bold>, additional details were shown in Supplementary Tables <xref ref-type="supplementary-material" rid="SM1">S4-1</xref>&#x2013;<xref ref-type="supplementary-material" rid="SM1">S4-3</xref>), all which indicated that the A&#x03B2;<sub>1-42</sub> levels can significantly influence the brain function.</p>
<fig id="F13" position="float">
<label>FIGURE 13</label>
<caption><p>The KEGG pathway enrichment of DEGs in brain transcriptome in the deficit rats induced by A&#x03B2;<sub>1-42</sub>. <bold>(A)</bold> The group of A&#x03B2;-10 vs. the Normal; <bold>(B)</bold> the group of A&#x03B2;-20 vs. the Normal; <bold>(C)</bold> the group of A&#x03B2;-20 vs. the A&#x03B2;-10.</p></caption>
<graphic xlink:href="fnagi-09-00403-g013.tif"/>
</fig>
</sec>
</sec></sec>
</sec>
<sec><title>Discussion</title>
<p>Increasing evidence suggests that the microbiota-gut-brain axis plays a key role in regulating brain functions, and prebiotics are widely considered to have potential as modulators of brain dysfunctions; however, only limited studies are yet available. Herein, we reported that fructooligosaccharides from <italic>M. officinalis</italic> could markedly modify the behavior, improve oxidative stress and inflammation disorder, regulate the synthesis and secretion of neurotransmitter, ameliorate the swelling of brain tissues, and reduce neuronal apoptosis. We also reported that OMO administration alters the diversity and stability of the microbial community, the expression of the genes of AD intracellular markers such as Tau and A&#x03B2;<sub>1-42</sub>. In addition, OMO administration exerted an adequate prebiotic role in regulating the composition and metabolism of gut microbiota in an overdose antibiotics-treated IBD mice model.</p>
<p>Gut microbiota plays a major role in maintaining normal physiological functions in the host. The changes in gut microbiota can lead to changes in brain function, thereby affecting the host behavior (<xref ref-type="bibr" rid="B65">Vuong et al., 2017</xref>). Recent studies showed a significant correlation between the changes in gut microbiota and cognitive behavior (<xref ref-type="bibr" rid="B19">Dinan and Cryan, 2017</xref>). The modulation of gut microbiota by germ-free animals, probiotics or antibiotics intervention, and fecal microbiota transplantation (FMT) can influence the cognitive behavior of the host (<xref ref-type="bibr" rid="B29">Hu et al., 2016</xref>). Our data were in agreement with previous studies, showing that the gut microbiota in two AD-like model rats was altered as compared to the normal rats, as the abundance of <italic>Clostridia</italic> and <italic>Clostridiales</italic> in A&#x03B2;<sub>1-42</sub>-induced groups increased significantly (<italic>p</italic> &#x003C; 0.05), while the groups administered OMO can reverse those changes, especially the probiotic <italic>Lactobacillus</italic> and <italic>Akkermansia</italic> increased distinctly (<italic>p</italic> &#x003C; 0.05).</p>
<p>The probiotic administration had a marked effect on the cognitive behavior. The prototype probiotic bacterium has been found to up-regulate the hormone oxytocin and systemic immune responses in order to achieve a broad range of health benefits involving wound healing, mental health, metabolism, and myoskeletal maintenance (<xref ref-type="bibr" rid="B55">Servin, 2004</xref>; <xref ref-type="bibr" rid="B20">Erdman and Poutahidis, 2016</xref>). Studies showed that <italic>Lactobacillus pentosus</italic> var. plantarum C29 from kimchi, a traditional food manufactured by fermenting vegetables (<xref ref-type="bibr" rid="B45">Park et al., 2014</xref>), was beneficial to health. It can also protect the memory deficits by inducing the expressions of BDNF and p-CREB in scopolamine-induced memory-deficient mice (<xref ref-type="bibr" rid="B33">Jung et al., 2012</xref>), anti-inflammatory amelioration of age-dependent memory impairment in Fischer 344 rats (<xref ref-type="bibr" rid="B31">Jeong et al., 2015</xref>), and ameliorate