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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Pharmacol.</journal-id>
<journal-title>Frontiers in Pharmacology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Pharmacol.</abbrev-journal-title>
<issn pub-type="epub">1663-9812</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">766120</article-id>
<article-id pub-id-type="doi">10.3389/fphar.2021.766120</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Pharmacology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>
<italic>Rheum tanguticum</italic> Alleviates Cognitive Impairment in APP/PS1 Mice by Regulating Drug-Responsive Bacteria and Their Corresponding Microbial Metabolites</article-title>
<alt-title alt-title-type="left-running-head">Gao et&#x20;al.</alt-title>
<alt-title alt-title-type="right-running-head">Rhubarb Regulates AD Microbial Metabolites</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Gao</surname>
<given-names>Demin</given-names>
</name>
<xref ref-type="fn" rid="fn1">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1579826/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhao</surname>
<given-names>Huizhen</given-names>
</name>
<xref ref-type="fn" rid="fn1">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1579880/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Yin</surname>
<given-names>Zhihui</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/1465814/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Han</surname>
<given-names>Chen</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/1523678/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Ying</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/1437894/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Luo</surname>
<given-names>Gan</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/887960/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Gao</surname>
<given-names>Xiaoyan</given-names>
</name>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/633442/overview"/>
</contrib>
</contrib-group>
<aff>School of Chinese Materia Medica, Beijing University of Chinese Medicine, <addr-line>Beijing</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>
<bold>Edited by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/531365/overview">Wenzhi Yang</ext-link>, Tianjin University of Traditional Chinese Medicine, China</p>
</fn>
<fn fn-type="edited-by">
<p>
<bold>Reviewed by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/597235/overview">Qiao Wang</ext-link>, Hebei Medical University, China</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/802726/overview">Feng-Qing Yang</ext-link>, Chongqing University, China</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Xiaoyan Gao, <email>gaoxiaoyan@bucm.edu.cn</email>
</corresp>
<fn fn-type="other">
<p>This article was submitted to Ethnopharmacology, a section of the journal Frontiers in Pharmacology</p>
</fn>
<fn fn-type="equal" id="fn1">
<label>
<sup>&#x2020;</sup>
</label>
<p>These authors have contributed equally to this&#x20;work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>15</day>
<month>12</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>766120</elocation-id>
<history>
<date date-type="received">
<day>28</day>
<month>08</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>24</day>
<month>11</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2021 Gao, Zhao, Yin, Han, Wang, Luo and Gao.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Gao, Zhao, Yin, Han, Wang, Luo and Gao</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) and the copyright owner(s) 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&#x20;terms.</p>
</license>
</permissions>
<abstract>
<p>Drugs targeting intestinal bacteria have shown great efficacy for alleviating symptoms of Alzheimer&#x2019;s disease (AD), and microbial metabolites are important messengers. Our previous work indicated that <italic>Rheum tanguticum</italic> effectively improved cognitive function and reshaped the gut microbial homeostasis in AD rats. However, its therapeutic mechanisms remain unclear. Herein, this study aimed to elaborate the mechanisms of rhubarb for the treatment of AD by identifying effective metabolites associated with rhubarb-responsive bacteria. The results found that rhubarb reduced hippocampal inflammation and neuronal damage in APP/PS1 transgenic (Tg) mice. 16S rRNA sequencing and metabolomic analysis revealed that gut microbiota and their metabolism in Tg mice were disturbed in an age-dependent manner. Rhubarb-responsive bacteria were further identified by real-time polymerase chain reaction (RT-PCR) sequencing. Four different metabolites reversed by rhubarb were found in the position of the important nodes on rhubarb-responsive bacteria and their corresponding metabolites combined with pathological indicators co-network. Furthermore, <italic>in&#x20;vitro</italic> experiments demonstrated <italic>o</italic>-tyrosine not only inhibited the viabilities of primary neurons as well as BV-2 cells, but also increased the levels of intracellular reactive oxygen species and nitric oxide. In the end, the results suggest that rhubarb ameliorates cognitive impairment in Tg mice through decreasing the abundance of <italic>o</italic>-tyrosine in the gut owing to the regulation of rhubarb-responsive bacteria. Our study provides a promising strategy for elaborating therapeutic mechanisms of bacteria-targeted drugs for&#x20;AD.</p>
</abstract>
<kwd-group>
<kwd>Alzheimer&#x2019;s disease</kwd>
<kwd>rhubarb</kwd>
<kwd>gut microbiota</kwd>
<kwd>drug-responsive bacteria</kwd>
<kwd>
<italic>o</italic>-tyrosine</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>Alzheimer&#x2019;s disease (AD) is a progressive neurodegenerative disease with high incidence, disability and death rates (<xref ref-type="bibr" rid="B47">Sierksma et&#x20;al., 2020</xref>). Clinically, AD patients are characterized by age-dependent memory loss, cognitive dysfunction and behavior abnormality (<xref ref-type="bibr" rid="B20">Jack et&#x20;al., 2018</xref>). It is widely believed that the pathological changes in the brains of AD patients belong to the accumulated amyloid-&#x3b2; (A&#x3b2;) induced oxidative stress and inflammatory responses in brain, causing oxidative damage and release of pro-inflammatory mediators, finally neuronal apoptosis (<xref ref-type="bibr" rid="B48">Stepanichev et&#x20;al., 2004</xref>; <xref ref-type="bibr" rid="B39">Pistollato et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B59">Wu Y. et&#x20;al., 2019</xref>). Emerging evidence has shown that gut microbial dysbiosis may mediate the pathogenesis of AD (<xref ref-type="bibr" rid="B32">Minter et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B27">Liu P. et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B55">Wang et&#x20;al., 2019</xref>). Therefore, remodeling gut microbial homeostasis may represent a more effective therapeutic strategy for the treatment of&#x20;AD.</p>
<p>Traditional Chinese medicine (TCM) has aroused increasing attention on account of its therapeutic effects in the prevention and treatment of AD (<xref ref-type="bibr" rid="B60">Xu et&#x20;al., 2017</xref>). Among them, rhubarb exhibits excellent therapeutic effect for AD by &#x201c;tonify the body by removing stasis&#x201d; and &#x201c;relaxing bowels and puzzle&#x201d; according to &#x201c;brain collateral damage due to toxin&#x201d; raised by theoretical system of TCM (<xref ref-type="bibr" rid="B25">Li et&#x20;al., 2019</xref>). Our previous studies have suggested that <italic>Rheum tanguticum</italic> effectively improves cognitive function and reshapes the gut microbial homeostasis in AD animal models (<xref ref-type="bibr" rid="B67">Zhao et&#x20;al., 2019</xref>). However, its therapeutic mechanisms remain unclear. Herein, considering the fact that a relatively low content of chemical ingredients in rhubarb permeated into the brain (<xref ref-type="bibr" rid="B49">Sun et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B10">Dong et&#x20;al., 2016</xref>), we hypothesized that therapeutic effects of rhubarb may attribute to remodeling gut microbiota. Thus, it is of great significance to the elaborating therapeutic mechanism of rhubarb for AD from the view of gut microbiota (<xref ref-type="bibr" rid="B30">Mancuso and Santangelo, 2018</xref>).</p>
<p>Among the researches involved in interaction between gut and brain, a growing body of evidence suggests that microbial metabolites are important messengers of intestinal bacteria responsible for regulation of physiological state in brain, although the mechanisms of gut-brain transmission have so far remained elusive (<xref ref-type="bibr" rid="B35">Nicholson et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B42">Rothhammer et&#x20;al., 2018</xref>). It has been found that harmful microbial metabolites, such as lipopolysaccharides (LPS) and Trimethylamine-<italic>N</italic>-oxide (<xref ref-type="bibr" rid="B53">Vogt et&#x20;al., 2018</xref>), are easy to enter the brain and destroy its homeostasis, because intestinal leakage and permeability of BBB are significantly increased in AD patients (<xref ref-type="bibr" rid="B22">Kim et&#x20;al., 2020</xref>). Accordingly, the regulation of gut microbiota-derived microbial metabolites is beneficial to alleviating symptoms of AD. Therefore, accurate identification of microbial metabolites associated with drug-responsive bacteria is crucial to elucidate the mechanisms of bacteria-targeted drugs for the treatment of&#x20;AD.</p>
<p>In terms of the progression in a disease as well as drug intervention, metabolomics is a powerful tool for comprehensive discovery of the disturbed metabolites in a biological system (<xref ref-type="bibr" rid="B31">Matysik et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B44">Shaffer et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B28">Luan et&#x20;al., 2019</xref>). However, it fails to distinguish the metabolites derived from drug-responsive bacteria. Because of the lack of direct identification methods, the alternative methods are diverse bacteria-based correlation analysis and co-network analysis combined with pathophysiological indicators (<xref ref-type="bibr" rid="B13">Feng et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B68">Zheng et&#x20;al., 2020</xref>). Over the last decade, microbiome research based on amplicon sequencing, such as 16S rRNA, offers the global relative abundance of bacteria in different taxonomies (<xref ref-type="bibr" rid="B16">Gohl et&#x20;al., 2016</xref>). However, comprehensive yet redundant data hinder accurate quantification of the drug-responsive bacteria. Given that relative abundance of bacteria could not reflect actual content of gut microbiota by 16S rRNA sequencing (<xref ref-type="bibr" rid="B11">Eisenstein, 2018</xref>; <xref ref-type="bibr" rid="B51">Tkacz et&#x20;al., 2018</xref>), meanwhile, uncertainty exists in peak area of the fragment ions and their real content in biological samples by metabolomics analysis (<xref ref-type="bibr" rid="B28">Luan et&#x20;al., 2019</xref>), there would be many false positives in identified microbial metabolites by 16S rRNA sequencing-based co-network analysis (<xref ref-type="bibr" rid="B37">Peisl et&#x20;al., 2018</xref>). Thus, it always gives obscure explanation of the therapeutic mechanisms of bacteria-targeted drugs. Therefore, it is urgent to improve the accuracy of identification for microbial metabolites associated with drug-responsive bacteria.</p>
<p>In recent years, real-time polymerase chain reaction (RT-PCR) has been adopted for quantifying microbiota significantly disturbed between the health individuals and patients (<xref ref-type="bibr" rid="B50">Tettamanti Boshier et&#x20;al., 2020</xref>). Based on the filtered specific intestinal bacteria in disease by 16S rRNA, RT-PCR as a complementary technology can obtain more precise drug-responsive bacteria by semi-quantitative comparative analysis between the treatment group and the disease group (<xref ref-type="bibr" rid="B34">Neyrinck et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B61">Xu et&#x20;al., 2021</xref>). To some extent, the above-mentioned method can eliminate false positive bacteria and contribute to unravel therapeutic mechanisms of bacteria-targeted drugs in a more accurate way. Hence, a co-network analysis proposed here, which consists of RT-PCR and different metabolites combined with measurable pathological indicators, can immensely improve the accuracy of identification for microbial metabolites associated with drug-responsive bacteria.</p>
<p>Based on the proposed strategy, the present study aimed to elaborate the mechanism of rhubarb for AD by identifying effective metabolites associated with rhubarb-responsive bacteria. First of all, the influence of long-term rhubarb treatment on the pathological indicator-related microbiota and corresponding metabolites was evaluated. And then, gut microbiota and metabolomic profiling based on a time series analysis were performed to filter the disturbed microbiota and metabolites with the progression of AD. Moreover, the rhubarb-responsive bacteria and their corresponding metabolites were discovered by the co-network analysis based on RT-PCR and different metabolites combined with pathological indicators. Finally, the effects of key metabolite on primary neurons and BV-2 cells were evaluated <italic>in&#x20;vitro</italic> to validate the bidirectional cross-talk between the gut and brain. Together, a more accurate co-network analysis employed in our study demonstrates that rhubarb ameliorates cognitive impairment by influencing effective metabolites in the gut through the regulation of rhubarb-responsive bacteria.</p>
</sec>
<sec sec-type="materials|methods" id="s2">
<title>Materials and Methods</title>
<sec id="s2-1">
<title>Animals</title>
<p>Eight-month-old male APP/PS1 Tg mice and littermate wild type (WT) mice were obtained from the Nanjing Biochemical Research Institute of Nanjing University and housed in environmentally controlled conditions (room temperature at 22&#x20;&#xb1; 1&#xb0;&#x421;, 12-h light/dark cycle) with access to standard food and water ad libitum. All experiments were approved and conducted in accordance with the guidelines of the Care and Use of Laboratory Animals approved by the Ethics Committee for Animal Care and Treatment at Beijing University of Chinese Medicine (BUCM-4-2018080101-3007).</p>
</sec>
<sec id="s2-2">
<title>Preparation of Drug Solutions</title>
<sec id="s2-2-1">
<title>Preparation of Rhubarb Decoction</title>
<p>Small pieces of rhubarb (<italic>Rheum tanguticum</italic>; 171202 ZISUN MEDICINE HEALTH CO.LTD. GuangZhou, China) herbal medicine (&#x223c;30&#xa0;g) were weighed and soaked in 300&#xa0;ml distilled water for 1&#xa0;h and decocted twice in boiling water for 30&#xa0;min on each occasion. The combined products from this water decoction were filtered and dried in a 60&#xb0;C water bath, then topped up to 50&#xa0;ml with ultrapure water to yield a 0.6&#xa0;g&#xa0;mL<sup>&#x2212;1</sup> solution (<xref ref-type="bibr" rid="B67">Zhao et&#x20;al., 2019</xref>).</p>
</sec>
<sec id="s2-2-2">
<title>Preparation of Donepezil Hydrochloride Solution</title>
<p>Donepezil hydrochloride solution was prepared by crushing one tablet containing 5&#xa0;mg donepezil hydrochloride and dissolving it in 100&#xa0;ml of normal saline by ultrasonication for 30&#xa0;min to obtain a 0.05&#xa0;mg&#xa0;ml<sup>&#x2212;1</sup> solution.</p>
</sec>
</sec>
<sec id="s2-3">
<title>Experimental Design</title>
<p>All the 8-month-old Tg mice were randomly divided into three groups (<italic>n</italic>&#x20;&#x3d; 9 per group): Tg model group, rhubarb administration group (TgR), and positive drug group (TgP). Littermate wild type mice (<italic>n</italic>&#x20;&#x3d; 9) were used as the wild type control group (WT). Mice in the TgR group were given a rhubarb decoction by gavage at 0.91&#xa0;g&#xa0;kg<sup>&#x2212;1</sup> every day for 60 consecutive days. Mice in the TgP group were given donepezil solution at 1.5&#xa0;mg&#xa0;kg<sup>&#x2212;1</sup> daily for 60&#xa0;days. The Tg model group and the WT control group were given 1&#xa0;ml normal saline every day. The fecal samples of all mice were collected from 8-month-old mice after 3&#xa0;days of acclimation. After 30-day-treatment, fecal samples of all mice were collected as 9-month-old samples. And after feeding for 60&#xa0;days, fecal were collected as 10-month-old samples.</p>
</sec>
<sec id="s2-4">
<title>Behavioral Test</title>
<sec id="s2-4-1">
<title>Morris Water Maze Test</title>
<p>The Morris water maze test was performed as described by Vorhees and Williams (<xref ref-type="bibr" rid="B54">Vorhees and Williams, 2006</xref>). The escape latency during the spatial learning phase and the number of platform crossings and the time spent in the target quadrant were recorded. The detailed experiments were provided in the <xref ref-type="sec" rid="s11">Supplementary Material</xref>.</p>
</sec>
<sec id="s2-4-2">
<title>Step-down&#x20;test</title>
<p>The step-down test was performed as described by <xref ref-type="bibr" rid="B43">Ruan et&#x20;al. (2016)</xref>. The error times during training, step-down delay and error times during experiments were recorded. The detailed experiments were provided in the <xref ref-type="sec" rid="s11">Supplementary Material</xref>.</p>
</sec>
</sec>
<sec id="s2-5">
<title>Tissue Collection</title>
<sec id="s2-5-1">
<title>Brain Tissue Collection</title>
<p>After the behavioral tests, mice were deeply anesthetized with 10% chloral hydrate and euthanized by cervical dislocation. After craniotomy on ice, the whole brain was removed and the hippocampus was quickly separated, weighed, and frozen at &#x2212;80&#xb0;C for subsequent enzyme-linked immunosorbent assay (ELISA) and neurotransmitter analyses. Brain tissue samples from mice in each group were also collected, fixed, paraffin-embedded, and sectioned at 5&#xa0;&#xb5;m for pathological staining.</p>
</sec>
<sec id="s2-5-2">
<title>Fecal Sample Collection</title>
<p>Fecal samples were collected from 8-month-old mice after 3&#xa0;days of acclimation. After feeding for 30&#xa0;days, fecal samples were collected from the mice at 9&#xa0;months of age. Finally, samples were collected at the age of 10&#xa0;months after feeding for 60&#xa0;days. Fecal samples of the same mice in the corresponding groups were collected at each time point and six samples from the WT, Tg and TgR groups were used for 16S rRNA gene sequencing and metabolomics analysis.</p>
</sec>
</sec>
<sec id="s2-6">