memory impairment and inflammation in <sc>D</sc>-galactose-induced accelerated aging mouse (<xref ref-type="bibr" rid="B70">Woo et al., 2014</xref>). Another study also showed that <italic>L. plantarum</italic> could attenuate anxiety-related behavior and protect against stress-induced dysbiosis in adult zebrafish (<xref ref-type="bibr" rid="B17">Davis et al., 2016</xref>). <italic>Lactobacilli</italic> and <italic>Bifidobacteria</italic> exhibited antagonistic activities against microbial pathogens (<xref ref-type="bibr" rid="B55">Servin, 2004</xref>). Our data were in agreement with previous studies showing that <italic>Lactobacillus</italic> can ameliorate memory deficiencies (<bold>Figure <xref ref-type="fig" rid="F4">4H</xref></bold>); the relative abundance of A&#x03B2;<sub>1-42</sub>-induced <italic>Lactobacillus</italic> was reduced starkly, especially in the high-dose group. As a result of OMO administration, the relative abundance of <italic>Lactobacillus</italic> was increased significantly; also, the MWM tests showed that the learning and memory abilities were improved (<bold>Figure <xref ref-type="fig" rid="F3">3B</xref></bold>). These results suggested that OMO can promote the abundance of <italic>Lactobacillus</italic> and ameliorate the memory deficiencies.</p>
<p>Fructo-oligosaccharides (FOS) are commonly regarded as a type of prebiotics, favorably stimulating the growth of <italic>Bifidobacteria</italic> and <italic>Lactobacilli</italic>. FOS from <italic>Stevia rebaudiana</italic> roots enhanced the growth of specific strains of both <italic>Bifidobacteria</italic> and <italic>Lactobacilli</italic>, especially, with respect to their fermentation ability (<xref ref-type="bibr" rid="B53">Sanches Lopes et al., 2016</xref>). FOS are reserve carbohydrates with important positive health effects and technological applications in the food industry. Another previous study indicated that short-chain fructooligosaccharides could be used optimally in combination with <italic>Bifidobacterium animalis</italic> or <italic>B. longum</italic> strains for the development of synbiotic foods or dietary supplements (<xref ref-type="bibr" rid="B61">Vald&#x00E9;s-Varela et al., 2017</xref>). Our results showed that FOS from <italic>M. officinalis</italic> also enhances the growth of some probiotics similar to that of <italic>Bifidobacteria</italic> and <italic>Lactobacilli.</italic></p>
<p>The microbiota can modulate the changes in the gut barrier as well as metabolic and inflammatory responses. Gut barrier function is a key to maintaining a balanced response between the host and its microbiome. This highly complex system involves numerous microbiota-derived factors. <italic>Akkermansia muciniphila</italic> is positively correlated with a lean phenotype, reduced body weight gain, amelioration of metabolic responses, and restoration of gut barrier function is effectuated by the modulation of mucus layer thickness (<xref ref-type="bibr" rid="B8">Bland, 2016</xref>; <xref ref-type="bibr" rid="B18">Derrien et al., 2016</xref>; <xref ref-type="bibr" rid="B25">Greer et al., 2016</xref>; <xref ref-type="bibr" rid="B27">Henning et al., 2017</xref>; <xref ref-type="bibr" rid="B62">Van Herreweghen et al., 2017</xref>). Our data in <sc>D</sc>-galactose-induced deficient rats showed that the <italic>Akkermansia</italic> were increased (<italic>p</italic> &#x003C; 0.05, <bold>Figure <xref ref-type="fig" rid="F2">2D</xref></bold>), and the intestinal pathological tissue changes (<bold>Figure <xref ref-type="fig" rid="F1">1E</xref></bold>) were improved after administration of OMO, thereby indicating that OMO administration can improve the gut barrier function via targeting the abundance of <italic>Akkermansia</italic>, but need more studies.</p>