<title>Congo Red Staining</title>
<p>The brain tissues of mice in various treatment groups were subjected to Congo Red staining to visualize amyloid plaques. Paraffin-embedded tissue sections were routinely dewaxed into water. The slices were immersed in alkaline solution for 20&#xa0;min and washed with water. Alkaline Congo Red solution was soaked for 20&#xa0;min and washed with water. The sections were immersed in alkaline solution for differentiation, observed under a microscope until the tissue staining contrast was clear, then washed with water to stop staining. Harris hematoxylin was applied for 5&#xa0;min and washed off. Afterward, 1% hydrochloric acid ethanol solution was added for differentiation for a few seconds and the sections were washed with water for 15&#xa0;min. The sections were dehydrated with gradient ethanol, hyalinized with xylene, and sealed with neutral&#x20;gum.</p>
</sec>
<sec id="s2-7">
<title>Hematoxylin and Eosin Staining</title>
<p>The brain tissues of mice were fixed with neutral formalin, dehydrated with ethanol, and removed with xylene. The brain tissues were embedded in paraffin and sectioned at 5&#xa0;&#x3bc;m. The paraffin sections were immersed in 100% xylene twice for 10&#xa0;min each time and soaked in 95, 80, and 70% alcohol for 3&#xa0;min in turn. Finally, phosphate-buffered saline (PBS) and distilled water were used to rinse the sections three times, for 2&#xa0;min each time. The sections were soaked in hematoxylin solution, stained for 10&#xa0;min, and washed with running water until the water was clear with no purple color. The cells were differentiated with 75% hydrochloric acid ethanol for 3&#xa0;s (three times) and washed with running water. The nuclei were confirmed to have turned blue under the microscope. Eosin staining was performed for 5&#xa0;min. The stained sections were dehydrated with pure alcohol and washed with xylene until the cut was transparent and sealed with neutral&#x20;gum.</p>
</sec>
<sec id="s2-8">
<title>Iba-1 Immunohistochemical Staining</title>
<p>Tissue sections of the whole brain were embedded with paraffin and prepared for immunohistochemical staining. After deparaffinization and rehydration in graded alcohols, antigen retrieval was performed with citrate buffer for 10&#xa0;min at 90&#xb0;&#x421;. Next, the sections were gradually cooled at room temperature to block endogenous peroxidase activity. The sections were then washed thrice with PBS and blocked with goat serum for 10&#xa0;min at room temperature. After the goat serum was removed, the sections were incubated with mouse-anti Iba-1 at 4&#xb0;&#x421; overnight, followed by intubation with biotin-labelled goat anti-mouse secondary antibody for 10&#xa0;min and streptomycin anti-biotin peroxidase for 10&#xa0;min at room temperature. Then, the sections were labelled with 3,3&#x2032;-diaminobenzidine, followed by hematoxylin counterstaining. Lastly, after washing, the sections were dehydrated through gradients of ethanol and xylene. PBS displacement of the primary antibody was used as the negative criterion.</p>
</sec>
<sec id="s2-9">
<title>Analysis of A&#x3b2;, A&#x3b2;<sub>42</sub>, Interleukin-1&#x3b2;, IL-18, and Tumor Necrosis Factor-&#x3b1; Levels with Enzyme-Linked Immunosorbent Assay</title>
<p>Hippocampus samples from the brain were homogenized and the concentrations of A&#x3b2;, A&#x3b2;<sub>42</sub>, IL-1&#x3b2;, IL-18, and TNF-&#x3b1; were measured using an ELISA kit (BlueGene Biotech, Shanghai, China) according to the instructions. The standard curve was established and used to calculate the levels of A&#x3b2;, A&#x3b2;<sub>42</sub>, IL-1&#x3b2;, IL-18, or TNF-&#x3b1; in the tissues. The obtained values were corrected for the wet weight of the brain sample and expressed as &#xb5;g/mg.</p>
</sec>
<sec id="s2-10">
<title>Quantification of Neurotransmitters in Brain Tissue</title>
<sec id="s2-10-1">
<title>Brain Tissue Sample Processing</title>
<p>The brain tissue was cut into pieces and mixed evenly. Afterward, 0.5&#xa0;ml of water-methanol (8:2, v/v) was added to every 0.25&#xa0;g brain tissue to remove protein and tissue homogenate was prepared in a homogenizer. The prepared homogenate was centrifuged twice at 4&#xb0;C 13709&#x20;&#xd7; g for 10&#xa0;min. After centrifugation, 200&#xa0;&#x3bc;l of homogenate supernatant solution was removed and added to 0.8&#xa0;ml 0.1% formic acid acetonitrile (40&#x2013;60%) followed by vortexing for 2&#xa0;min. The prepared solution was centrifuged at 4&#xb0;C, 13709&#x20;&#xd7; g for 10&#xa0;min and placed in an injection&#x20;vial.</p>
</sec>
<sec id="s2-10-2">
<title>Liquid Chromatography&#x2013;Mass Spectrometry Method</title>
<p>Ultra-Performance Liquid Chromatography (UPLC) analysis was performed on a Waters Acquity UPLC system (Waters Corporation, Milford, MA, United&#x20;States) consisting of a binary solvent system, an autosampler, and a column temperature controller. Chromatographic separation was carried out on an ACQUITY BEH C18 column (2.1&#xa0;mm &#xd7; 100&#xa0;mm, 1.7&#xa0;&#x3bc;m, Waters, United&#x20;Kingdom). The mobile phase was composed of eluent A (0.3% formic acid in water) and eluent B (acetonitrile). The line gradient program was optimized as follows: 0&#x2013;2&#xa0;min, maintained at 2% B; 2&#x2013;3&#xa0;min, increased from 2% B to 30% B; 3&#x2013;3.5&#xa0;min, increased from 30% B to 90% B; 3.5&#x2013;5&#xa0;min, maintained at 90% B; 5&#x2013;5.1&#xa0;min decreased from 90% B to 2% B; 5.1&#x2013;7&#xa0;min maintained at 2% B for column equilibrium. The column temperature was set at 30&#xb0;C and the sample chamber temperature was set at 4&#xb0;C. The mobile phase flow rate was set at 0.3&#xa0;ml/min, and the injection volume was 2&#xa0;&#x3bc;l for each&#x20;run.</p>
<p>MS data were recorded using the Waters XEVO TQ-S system (Waters Corporation, Manchester, United&#x20;Kingdom) equipped with an electrospray ionization source in positive ion mode with multiple reaction monitoring (MRM) of the transition of <italic>m/z</italic> 176.9360 &#x2192; 160.1180 for serotonin (5-HT); <italic>m/z</italic> 146.0780 &#x2192; 87.0840 for acetylcholine (Ach); <italic>m/z</italic> 154.3020 &#x2192; 137.1390 for dopamine (DA); <italic>m/z</italic> 103.9040 &#x2192; 86.9900 for &#x3b3;-aminobutyric acid (GABA); <italic>m/z</italic> 148.2130 &#x2192; 84.1240 for glutamate (Glu), and <italic>m/z</italic> 169.9140 &#x2192; 152.1190 for norepinephrine (NE). The MS parameters were optimized as follows: the ion spray voltage was 4000&#xa0;V; capillary voltage was 3.0&#xa0;kV; cone voltage was 30&#xa0;V; nitrogen was used as the desolvation gas and the cone gas with flow rates of 800 and 150&#xa0;L/h, respectively; the source and desolvation temperatures were set at 150 and 400&#xb0;C, respectively; the sheath and auxiliary gas pressures were 20 psi and 10 psi, respectively. Thereafter, the MS/MS conditions were optimized for the internal standard by infusing the individual solution into the electro-spray source. The optimized cone voltage and collision energy were 2&#xa0;V and 10&#xa0;eV for 5-HT, 32&#xa0;V and 12&#xa0;eV for Ach, 2&#xa0;V and 8&#xa0;eV for DA, 22&#xa0;V and 8&#xa0;eV for GABA, 2&#xa0;V and 14&#xa0;eV for Glu, and 72&#xa0;V and 6&#xa0;eV for NE, respectively.</p>
</sec>
</sec>
<sec id="s2-11">
<title>16S rRNA Microbial Community Analysis</title>
<sec id="s2-11-1">
<title>Illumina MiSeq Sequencing</title>
<p>The 16S rRNA sequencing was performed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China). Purified amplicons were pooled in equimolar and paired-end sequences (2 &#xd7; 300) on an Illumina MiSeq platform (Illumina, San Diego, United&#x20;States) according to the standard protocols provided by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China). The detailed method of RNA extraction, PCR amplification and data processing is provided in the <xref ref-type="sec" rid="s11">Supplementary Material</xref>.</p>
</sec>
<sec id="s2-11-2">
<title>Data Analysis</title>
<p>Association network analysis was performed using the Co-Net v1.1.1. beta tool (<xref ref-type="bibr" rid="B12">Faust and Raes, 2016</xref>) on Cytoscape v3.7.2. (<xref ref-type="bibr" rid="B45">Shannon et&#x20;al., 2003</xref>). Taxa below a sum of 120 and 12 occurrences per condition were discarded and the relative abundances were calculated. Networks were inferred based on the 1000 top and bottom edges for each of the Pearson, Spearman, Bray, and Kullback-Leibler correlation methods with 1000 iterations. The final <italic>p</italic>-values were computed during bootstrapping and adjusted with Benjamini-Hochberg correction for multiple testing.</p>
</sec>
</sec>
<sec id="s2-12">
<title>Metabolomics Analysis</title>
<p>Hundred-milligram fecal samples from each mouse were weighed and placed in a 2&#xa0;ml centrifuge tube. Three times the volume of 50% methanol aqueous solution was added for 5&#xa0;min, and centrifuged at 13709&#x20;&#xd7; g for 10&#xa0;min. The supernatant was dried with nitrogen and 100&#xa0;&#x3bc;l of 50% methanol aqueous solution was added for re-dissolution. After shaking for 30&#xa0;s and standing for 10&#xa0;min, the supernatant was centrifuged at 13709&#x20;&#xd7; g at 4&#xb0;C for 10&#xa0;min and the supernatant was placed in an injection&#x20;vial.</p>
<p>UPLC analysis was carried out on a Waters Acquity&#x2122; UPLC system (Waters Corporation, Milford, MA, United&#x20;States) consisting of a binary solvent system, an autosampler, and a column temperature controller. Chromatographic separation was carried out on an ACQUITY UPLC<sup>&#xae;</sup> HSS T3 column (2.1&#xa0;mm &#xd7; 100&#xa0;mm, 1.8&#xa0;&#x3bc;m, Waters, United&#x20;Kingdom). The mobile phase was composed of eluent A (0.1% formic acid in water) and eluent B (acetonitrile). The line gradient program was optimized as follows: 0&#x2013;0.5&#xa0;min, 1% B; 0.5&#x2013;4&#xa0;min, 1&#x2013;20% B; 4&#x2013;8&#xa0;min, 20&#x2013;100% B; 8&#x2013;9&#xa0;min, 100% B; 9&#x2013;9.5&#xa0;min, 100&#x2013;1% B; 9.5&#x2013;11&#xa0;min 1% B. The column temperature was set at 45&#xb0;C and the sample chamber temperature was set at 4&#xb0;C. The mobile phase flow rate was set at 0.3&#xa0;ml/min and the injection volume was 3&#xa0;&#x3bc;l for each&#x20;run.</p>
<p>MS analysis was carried out with a Waters SYNAPT G2-SI MS system (Waters, United&#x20;States) equipped with an electrospray ionization source. The analysis was performed in the positive and negative ion electrospray modes. The source parameters were set as follows: capillary voltage, 3.0&#xa0;kV; cone voltage, 28&#xa0;V; source temperature, 100&#xb0;C; desolvation temperature, 400&#xb0;C; the cone gas flow, 35&#xa0;L/h; desolvation gas flow, 800&#xa0;L/h. The low collision energy was 6&#xa0;eV and the high collision energy was 10&#x2013;65&#xa0;eV. Mass spectra were recorded across the <italic>m/z</italic> range of 50&#x2013;1200 and 3D data were collected in the continuum mode. The mass spectrometry data were acquired and processed with Waters MassLynx V4.1 software.</p>
</sec>
<sec id="s2-13">
<title>Data Processing and Multivariate Data Analysis</title>
<p>The UPLC-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) data for the fecal samples were imported into Progenesis QI v1.0 (Nolinear Dynamics, Newcastle, United&#x20;Kingdom) for peak selection and alignment. After normalizing the data using the total ion intensity, a data matrix of interesting features containing the retention time, <italic>m/z</italic> value, and normalized peak intensity was imported into Metaboanalysis 4.0 for principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) and further confirmed using analysis of variance (ANOVA). The differences in the trends were processed with an unsupervised PCA method. Supervised PLS-DA was used to search for interesting biomarkers. Then, the peak height intensities of the differential metabolites were compared with t-tests using statistical software to confirm the biomarker alterations between the WT and Tg groups at the age of 8, 9, and 10&#xa0;months. A <italic>p</italic> value &#x3c; 0.05 was set as the threshold. As a small sample set, a pooled quality control (QC) sample containing equal aliquots of all the samples was run at the beginning of the sample queue for column conditions and injected at regular intervals and the end of the run (<xref ref-type="bibr" rid="B57">Want et&#x20;al., 2010</xref>). Mass data acquisition was performed for the evaluation of the sensitivity and stability of instrument performance with regard to mass accuracy, retention time stability, and the coefficient of variation (CV). All samples were kept at 4&#xb0;C during the analysis.</p>
</sec>
<sec id="s2-14">
<title>Analysis of Fecal Metabolites and Their Metabolic Pathways</title>
<p>Metabolite peaks were assigned based on MS/MS analysis using the MassFragment&#x2122; application manager (Waters Corp., Milford, United&#x20;States). After applying chemically intelligent peak-matching algorithms, the molecular composition of each metabolite and its fragments were structure-matched using available biochemical databases such as HMDB (<ext-link ext-link-type="uri" xlink:href="http://www.hmdb.ca/">http://www.hmdb.ca/</ext-link>), Kyoto Encyclopedia of Genes and Genomes (KEGG; <ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/kegg/">http://www.genome.jp/kegg/</ext-link>), LIPIDMAPS (<ext-link ext-link-type="uri" xlink:href="http://www.lipidmaps.org/">http://www.lipidmaps.org/</ext-link>), and Chemspider (<ext-link ext-link-type="uri" xlink:href="http://www.chemspider.com">http://www.chemspider.com</ext-link>). The identified metabolites were subjected to KEGG pathway mapping for metabolic pathway analysis. The KEGG database contains a collection of manually curated pathway maps from genomics, transcriptomics, proteomics, and metabolomics and provides molecular interactions and reaction networks.</p>
</sec>
<sec id="s2-15">
<title>HPLC Fingerprinting of Rhubarb Extraction</title>
<sec id="s2-15-1">
<title>Chromatographic Conditions</title>
<p>Chromatographic analysis was performed on a Thermo UltiMate 3000 HPLC system (Thermo Scientific, United&#x20;States). The separations were achieved on an Agilent SB-C18 column (250&#xa0;mm &#xd7; 4.6 mm, 5&#xa0;&#x3bc;m) with the column temperature at 40&#xb0;C. The mobile phases consisted of acetonitrile (A) and an aqueous solution containing 0.05% phosphoric acid (B) using a gradient elution as follows: 0&#x2013;10&#xa0;min 96&#x2013;89% B, 10&#x2013;25&#xa0;min 89&#x2013;87% B, 25&#x2013;50&#xa0;min 87&#x2013;85% B, 50&#x2013;70&#xa0;min 85&#x2013;80% B, 70&#x2013;100&#xa0;min 80&#x2013;67% B, 100&#x2013;115&#xa0;min 67&#x2013;40% B, and 115&#x2013;140&#xa0;min 40% B with a flow rate of 1.0&#xa0;ml/min. The injection volume was 10&#xa0;&#x3bc;l and the detection wavelength was at 268&#xa0;nm.</p>
</sec>
<sec id="s2-15-2">
<title>Preparation of Reference Compound Solution</title>
<p>Stock solutions were prepared by dissolving seven substances (emodin (BP0532), 1.95&#xa0;mg; rhein (BP1208), 1.95&#xa0;mg; chrysophanol (BP0348), 1.51&#xa0;mg; physcion (BP1092), 1.61&#xa0;mg; aloe-emodin (BP0146), 1.75&#xa0;mg; sennoside A (BP1292), 1.50&#xa0;mg; sennoside B (BP1293), 2.36&#xa0;mg) in 200&#xa0;&#xb5;l dimethyl sulfoxide (DMSO) as described in our previous paper (<xref ref-type="bibr" rid="B15">Gao et&#x20;al., 2009</xref>) and distilled water was added to a constant volume of 5&#xa0;ml. All the compounds were obtained from Chengdu Biopurify Phytochemicals Ltd. and the purity of these compound is over 98.0%. Subsequently, each reference compound solution was diluted to 100&#x20;times with distilled water and the diluent was filtered through a 0.22&#xa0;&#x3bc;m microporous membrane and placed in an injection&#x20;vial.</p>
</sec>
<sec id="s2-15-3">
<title>Method Validation</title>
<p>The precision was determined by successively analyzing the same sample solution six times. The repeatability was assessed by analyzing six independently prepared sample solutions. The stability was evaluated with the same sample solution at different periods in 1&#xa0;day (0, 2, 4, 8, 16, 24&#xa0;h). Each sample solution was tested twice in parallel.</p>
</sec>
<sec id="s2-15-4">
<title>Data Analysis</title>
<p>The data analysis was performed on a &#x201c;TCM chromatographic fingerprint similarity evaluation system (version 2012, Chinese Pharmacopoeia Commission)&#x201d;.</p>
</sec>
</sec>
<sec id="s2-16">
<title>RT-PCR</title>
<p>The total bacterial DNA was extracted from the fecal samples of mice in each group with the E.Z.N.A &#x2122;. Stool DNA kit (D4015, Omega Biotek, United&#x20;States), and the procedures were carried out according to the manufacturer&#x2019;s instructions. First, fecal samples were removed from a &#x2212;80&#xb0;C refrigerator, 200&#xa0;mg of feces from each sample was measured into a 1.5&#xa0;ml sterile centrifuge tube, and genomic DNA was detected with 2% agarose gel electrophoresis. For detection of the bacteria <italic>Marvinbryantia</italic> (<xref ref-type="bibr" rid="B8">Desai et&#x20;al., 2016</xref>) and <italic>Erysipelatoclostridium</italic> (<xref ref-type="bibr" rid="B63">Zakham et&#x20;al., 2019</xref>), extracted bacterial DNA was subjected to RT-PCR using the CFX Connect real-time PCR system (Bio-rad Laboratories, Hercules California, United&#x20;States). PCR was performed with a 10&#xa0;&#x3bc;l sample containing 5&#xa0;&#x3bc;l SG Green qPCR Mix (with ROX Q1002, SinoGene), 0.2&#xa0;&#x3bc;l 20&#xa0;&#x3bc;m upstream and downstream primers, 1&#xa0;&#x3bc;l bacterial genomic DNA template, and 3.6&#xa0;&#x3bc;l deionized water. In the blank control, the template DNA was replaced with deionized water. After the PCR reaction, the melting curve temperature was set at 60&#x2013;95&#xb0;C and increased by 0.5&#xb0;C/s. For detection of the bacteria <italic>Bacteroides</italic> (<xref ref-type="bibr" rid="B17">Haugland et&#x20;al., 2010</xref>) and <italic>norank_f_Ruminococcaceae</italic> (<xref ref-type="bibr" rid="B21">Jiang et&#x20;al., 2017</xref>), extracted bacterial DNA was subjected to RT-PCR using the LineGene 9600 Plus real-time PCR system (Bioer Technology, Hangzhou, China). PCR was performed with a 20&#xa0;&#x3bc;l sample containing 10&#xa0;&#x3bc;l ChamQ SYBR Color qPCR Master MiX (Vazyme Biotech Co., Ltd, Nanjing China), 0.4&#xa0;&#x3bc;l 5&#xa0;&#x3bc;m upstream and downstream primers, 2&#xa0;&#x3bc;l bacterial genomic DNA template, and 7.2&#xa0;&#x3bc;l deionized water. In the blank control, the template DNA was replaced with deionized water. After PCR reaction, the melting curve temperature was set at 60&#x2013;95&#xb0;C and increased by 0.5&#xb0;C/s. <xref ref-type="table" rid="T1">Table&#x20;1</xref> shows the sequences for each primer set, which targeted the 16S rRNA genes for each bacteria group. Each standard curve was prepared based on the cell numbers measured using a bacterial counting chamber with each strain indicated. DNA from each standard strain was extracted as described above and used for RT-PCR. All RT-PCR experiments were performed with duplicates for each sample. The detailed PCR reaction information is listed in the <xref ref-type="sec" rid="s11">Supplementary Material</xref>.</p>