<p>Increased gut permeability (leaky gut) and alterations in gut microbiota are now widely accepted as an important link with the etiology, course, and treatment of several neuropsychiatric disorders (<xref ref-type="bibr" rid="B5">Anderson et al., 2016</xref>). Gut microbiota-released LPS contributes to chronic inflammation and oxidative stress (<xref ref-type="bibr" rid="B34">Le Sage et al., 2017</xref>). Moreover, inflammation was first implicated in AD pathology and development, with the neuropathological findings of activated inflammatory cells (microglia and astrocytes) and inflammatory proteins (for example, cytokines and complement), surrounding the amyloid plaques and the nerve fiber tangles (<xref ref-type="bibr" rid="B3">Alkasir et al., 2017</xref>). Our study showed that OMO administration could reduce the levels of LPS in TNBS-induced IBD mice and some pro-inflammatory cytokines in both A&#x03B2;<sub>1-42</sub> induced deficit rats (<bold>Figure <xref ref-type="fig" rid="F3">3C</xref></bold>) and TNBS-induced IBD mice (<bold>Figures <xref ref-type="fig" rid="F5">5C</xref></bold>, <bold><xref ref-type="fig" rid="F6">6</xref></bold>). On the other hand, it can increase the levels of some anti-inflammatory cytokines, which suggested that the administration of OMO (prebiotics) can improve the host inflammatory immune response. The data also showed that OMO administration could enhance the oxidative stress, similar to elevated SOD, MDA, CAT, and inhibiting the MDA production in the <sc>D</sc>-galactose-induced deficit rats (<bold>Figure <xref ref-type="fig" rid="F1">1D</xref></bold>). The gut microbiota is known to play a vital role in those responses (<xref ref-type="bibr" rid="B64">Vanegas et al., 2017</xref>), although not fully understood. Taken together, we can summarize that OMO administration influences the host inflammatory immune response and oxidative stress by regulating the gut microbiota.</p>
<p>Preliminary data suggested that FOS increases fecal <italic>Bifidobacteria</italic>, induce immunoregulatory dendritic cell (DC) responses, and reduce the disease activity in patients with Crohn&#x2019;s disease (<xref ref-type="bibr" rid="B7">Benjamin et al., 2011</xref>). Moreover, <italic>Bifidobacteria</italic> are predominant bacterial species in the human gut microbiota and have been considered to exert a beneficial effect on human health by maintaining the equilibrium of the resident organisms. <italic>B. longum</italic> with FOS reduces TNF-&#x03B1;, CRP, serum AST levels, HOMA-IR, serum endotoxin, steatosis, and the non-alcoholic steatohepatitis activity index significantly (<xref ref-type="bibr" rid="B42">Malaguarnera et al., 2012</xref>). Human milk contains <italic>B. breve</italic>, <italic>Streptococcus thermophilus</italic>, and short-chain galactooligosaccharides/long-chain fructooligosaccharides with pectin-derived acidic oligosaccharides conferring a protective role against gastrointestinal infections: ameliorating the AD symptoms, modulating the immune response, binding the viral particles, and protecting against rotavirus infection (<xref ref-type="bibr" rid="B51">Rigo-Adrover et al., 2017</xref>). The combination of fermented formula with short-chain galactooligosaccharides and long-chain fructooligosaccharides was well-tolerated showing a low overall crying time, low incidence of infantile colic infection, and a stool-softening effect in healthy term infants (<xref ref-type="bibr" rid="B63">Vandenplas et al., 2017</xref>). After a broad spectrum antibiotics treatment, the IBD mice model showed that FOS from <italic>M. officinalis</italic> also increases fecal <italic>Bifidobacteria</italic>, ameliorates the symptoms of IBD, and modulates the immune response; the A&#x03B2;<sub>1-42</sub> induced deficient rats showed a similar effect.</p>