<table-wrap id="T1" position="float">
<label>TABLE 1</label>
<caption>
<p>Primer sets used in this&#x20;study.</p>
</caption>
<table>
<thead valign="top">
<tr>
<th align="left">Target Bacteria</th>
<th align="center">Sense primer</th>
<th align="center">Anti-sense primer</th>
</tr>
</thead>
<tbody valign="top">
<tr>
<td align="left">
<italic>Bacteroides</italic>
</td>
<td align="left">5&#x2032;-CAT&#x200b;GTG&#x200b;GTT&#x200b;TAA&#x200b;TTC&#x200b;GAT&#x200b;GAT-3&#x2032;</td>
<td align="left">5&#x2032;-AGC&#x200b;TGA&#x200b;CGA&#x200b;CAA&#x200b;CCA&#x200b;TGC&#x200b;AG-3&#x2032;</td>
</tr>
<tr>
<td align="left">
<italic>Erysipelatoclostridium</italic>
</td>
<td align="left">5&#x2032;-GAC&#x200b;ACT&#x200b;GCA&#x200b;TGG&#x200b;TGA&#x200b;CC-3&#x2032;</td>
<td align="left">5&#x2032;-GGT&#x200b;TTC&#x200b;TAT&#x200b;GGC&#x200b;TTA&#x200b;CTG-3&#x2032;</td>
</tr>
<tr>
<td align="left">
<italic>Marvinbryantia</italic>
</td>
<td align="left">5&#x2032;-CAG&#x200b;GGA&#x200b;TTT&#x200b;TAC&#x200b;GTG&#x200b;CTT&#x200b;TAT&#x200b;TTT&#x200b;AGT&#x200b;TAT-3&#x2032;</td>
<td align="left">5&#x2032;-AGT&#x200b;TCG&#x200b;GAT&#x200b;TCG&#x200b;CTC&#x200b;GTA&#x200b;TTT&#x200b;TCT-3&#x2032;</td>
</tr>
<tr>
<td align="left">
<italic>norank_f_Ruminococcaceae</italic>
</td>
<td align="left">5&#x2032;-TGT&#x200b;TAA&#x200b;CAG&#x200b;AGG&#x200b;GAA&#x200b;GCA&#x200b;AAG&#x200b;CA-3&#x2032;</td>
<td align="left">5&#x2032;-TGC&#x200b;AGC&#x200b;CTA&#x200b;CAA&#x200b;TCC&#x200b;GAA&#x200b;CTA&#x200b;A-3&#x2032;</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s2-17">
<title>Cell Culture</title>
<sec id="s2-17-1">
<title>Primary Culture of Rat Neurons</title>
<p>Twenty specific-pathogen-free Sprague-Dawley (SD) neonatal rats were purchased from SPF Biotechnology Co., Ltd (Beijing). The healthy SD neonatal rats were sterilized with 75% alcohol within 24&#xa0;h after birth and decapitated under sterile conditions. The scalp and skull were cut. Brain tissue was taken out and placed in a dish containing cold D-Hank&#x2019;s solution with pH 7.2 free of calcium and magnesium. The brain tissue was peeled under sterile conditions and the cerebellum, hippocampus, and medulla were removed. The cortex was isolated and the meninges and blood vessels were carefully peeled off. The tissue was cut into blocks of about 1&#xa0;mm<sup>3</sup> using iris scissors, digested in 0.125% trypsin for 20&#xa0;min at 37&#xb0;C and shaken two to three times. The supernatant was discarded and complete media was added to terminate digestion. The tissues were rinsed twice and gently pipetted 20&#x20;times using a Pasteur pipette. The cell suspension was allowed to stand for 2&#xa0;min. The cell suspension was collected in a new centrifuge tube and centrifuged at 95&#x20;&#xd7; g at 4&#xb0;C for 10&#xa0;min. The supernatant was discarded. The cells were resuspended in complete media and filtered with a 200 mesh stainless steel filter. The filtrate was stained using trypan blue and the cells were counted using a hemocytometer under a microscope. The cells were inoculated at an intensity of 8.0 &#xd7; 10<sup>4</sup> to 1.0 &#xd7; 10<sup>5</sup>&#xa0;ml with 100&#xa0;&#x3bc;l/well into a 96-well plate pre-coated with poly-L-lysine. The cells were cultured for 4&#x2013;6&#xa0;h in an incubator at 37&#xb0;C with 5% CO<sub>2</sub> and the medium was replaced with serum-free media. After culturing for 3&#xa0;days, Ara-C working solution was added to inhibit over-proliferation of non-neuronal cells and aspirated after 24&#xa0;h. Thereafter, half of the medium was replaced every 3&#xa0;days. Cells collected from days 7&#x2013;21 of culture were used for the experiment.</p>
</sec>
</sec>
<sec id="s2-18">
<title>Cell Culture of Rat Microglial Cells</title>
<p>The murine microglial cell line BV-2 was cultured in high-glucose Dulbecco&#x2019;s modified Eagle&#x2019;s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in a humidified incubator with 5% CO<sub>2</sub> at 37&#xb0;C. BV-2 cells were plated into 96-well plates (1.0 &#xd7; 10<sup>5</sup> cells/well) and incubated overnight for subsequent experiments.</p>
</sec>
<sec id="s2-19">
<title>MTT Analysis</title>
<p>The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay is based on the protocol described by <xref ref-type="bibr" rid="B33">Mosmann (1983)</xref>. The assay was optimized for the cells used in the experiments. Briefly, after the cells were incubated with different concentrations of <italic>o</italic>-tyrosine (<italic>o</italic>-tyr) (0.5, 1, and 2&#xa0;mM) for 48&#xa0;h at 37&#xb0;&#x421; (<xref ref-type="bibr" rid="B38">Pennathur et&#x20;al., 1999</xref>), the culture medium was removed,&#x20;then the cells were incubated for 4&#xa0;h with 0.5&#xa0;mg&#xa0;ml<sup>&#x2212;1</sup> of MTT and dissolved in serum free medium. Washing with PBS was followed by the addition of 100&#xa0;&#xb5;l DMSO and gentle shaking for 10&#xa0;min to facilitate complete dissolution. After the formazan crystals had dissolved, the absorbance was determined spectrophotometrically at 490&#xa0;nm on an ELX800 UV universal microplate reader. The results were analyzed with the Soft max pro software (version 2.2.2) and are presented as a percentage of the control values.</p>
</sec>
<sec id="s2-20">
<title>Active Oxygen Detection</title>
<p>Reactive oxygen species (ROS) production in neuronal and BV-2 cells was assessed with a 2&#x2032;,7&#x2032;-dichlorodihydrofluorescein diacetate (DCFH-DA) probe. Different concentrations of <italic>o</italic>-tyr (0.5, 1, and 2&#xa0;mM) were incubated with the cells for 48&#xa0;h at 37&#xb0;&#x421;. After the culture medium was removed, the cells were treated with 5&#xa0;&#xb5;M DCFH-DA at 37&#xb0;&#x421; for 30&#xa0;min. Washing with PBS three times was followed by the addition of 100&#xa0;&#xb5;l PBS and the intracellular ROS levels in the cells were viewed with a fluorescence microscope (Nikon Eclipse).</p>
</sec>
<sec id="s2-21">
<title>Measurement of Nitric Oxide</title>
<p>Nitric oxide (NO) production in neuronal and BV-2 cells was performed using 2&#x2032;,7&#x2032;-dichlorodihydrofluorescein diacetate (DAF-FM DA). Different concentrations of <italic>o</italic>-tyr (0.5, 1, and 2&#xa0;mM) were incubated with the cells for 48&#xa0;h at 37&#xb0;&#x421;. After the culture medium was removed, DAF-FM DA (5&#xa0;&#xb5;M) was added to the wells. After incubating at 37&#xb0;&#x421; for 20&#xa0;min, the chemical was removed and the cells were washed three times with PBS followed by measurement with a fluorescence microscope.</p>
</sec>
<sec id="s2-22">
<title>Statistical Analysis</title>
<p>Statistical analyses were performed using R 2.15.0 and GraphPad Prism software v 8.0. All the data were presented as the mean&#x20;&#xb1; SEM. The significance of the differences between two groups was analyzed using the Student&#x2019;s unpaired <italic>t</italic>-test and multiple comparisons were analyzed using one-way ANOVA followed by Dunnett&#x2019;s post hoc test. The differential abundances of genera and metabolites were determined using non-parametric tests including the Wilcoxon rank sum test and Mann&#x2013;Whitney U test. The correlations among fecal metabolites, 16S levels, and physiological and biochemical indexes were tested with both the Pearson Correlation Coefficient and Spearman rank correlation. <italic>p</italic> values were corrected for multiple comparisons using the Benjamini&#x2013;Hochberg false discovery rate (FDR) and <italic>p</italic>&#x20;&#x3c; 0.05 was statistically significant.</p>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>Results</title>
<sec id="s3-1">
<title>Rhubarb Alleviates Cognitive Impairment in APP/PS1 Transgenic Mice</title>
<p>Our previous study revealed that <italic>Rheum tanguticum</italic> ameliorated cognitive impairment in AD rat model, possibly due to the regulation of the gut microbiota (<xref ref-type="bibr" rid="B67">Zhao et&#x20;al., 2019</xref>). In this study, to further verify the therapeutic effects for the treatment of AD, rhubarb extraction with a uniform and stable quality (<xref ref-type="sec" rid="s11">Supplementary Figure S1A</xref>) and donepezil as positive drug were administrated to APP/PS1 transgenic mice for 2&#xa0;months, named the TgR and TgP group, respectively. The main content of this study was shown in <xref ref-type="fig" rid="F1">Figure&#x20;1</xref>. The effect of rhubarb on the learning and memory abilities of the Tg mice was tested by the Morris water maze. During the training period, the escape latencies of the mice in each group were similar on the first day, and gradually decreased in the next 5&#xa0;days (<xref ref-type="fig" rid="F2">Figure&#x20;2A</xref>). On the sixth day, the escape latency of Tg mice was significantly longer than that of wild-type (WT) mice. After the treatment of rhubarb or donepezil, the escape latency of Tg mice was significantly shortened and there was no significant difference between them. In the probe trial, Tg mice exhibited a lower platform passing times (<xref ref-type="fig" rid="F2">Figure&#x20;2B</xref>) and shorter swimming time in target zone (<xref ref-type="fig" rid="F2">Figure&#x20;2C</xref>). However, rhubarb or donepezil treatment significantly reversed these defects in Tg mice. These results indicated that rhubarb could attenuate spatial learning and memory deficits in APP/PS1 mice (<xref ref-type="fig" rid="F2">Figure&#x20;2D</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>The main content of this study.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g001.tif"/>