<p>The gut microbiota can regulate the activity in the peripheral and central nervous system by various means of communication including vagal nerve and adrenergic nerve activation as well as producing several molecular candidates such as neurotransmitters, neuropeptides, endocrine hormones, and immunomodulators. Host stress hormones, such as noradrenaline, might affect the bacterial activities or signal between bacteria may change the microbial diversity and actions of the gut microbiota. However, these bacteria are capable of synthesizing and releasing several neurotransmitters and neuromodulators or eliciting the synthesis and release of neuropeptides from enteroendocrine cells. Previous studies showed that <italic>Lactobacillus</italic> and <italic>Bifidobacterium</italic> species could produce short-chain fatty acids; <italic>Escherichia</italic>, <italic>Bacillus</italic>, and <italic>Saccharomyces</italic> spp. can produce norepinephrine; spore-forming microbes can produce 5-HT; <italic>Bacillus</italic> can produce dopamine, and <italic>Lactobacillus</italic> can produce acetylcholine (<xref ref-type="bibr" rid="B66">Wall et al., 2014</xref>; <xref ref-type="bibr" rid="B48">Potgieter et al., 2015</xref>; <xref ref-type="bibr" rid="B71">Yano et al., 2015</xref>; <xref ref-type="bibr" rid="B3">Alkasir et al., 2017</xref>). In this study, the monoamine neurotransmitter (NE, DA, 5-HT, and 5-HIAA) levels in the brain tissue were reduced in A&#x03B2;<sub>1-42</sub> induced deficient rats, and the OMO administration can reverse this decreasing tendency. Thus, we can conclude that OMO influences some bacteria that affect the synthesis and release of some neurotransmitters and neuromodulators. Similar effects were observed in mice subjected to chronic stress, where the observed behavioral, neurochemical, genetic, and neuroendocrine changes after prebiotic (fructooligosaccharides and galactooligosaccharides) administration could be mediated partially by short chain fatty acids (SCFAs) (<xref ref-type="bibr" rid="B9">Burokas et al., 2017</xref>); the increased levels of acetate, propionate, and n-butyrate correlated with behavior and gene expression.</p>
<p>We also observed novel changes in microbiota composition, especially the increase in <italic>Bifidobacterium</italic>, immunological enhancement (<bold>Figures <xref ref-type="fig" rid="F5">5</xref></bold>, <bold><xref ref-type="fig" rid="F6">6</xref></bold>), and gut barrier impairment (<bold>Figure <xref ref-type="fig" rid="F5">5</xref></bold>) in TNBS-induced IBD mice. Previous reports showed that <italic>Bifidobacterium</italic> combined with <italic>L. acidophilus</italic>, <italic>L. casei</italic>, and <italic>L. fermentum</italic> for 12 weeks can affect the cognitive function and some metabolic statuses in AD patients (<xref ref-type="bibr" rid="B2">Akbari et al., 2016</xref>), and <italic>B. longum</italic> 1714 reduced the stress and improved the memory in healthy volunteers (<xref ref-type="bibr" rid="B4">Allen et al., 2016</xref>). The abundance of <italic>Bacteroides</italic> was also increased with OMO administration in the two AD-like animal models (<bold>Figures <xref ref-type="fig" rid="F3">3</xref></bold>, <bold><xref ref-type="fig" rid="F5">5</xref></bold>). <italic>Bacteroides</italic> are strict anaerobes critical since the initiation of life (<xref ref-type="bibr" rid="B6">Arboleya et al., 2015</xref>), and some strains have been used as probiotics. Previous studies have shown that <italic>Bacteroides fragilis</italic> could reverse the autism-like behavior in mice (<xref ref-type="bibr" rid="B28">Hsiao et al., 2013</xref>).</p>
<p>The gut microbiota contains highly diverse microbial communities that play a critical role in the metabolic, immunological, and protective functions in health. This phenomenon is influenced by several factors including genetics, host physiology (age of the host, disease, and stress) and environmental factors such as living conditions and use of medications. Increasingly, diet has been recognized as a key environmental factor that mediates the composition and metabolic function of the gut microbiota. Furthermore, the consumption of specific dietary ingredients, such as oil, fibers, and prebiotics, is an avenue that modulates the microbiota. Studies on pigs also suggests that the combination with fructooligosaccharides might represent a valuable