</fig>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Effects of rhubarb on memory and cognitive function of APP/PS1 mice. <bold>(A&#x2013;D)</bold> Morris water maze test, including assessments of escape latency <bold>(A)</bold>, platform crossing times <bold>(B)</bold>, swimming time in the target quadrant <bold>(C)</bold>, representative swimming path <bold>(D)</bold>. <bold>(E&#x2013;G)</bold> Step-down test, including assessments of error times during training <bold>(E)</bold>, step-down delay <bold>(F)</bold>, error times during experiments <bold>(G)</bold>. Values are expressed as the mean&#x20;&#xb1; S.E.M.; <italic>n</italic>&#x20;&#x3d; 9, &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Tg, &#x23;<italic>p</italic>&#x20;&#x3c;0.05 versus TgP, by Student&#x2019;s unpaired <italic>t</italic>-test.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g002.tif"/>
</fig>
<p>The step-down test was performed to investigate the passive avoidance ability of Tg mice. Compared with the WT mice, Tg mice showed more errors times during the training period (<xref ref-type="fig" rid="F2">Figure&#x20;2E</xref>) and shorter step-down delay (<xref ref-type="fig" rid="F2">Figure&#x20;2F</xref>) accompanied by a greater number of errors (<xref ref-type="fig" rid="F2">Figure&#x20;2G</xref>) during the experimental period. Fortunately, rhubarb or donepezil treatment reduced the errors times during the training period, increased the step-down delay, and reduced the number of errors during the experimental period in Tg mice with no significant difference. These results suggested that rhubarb extract could alleviate the stimulation avoidance response and cognitive impairment in APP/PS1&#x20;mice.</p>
</sec>
<sec id="s3-2">
<title>Rhubarb Reverses the Pathological Changes in Tg Mice</title>
<p>After the behavioral tests, the mice were sacrificed to further investigate the effect of rhubarb on the pathological changes in the brain of Tg mice, including A&#x3b2; deposition, activated microglia, neuronal damage and neurotransmitter disorders. The main pathological feature of AD is senile plaques composed of extracellular A&#x3b2;, which mainly deposited in the brain parenchyma and cerebral vessels (<xref ref-type="bibr" rid="B39">Pistollato et&#x20;al., 2016</xref>; <xref ref-type="bibr" rid="B14">Friedland and Chapman, 2017</xref>). Here, A&#x3b2; deposition in the brain of Tg mice was stained by Congo Red, and the amount of total A&#x3b2; and A&#x3b2;<sub>42</sub> were quantified by ELISA. As expected, cerebral A&#x3b2; deposition (<xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>), and the levels of hippocampal A&#x3b2; and A&#x3b2;<sub>42</sub> (<xref ref-type="fig" rid="F3">Figures 3B,C</xref>) in Tg mice was significantly higher than that of WT mice. After the treatment of rhubarb or donepezil, A&#x3b2; deposition in the brain of Tg mice was significantly reduced (<xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>). Moreover, although there was no significant difference in the level of total A&#x3b2; between the TgR and Tg group, the level of A&#x3b2;<sub>42</sub> was markedly reduced in the TgR group (<xref ref-type="fig" rid="F3">Figures 3B,C</xref>). Donepezil treatment significantly reduced both the levels of total A&#x3b2; and A&#x3b2;<sub>42</sub>.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>Rhubarb alleviates the pathological changes in APP/PS1 mice. <bold>(A)</bold> Histopathology examination of the hippocampus in the brain. (Scale bar: 100&#xa0;&#x3bc;m). <bold>(B&#x2013;L)</bold> Levels of &#x3b2;-amyloids, pro-inflammatory cytokines, and neurotransmitters in the brain. A&#x3b2;<sub>42</sub> (B), A&#x3b2; <bold>(C)</bold>, IL-1&#x3b2; <bold>(D)</bold>, IL-18 <bold>(E)</bold>, TNF-&#x3b1; <bold>(F)</bold>, norepinephrine (NE) <bold>(G)</bold>, glutamate (Glu) <bold>(H)</bold>, &#x3b3;-aminobutyric acid (GABA) <bold>(I)</bold>, Acetylcholine (Ach) <bold>(J)</bold>, serotonin (5-HT) <bold>(K)</bold>, dopamine (DA) <bold>(L)</bold>. Values are expressed as the mean&#x20;&#xb1; S.E.M.; <italic>n</italic>&#x20;&#x3d; 9; &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.01 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.001 versus Tg, by Student&#x2019;s unpaired <italic>t</italic>-test.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g003.tif"/>
</fig>
<p>Recent studies have shown that A&#x3b2; deposition in the brain can activate microglia and release inflammatory factors (<xref ref-type="bibr" rid="B59">Wu Y. et&#x20;al., 2019</xref>). Therefore, the activation of microglia in the brain and the content of inflammatory factors in the hippocampus were evaluated by Iba-1 immunohistochemistry and ELISA, respectively. Compared with the WT mice, both the density and the number of activated microglia in the hippocampus of Tg mice were larger (<xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>). In addition, the levels of IL-1&#x3b2; and IL-18 in Tg mice were significantly higher than that of WT mice, and the level of and TNF-&#x3b1; was slightly higher (<xref ref-type="fig" rid="F3">Figures 3D&#x2013;F</xref>). As shown in <xref ref-type="fig" rid="F3">Figure&#x20;3</xref>, rhubarb treatment exhibited a significant decrease in the number of activated microglia, and the levels of IL-18 and IL-1&#x3b2; (<xref ref-type="fig" rid="F3">Figure&#x20;3</xref>) alone with a slight decrease of TNF-&#x3b1; similar to the donepezil treatment.</p>
<p>Activated microglia release inflammatory factors and induce neuroinflammation reaction, and eventually lead to neuronal apoptosis, resulting in the decline of learning and memory abilities (<xref ref-type="bibr" rid="B42">Rothhammer et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B59">Wu Y. et&#x20;al., 2019</xref>). Therefore, the morphology of neurons in the brain tissue of mice was observed by HE staining. The results showed the disordered arrangement of neurons, condensed cytoplasm and karyopyknosis, and decreased number of neurons were observed in Tg mice (<xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>). Rhubarb or donepezil treatment reversed the above histopathological changes.</p>
<p>Neuronal injury can lead to the neurotransmitter disorders in the brain. Different kinds of neurotransmitters participate in neural activities in multiple brain regions. Therefore, the levels of 5-HT, DA, NE, Ach, Glu, and GABA in the brain of mice were detected by UPLC-TQ/MS. Compared with the WT mice, the levels of NE, Ach, 5-HT, and DA in the brain of Tg mice were significantly decreased, and the levels of Glu and GABA were slightly reduced (<xref ref-type="fig" rid="F3">Figures 3G&#x2013;L</xref>). As illustrated in <xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>, rhubarb and donepezil showed a favourable regulation in neurotransmitters in brain of Tg mice. Altogether, these results provided evidence that rhubarb could alleviate the pathological changes in Tg mice. Moreover, after 60&#xa0;days treatment with rhubarb, there were no obvious abnormalities in body weight (<xref ref-type="sec" rid="s11">Supplementary Figure S2A</xref>) and also no tissue damage or any other adverse effect in brain tissues (<xref ref-type="sec" rid="s11">Supplementary Figure&#x20;S2B</xref>).</p>
</sec>
<sec id="s3-3">
<title>Screening Drug-Responsive Bacteria in Rhubarb Treated Tg Mice in an Age-dependent Alteration by RT-PCR Analysis</title>
<p>In order to explore the changes in intestinal microbiota during the progression of AD, gut microbial dysbiosis in Tg mice in an age-dependent alteration (six samples per time point, <italic>n</italic>&#x20;&#x3d; 36) was evaluated, and distributed intestinal microbiota was identified by 16S rRNA gene sequencing. As a result, a total of 1237622 valid sequences were obtained from 36 samples (average 34378&#x20;&#xb1; 9394 reads per sample). These sequences were classified into 521 OTUs with a 97% similarity level. The &#x3b1;-diversity index includes the Chao1, Shannon, and Simpson indexes, which were used to determine the ecological diversity of the microbial community. The results showed that the &#x3b1;-diversity of gut microbiota in Tg mice decreased to a certain extent compared with the value of WT mice (<xref ref-type="fig" rid="F4">Figures 4A&#x2013;D</xref>). The dominant microbiota at the phylum level in the WT mice changed regularly with age (<xref ref-type="fig" rid="F4">Figure&#x20;4E</xref>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>Alteration of gut microbiota profile in AD model <bold>(A&#x2013;D)</bold> &#x3b1; diversity of WT (<italic>n</italic>&#x20;&#x3d; 6) and Tg mice (<italic>n</italic>&#x20;&#x3d; 6) evaluated by Shannon <bold>(A)</bold>, Simpson <bold>(B)</bold>, Chao1&#x20;<bold>(C)</bold>, and Shannon even indices <bold>(D)</bold>. Error bars represent mean&#x20;&#xb1; S.E.M. &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.01 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.001 versus Tg, &#x2a;&#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.0001 versus Tg, by Wilcoxon rank-sum test. <bold>(E)</bold> Bacterial taxonomic profiling at phylum level. Number in the group name represents months of age. <bold>(F)</bold> Principal component analysis (PCoA) based on unweighted UniFrac distances.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g004.tif"/>