symbiotic strategy to increase the probiotic levels of bacteria and survival in the gastrointestinal tracts for feed and food applications (<xref ref-type="bibr" rid="B59">Tanner et al., 2015</xref>). The administration of such oligosaccharides is attributable to high interindividual variation of the communities in fecal bacteria from pet cats and dogs (<xref ref-type="bibr" rid="B22">Garcia-Mazcorro et al., 2017</xref>). In this study, the fructooligosaccharides were extracted from <italic>M</italic>. <italic>officinalis</italic>, which was widely used in soup, wine, and sweetmeats in South China. Fructo-oligosaccharides are soluble fiber extensively used as prebiotics that is conventionally associated with the stimulation of beneficial bacteria such as <italic>Bifidobacteria</italic> and <italic>Lactobacilli</italic>, among other gut members. However, the mechanisms underlying the fructooligosaccharides stimulation of the beneficial bacteria are yet unknown. A previous study showed that the obtained nutrients process of bacteria require cell membrane protein machines called SusCD complexes (extracellular substrate binding proteins and SusC transporter) (<xref ref-type="bibr" rid="B24">Glenwright et al., 2017</xref>), in order to detect the binding capacities between SusCD and nutrients (as starch and other dietary polysaccharides) can evaluate the activity of prebiotics of nutritional ingredients. In this study, the molecular docking analysis was carried out for the evaluation of the binding capacities between SusCD and fructooligosaccharides from <italic>M. officinalis</italic>. The molecular docking study was conducted using the CDOCKER protocol for the four polysaccharides from <italic>M. officinalis</italic> using the Discovery Studio 2.5 (DS2.5) Provisional software. A total of four components (<bold>Figures <xref ref-type="fig" rid="F14">14A,B</xref></bold>) from <italic>M. officinalis</italic> were assimilated by literature search, and 1048 poses were generated for all the compounds investigated. The docked poses were ranked by the CDOCKER-ENERGY, and the top 10 poses with the co-crystal ligand for SusCD were retained (<bold>Figure <xref ref-type="fig" rid="F14">14</xref></bold>). The data revealed 4 hits namely, compounds 3 (Nystose), 4 (<italic>F</italic>-fructofuranosylnystose), 5 (fructooligosaccharide, GF5), and 6 (fructooligosaccharide, GF6) with CDOCKER-ENERGY -52.0244180, -75.5881, -101.88, and -110.387, respectively (<bold>Figure <xref ref-type="fig" rid="F14">14C</xref></bold>). This indicated that the 4 polysaccharides might exert a potent binding activity on SusCD. The interaction between the SusCD protein and the four compounds was further analyzed using the receptor-ligand interaction module in DS. The analysis between SusCD and compound 3 revealed that 9 hydrogen bond interactions appeared in the docked pose. The analysis between SusCD and compound 5 revealed that 9 hydrogen bond interactions appeared in the docked pose. The analysis between SusCD and compound 5 revealed that 7 hydrogen bond interactions appeared in the docked pose. The analysis between SusCD and compound 6 revealed that 9 hydrogen bond interactions appeared in the docked pose. These results suggested that the fructooligosaccharides from <italic>M. officinalis</italic> could be absorbed sufficiently by bacteria with the help of SusCD, serving as optimal nutritional ingredients or prebiotics for bacteria.</p>
<fig id="F14" position="float">
<label>FIGURE 14</label>
<caption><p>Binding pattern of fructooligosaccharides from <italic>Morinda officinalis</italic>: <bold>(A)</bold> HPLC-ELSD analysis of fructooligosaccharides from <italic>M. officinalis</italic>. <bold>(B)</bold> The chemical structure of nystose (3), <italic>F</italic>-fructofuranose nystose (4), fructooligosaccharide (GF5, 5), fructooligosaccharide (GF6, 6); <bold>(C)</bold> The docked poses were ranked by CDOCKER- ENERGY and the top 10 poses with the co-crystal ligand for SusCD were retained. The data revealed compounds 3, 4, 5, and 6 with CDOCKER-ENERGY of &#x2013;52.0244180, &#x2013;75.5881, &#x2013;101.88, and &#x2013;110.387, respectively.</p></caption>