</fig>
<p>The <italic>&#x3b2;</italic> diversity of all bacteria in the six groups was calculated by the unweighted UniFrac metric and visualized by principal coordinate analysis, respectively. We found that the gut microbiota composition between WT and Tg mice changed similarly with time, but the variation in Tg mice was more significant (<xref ref-type="fig" rid="F4">Figure&#x20;4F</xref>).</p>
<p>To further explore the microbiota that was related to the aggravation of the disease, the gut microbiota in WT and Tg mice was compared based on a PLS-DA model. According to the VIP &#x3e; 0.7, 72 differential bacterial genera were screened at 8&#xa0;months of age (<xref ref-type="fig" rid="F5">Figure&#x20;5A</xref>), 76 at 9&#xa0;months of age (<xref ref-type="fig" rid="F5">Figure&#x20;5B</xref>), and 69 at 10&#xa0;months of age (<xref ref-type="fig" rid="F5">Figure&#x20;5C</xref>), respectively. However, only nine genera exhibited the same trends at the three time points. In the Tg group, the relative abundances of <italic>Tyzzerella</italic>, <italic>Ruminococcaceae_UCG_009</italic>, <italic>Bacteroides</italic>, <italic>Escherichia-Shigella,</italic> and <italic>Marvinbryantia</italic>, <italic>norank_f_Ruminococcaceae</italic> and <italic>Erysipelatoclostridium</italic> increased gradually, while <italic>Odoribacter</italic> and <italic>Akkermansia</italic> decreased gradually (<xref ref-type="fig" rid="F5">Figure&#x20;5D</xref>).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption>
<p>The gut microbiota of Tg mice exhibited a common trend with age. <bold>(A&#x2013;C)</bold> PLS-DA score plots of WT and Tg groups. Number in the group name represents months of age. <bold>(D)</bold> Heatmap formed by the abundance of genera. <bold>(E&#x2013;H)</bold> Abundance of the key bacteria in the network, quantified by species-specific quantitative PCR. &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.01 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.001 versus Tg, &#x2a;&#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.0001 versus Tg, by Wilcoxon rank-sum test. <bold>(I)</bold> Co-network constructed by all OTUs in the fecal samples of Tg mice at three time points. The size of the node indicates the relative OTU abundance; the color of the node indicates different phyla; the lines between the nodes indicate co-abundance (red) or co-exclusion (blue) between the&#x20;nodes.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g005.tif"/>
</fig>
<p>After that, drug-responsive bacteria between the Tg and TgR group were identified by RT-PCR analysis. As shown in <xref ref-type="fig" rid="F5">Figures 5E&#x2013;H</xref>, rhubarb treatment increased the number of <italic>norank_f_Ruminococcaceae</italic>, <italic>Erysipelatoclostridium</italic> and <italic>Bacteroides</italic> and reduced the number of <italic>Marvinbryantia</italic> compared with the Tg group. To confirm the changes in the gut microbiota in Tg mice with age, co-network analysis was conducted on all OTUs detected in fecal samples from Tg mice at three time points (<xref ref-type="fig" rid="F5">Figure&#x20;5I</xref>, <xref ref-type="sec" rid="s11">Supplementary Figure S3</xref>). The results showed that there were close interactions between the intestinal microbiota, which increased or decreased together.</p>
</sec>
<sec id="s3-4">
<title>Screening Microbial Metabolites in Rhubarb Treated Tg Mice in an Age-dependent Alteration by Metabolomics Analysis</title>
<p>To clarify the effects of gut microbiota changes on AD-related pathological changes in mice, the metabolic profiles of fecal metabolites from the Tg and WT groups at 8, 9, and 10&#xa0;months of age were analysed by UPLC-Q-TOF/MS in positive and negative ion modes. BPIs of the metabolomic profiles of Tg sample in the negative ion modes is shown in <xref ref-type="fig" rid="F6">Figure&#x20;6A</xref>. A total of 9941 features in the positive ion mode and 5139 features in the negative ion mode were detected in all samples from the WT and Tg groups.</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption>
<p>Fecal metabolomics profile of Tg mice <bold>(A&#x2013;D)</bold>. <bold>(A)</bold> Representative base peak ion chromatogram (BPI) of fecal metabolites from Tg sample. PCA score plots in positive <bold>(B)</bold> and negative <bold>(C)</bold> ion mode. <bold>(D)</bold> Heatmap showing the trend of metabolomic profiling in all the Tg groups. Effects of rhubarb on the fecal metabolomics of AD model <bold>(E,F)</bold>. PCA score plots based on fecal metabolic profiles under the negative ion mode. TgR mice received rhubarb intervention 30&#xa0;days <bold>(E)</bold> and 60&#xa0;days <bold>(F)</bold>. <bold>(G)</bold> Pathway enrichment of different metabolites in WT and Tg mice and the metabolites recovered after rhubarb administration. The size of the node represents the path impact value and the colour represents the &#x2212;log<sub>10</sub> (<italic>p</italic>) value of the pathway.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g006.tif"/>
</fig>
<p>The fecal metabolic profiles of the WT and Tg mice were analysed with PCA. Different metabolites were observed among the groups at 8, 9, and 10&#xa0;months of age. The PCA scores for the WT and Tg at three time points are shown in <xref ref-type="fig" rid="F6">Figure&#x20;6B</xref> (positive ion mode) and <xref ref-type="fig" rid="F6">Figure&#x20;6C</xref> (negative ion mode). It can be observed that the profile for the fecal metabolites showed age-dependent changes. The obvious difference between the WT and Tg groups indicated that the fecal metabolites of Tg mice had changed significantly. To explore potential biomarkers related to the pathogenesis of AD, the fecal metabolomics data for WT and Tg mice was compared by a PLS-DA model (<xref ref-type="sec" rid="s11">Supplementary Figure S4</xref>). According to PLS-DA model with a VIP value greater than 1 and a <italic>p</italic> value less than 0.05 for the ANOVA <italic>t</italic>-test, differential metabolites were identified based on the fragment information and accurate mass number. Through a search and comparison of the HMDB, Metlin, and Chemspider databases, 50 differential metabolites with similar trends were found in the feces of Tg mice at three time points (<xref ref-type="fig" rid="F6">Figure&#x20;6D</xref>). We speculate that some of these 50 differential metabolites were directly related to the pathological process in&#x20;AD.</p>
<p>Drug-specific responsive microbial metabolites in the TgR group were screened by metabolomics analysis. After the administration of rhubarb extract for 30 and 60&#xa0;days, the fecal metabolic profile for Tg mice showed a gradual recovery to a profile similar to that of WT mice (<xref ref-type="fig" rid="F6">Figures 6E,F</xref>, <xref ref-type="sec" rid="s11">Supplementary Figures S1B,C</xref>). Further, 27 of the 50 metabolites (<xref ref-type="fig" rid="F6">Figure&#x20;6D</xref>) present at both time points in the TgR group showed a rhubarb intervention-dependent&#x20;trend.</p>
<p>To gain insight into the mechanism underlying the rhubarb-induced improvement of cognitive impairment in AD mice, the metabolic pathways for 50&#x20;age-dependent metabolites with differences between the WT and Tg groups and 27 biomarkers for the long-term effects of rhubarb on AD cognitive impairment were evaluated. The results showed that the main metabolic pathways for rhubarb were histidine metabolism, D-glutamine, and D-glutamic acid metabolism, aminoacyl tRNA biosynthesis, alanine, aspartic acid, and glutamic acid metabolism (<xref ref-type="fig" rid="F6">Figure&#x20;6G</xref>).</p>
</sec>
<sec id="s3-5">
<title>Screening Microbial Metabolites Associated With Rhubarb-Responsive Bacteria by Co-network Analysis</title>