<graphic xlink:href="fnagi-09-00403-g014.tif"/>
</fig>
<p>The changes in behavior and gut microbiota, as a result of different concentrations of A&#x03B2;<sub>1-42</sub>, coincided with the alterations in gene expression in critical brain and intestinal regions. The transcriptome analysis of intestine and brain tissues at the 5th week induced by A&#x03B2;<sub>1-42</sub> showed that the expression of some genes changed significantly (<bold>Figures <xref ref-type="fig" rid="F10">10</xref></bold>, <bold><xref ref-type="fig" rid="F12">12</xref></bold>). Furthermore, to understand the genetic pathways of the gut-brain axis, the significant DEGs both in the brain and intestine were analyzed to identify the gene elements by an interactive information using the Wayne chart (<bold>Figures <xref ref-type="fig" rid="F15">15A</xref>&#x2013;<xref ref-type="fig" rid="F15">C</xref></bold>), which revealed that the interactive genes were increased by the A&#x03B2;<sub>1-42</sub> levels (14 for A&#x03B2;-10 vs. normal, while 25 for A&#x03B2;-20 vs. normal, <italic>p</italic> &#x003C; 0.05). The KEGG pathway enrichment analysis showed that the DEGs were primarily enriched in protein digestion and absorption and platelet activation for A&#x03B2;-10 induced group (<bold>Figure <xref ref-type="fig" rid="F15">15D</xref></bold>). This phenomenon might be attributed to the colonic bacteria that might not be able to run well or are lost, the non-digestible peptides and proteins (collagen) could not be fermented, and some short-chain fatty acids such as butyrate, propionate, and acetate are deficient, which resulted in platelet activation. Thus, the expressions of Col1a1, Col3a1, and Col14a1 mRNA were changed. With the altered mRNA expression of Lamc2, Sstr3, Nts, Spp1, Il6r, Vip, Kcnk3, and Nr4a1, the PI3K-Akt signaling pathway, neuroactive ligand-receptor interaction, focal adhesion, and ECM-receptor interaction were activated in the A&#x03B2;-20-induced group (<bold>Figure <xref ref-type="fig" rid="F15">15E</xref></bold>). With the increased levels of A&#x03B2;<sub>1-42</sub> levels, the mRNA expressions of Igsf8, Kcnk3, and Mef2c were changed, and the KEGG pathway enrichment analysis showed that the aldosterone synthesis and secretion and MAPK signaling pathway were influenced (<bold>Figure <xref ref-type="fig" rid="F15">15F</xref></bold>). Together with the changes in the gut microbiota community diversity shown in <bold>Figure <xref ref-type="fig" rid="F8">8</xref></bold>, and the transcriptome analysis data of intestine and brain, we concluded that the A&#x03B2;<sub>1-42</sub> levels in hippocampus interact the gut and microbiota, although further studies are essential for substantiation.</p>
<fig id="F15" position="float">
<label>FIGURE 15</label>
<caption><p>The interactive information analysis of DEGs in brain and intestine in deficient rats by injected A&#x03B2;<sub>1-42</sub>. <bold>(A&#x2013;C)</bold> Wayne chart of DEGs in the brain and intestine transcriptome. <bold>(D&#x2013;F)</bold> KEGG pathway enrichment of DEGs in the brain and intestine transcriptome.</p></caption>
<graphic xlink:href="fnagi-09-00403-g015.tif"/>
</fig>
<p>Antibiotics intervention in APPSWE/PS1&#x0394;E9 mouse model suggests that the diversity of the gut microbiota community can regulate the host innate immunity mechanisms that impact A&#x03B2; amyloidosis (<xref ref-type="bibr" rid="B44">Minter et al., 2016</xref>). The fecal microbiota transplantation implemented from A&#x03B2; precursor protein (APP) transgenic mice to non-transgenic wild-type mice showed a drastically increased level of cerebral A&#x03B2; levels, thereby indicating a microbial involvement in the development of A&#x03B2; pathology, and microbiota contributes to the development of neurodegenerative diseases (<xref ref-type="bibr" rid="B26">Harach et al., 2017</xref>; <xref ref-type="bibr" rid="B41">Liu et al., 2017</xref>). We also observed that the diversity in the gut microbiota community altered with the levels of A&#x03B2; and the induced time (<bold>Figure <xref ref-type="fig" rid="F8">8</xref></bold>). Although the complex networks of communication between the gut microbiota and the brain are not yet fully elucidates, it is clear that prebiotics strongly modulates the ecology of the microbiota. However, the role of the microbial composition and the vast quantity, diversity, and functional capabilities of all these gut microorganisms on the brain and behavior are yet to be determined.</p>
</sec>
<sec><title>Conclusion</title>
<p>Taken together, these data provide further evidence for a beneficial role of fructooligosaccharides (prebiotics) from <italic>M. officinalis</italic> and the effects on microbiota-brain-gut axis in AD, but need more studies. This study characterized OMO as a promising naturally occurring chemical constituent and suggested microbiota-brain-gut axis as a putative new therapeutic target for the treatment of various neurological diseases by using <italic>M. officinalis</italic> in conventional medicine.</p>
</sec>
<sec><title>Ethics Statement</title>
<p>The animal protocols used in this work were approved by the Institutional Animal Care and Use committee of the Center of Laboratory Animals of the Guangdong Institute of Microbiology (GT-IACUC20160426).</p>
</sec>
<sec><title>Author Contributions</title>
<p>DC designed the study, carried out the computational analyses and wrote the manuscript. JY and GL collected animal physiological data and fecal samples and extracted ruminal DNA. XY and XT collected animal physiological data and brain samples. DC, TY, and OS collected data regarding the microbial metabolic networks and transcriptome analysis. YX and QW helped to design the study and to develop the metagenomic analysis tools and wrote the manuscript. GZ helped with computational tool development and statistical analyses (PCA). All authors read and approved the final manuscript.</p>
</sec>
<sec><title>Conflict of Interest Statement</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
</body>
<back>
<fn-group>
<fn fn-type="financial-disclosure">
<p><bold>Funding.</bold> The present work was supported by the financial support from the Guangdong Science and Technology Plan Projects (2015A020211021; 2016A050502032), the Guangzhou Science and Technology Plan Projects (201504281708257; 201604020009), the High-level Leading Talent Introduction Program of GDAS (2016GDASRC-0102), and the Nanyue Microbial Talents Cultivation Fund of Guangdong Institute of Microbiology and the Guangzhou Medical University Research Projects (2016C28).</p>
</fn>
</fn-group>
<ack>
<p>The authors would like to thank Zhang Heming, Burton B. Yang for helpful discussions in the preparation of this manuscript. Sequencing service was provided by Personal Biotechnology Co., Ltd., Shanghai, China.</p>
</ack>
<sec sec-type="supplementary material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fnagi.2017.00403/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fnagi.2017.00403/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Presentation_1.PDF" id="SM1" mimetype="application/pdf" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
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<fn id="fn01"><label>1</label><p><ext-link ext-link-type="uri" xlink:href="http://deweylab.biostat.wisc.edu/rsem/">http://deweylab.biostat.wisc.edu/rsem/</ext-link></p></fn>
<fn id="fn02"><label>2</label><p><ext-link ext-link-type="uri" xlink:href="http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html">http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html</ext-link></p></fn>
<fn id="fn03"><label>3</label><p><ext-link ext-link-type="uri" xlink:href="https://github.com/tanghaibao/Goatools">https://github.com/tanghaibao/Goatools</ext-link></p></fn>
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