<p>To further screen the microbial metabolites associated with bacteria in response to rhubarb, an improved co-network analysis was conducted based on the gut microbiota data at the OTU level and 50 differential metabolites detected in mouse fecal samples, with five pathological indicators and six neurotransmitters. As shown in <xref ref-type="fig" rid="F7">Figure&#x20;7</xref>, <italic>Bacteroides</italic>, <italic>Marvinbryantia</italic>, <italic>norank_f_Ruminococcaceae,</italic> and <italic>Erysipelatoclostridium</italic> were significantly correlated with several biomarkers and pathological indicators. Phosphatidylcholine (PC; 15:0/18:2(9Z,12Z)), <italic>o-</italic>tyr, 3-hydroxyundecanoyl carnitine, L-glutamic acid, LysoPE (14:0/0:0), 3-hydroxytetradecanedioic acid, and pyroglutamic acid showed strong correlations with both the microbiota and indicator nodes. Interestingly, <italic>o-</italic>tyr showed a significant correlation with both the microbiota and indicator nodes (<xref ref-type="sec" rid="s11">Supplementary Table S6</xref>), suggesting that <italic>o-</italic>tyr may lay on an important node in this network. We speculated that these four genera and their related metabolites and pathways may influence AD-related pathological indicators and play an important role in the progression of AD. A variety of pathological indicators for AD are related to intestinal microbiota disorders and metabolic disorders (<xref ref-type="sec" rid="s11">Supplementary Figure S5</xref>). It suggested that the decline of cognitive function in AD was related to the microbiota composition and metabolites and further aggravates cognitive impairment.</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption>
<p>Rhubarb regulates the microbial-metabolite-indicator network of AD model. <bold>(A)</bold> Correlation network for microbiota, metabolites, and pathological indicators for Tg mice. The blue triangle represents bacteria, the yellow circle represents metabolites, and the green diamond represents physiological and biochemical indicators. Lines between nodes indicate positive (red) or negative (blue) correlations. The width of the line indicates the correlation value. <bold>(B&#x2013;H)</bold> Rhubarb regulates abundance of key metabolites in the network quantified by peak areas. Values are expressed as the mean&#x20;&#xb1; S.E.M.; <italic>n</italic>&#x20;&#x3d; 9; &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.01 versus Tg; &#x2a;&#x2a;<italic>p</italic>&#x20;&#x3c; 0.001 versus Tg, by Student&#x2019;s unpaired <italic>t</italic>-test.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g007.tif"/>
</fig>
<p>As shown in <xref ref-type="fig" rid="F7">Figure&#x20;7</xref>, some bacteria and metabolites play pivotal roles in the microbiota-metabolite-indicator network and may react specifically to rhubarb. To understand the potential effect of rhubarb on the microbiota-metabolite-indicator network, metabolite nodes with higher node degrees were analysed. Interestingly, the abundance of <italic>o-</italic>tyr, 3-hydroxyundecanoyl carnitine, L-glutamic acid, LysoPE (14:0/0:0), 3-Hydroxytetradecanedioic acid, and pyroglutamic acid, which connected the microbiota and indicator nodes in the network, were recovered after rhubarb treatment (<xref ref-type="fig" rid="F7">Figures 7B&#x2013;H</xref>).</p>
</sec>
<sec id="s3-6">
<title>Validation of <italic>o</italic>-tyr as Key Microbial Metabolites Mediating the Pathological Changes in Alzheimer&#x2019;s disease</title>
<p>As mentioned above, the relative peak area of <italic>o-</italic>tyr in the feces of&#x20;the Tg group continued to increase with age. The level of <italic>o-</italic>tyr was significantly reduced by rhubarb intervention (<xref ref-type="fig" rid="F7">Figure&#x20;7B</xref>). In the microbiota-metabolites-indicators network, <italic>o-</italic>tyr was significantly correlated with two types of bacteria, four pathological indicators, and seven metabolites, suggesting it may play a pivotal role in connecting the microbiota to the&#x20;pathological indicators in the microbiota-metabolites-indicators network.</p>
<p>It has been reported that <italic>o</italic>-tyrosine could not only produce intracellular hydroxyl radicals, but other reactive oxygen species (ROS), such as hydrogen peroxide and superoxide radical anion (<xref ref-type="bibr" rid="B19">Ipson and Fisher, 2016</xref>). We speculated that in the process of aging, <italic>o-</italic>tyr from bacteria could enter the brain due to the increased permeability of the blood-brain barrier, induced neuronal oxidative stress and apoptosis. In this study, <italic>in&#x20;vitro</italic> experiments on primary neurons and BV-2 cells were performed to validate whether <italic>o-</italic>tyr could promote the pathology of AD. ROS is considered to participate in the pathogenesis of AD, which can cause oxidative stress and trigger damages to cells in the brain. The intracellular ROS levels in neuronal and BV-2 cells were determined with DCFH-DA and the fluorescence intensity was further monitored by fluorescence microscope. As shown in <xref ref-type="fig" rid="F8">Figures 8A,C,F,H</xref>, as the increase of <italic>o-</italic>tyr concentration, the fluorescence intensity of both cells significantly enhanced.</p>
<fig id="F8" position="float">
<label>FIGURE 8</label>
<caption>
<p>Effects of <italic>o</italic>-tyr on oxidative stress and cell viability of BV-2 and neurons. <bold>(A,B)</bold> Fluorescent images of ROS <bold>(A)</bold> and NO <bold>(B)</bold> in BV-2 cells, with <italic>in situ</italic> signals quantified in <bold>(C)</bold> and <bold>(D)</bold>. <bold>(E)</bold> Effect of <italic>o</italic>-tyr on the viability of BV-2 cells. <bold>(F,G)</bold> Fluorescent images of ROS <bold>(F)</bold> and NO <bold>(G)</bold> in BV-2 cells, with <italic>in situ</italic> signals quantified in <bold>(H)</bold> and <bold>(I)</bold>. <bold>(J)</bold> Effect of <italic>o</italic>-tyr on the viability of neuronal cells. Values are expressed as the mean&#x20;&#xb1; S.E.M.; <italic>n</italic>&#x20;&#x3d; 6; &#x2a;<italic>p</italic>&#x20;&#x3c; 0.05 versus Con, by Student&#x2019;s unpaired <italic>t</italic>-test.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g008.tif"/>
</fig>
<p>NO, as an inflammatory factor, plays an important role in neuronal death. To investigate the effect of <italic>o-</italic>tyr on the inflammatory response in neuronal and BV-2 cells, DAF-FM DA was used as a probe for NO. As shown in <xref ref-type="fig" rid="F8">Figure&#x20;8</xref>, the fluorescence intensity in both neuronal and BV-2 cells significantly enhanced with the increase of the <italic>o-</italic>tyr concentration.</p>
<p>Studies have shown the potential of <italic>o-</italic>tyr to induce apoptosis. Therefore, the impact of <italic>o-</italic>tyr on the viability of neuronal and BV-2 cells was evaluated by the MTT assay. As shown in <xref ref-type="fig" rid="F8">Figure&#x20;8</xref>, both of the two cells treated with 2&#xa0;mM <italic>o-</italic>tyr reduced the cell viability to approximately 50%. These results demonstrated that <italic>o-</italic>tyr adversely affected the function and viability of the neuronal and BV-2&#x20;cells.</p>
</sec>
</sec>
<sec sec-type="discussion" id="s4">
<title>Discussion</title>
<p>In this study, we found that there were age-dependent alterations in both gut microbiota and fecal metabolites in Tg mice, indicating a dynamic change in microbial community and related metabolites during the development of AD. Through a more accurate co-network analysis based on indicator and multi-omics correlation analyses, we found a significant correlation between the metabolites and microbiota with the development of AD disease. <italic>In vitro</italic> experiments were conducted to confirm the toxicity of the microbial metabolite <italic>o-</italic>tyr, which was closely related to the microbiota and pathological indicators in response to rhubarb intervention. The therapeutic mechanisms by which rhubarb acts on key gut microbiota, affects the related metabolites, and improves pathological indicators and finally cognitive impairment in Tg mice were further examined.</p>
<p>It has been reported that APP/PS1 mice show amyloid deposition at 2&#xa0;months of age, amyloid plaques at 5&#xa0;months of age, synaptic loss after 7&#x2013;9&#xa0;months, and severe cognitive impairment (<xref ref-type="bibr" rid="B57">Want et&#x20;al., 2010</xref>). In addition, age-dependent alterations in the microbiome of APP/PS1 Tg mice have been reported (<xref ref-type="bibr" rid="B46">Shen et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B2">Bauerl et&#x20;al., 2018</xref>). These reports indicate that pathological changes in AD are a dynamic process; hence, disturbed intestinal bacteria based on a single time point are not enough to reflect the pathological process of AD. Accordingly, our study confirmed that the gut microbiota community structure changed with the age of the Tg mice by 16S rRNA analysis. The abundance of <italic>Akkermansia</italic> in the Tg group decreased significantly with the increase of age and was negatively correlated with the A&#x3b2;<sub>42</sub> content in the hippocampus. As a next generation probiotic (<xref ref-type="bibr" rid="B65">Zhang T. et&#x20;al., 2019</xref>), <italic>Akkermansia muciniphila</italic> is considered the most abundant mucolytic bacteria in a healthy gut (<xref ref-type="bibr" rid="B3">Belzer and de Vos, 2012</xref>). The continuous decrease of <italic>Akkermansia</italic> in the gut during aging may lead to the thinning of intestinal mucosa and the weakening of the intestinal barrier function, and subsequently the translocation of endotoxins and other proinflammatory bacterial products (<xref ref-type="bibr" rid="B5">Bodogai et&#x20;al., 2018</xref>). The abundance of <italic>Escherichia-Shigella</italic> in the Tg group also increased with age. A clinical study showed that the abundance of <italic>Escherichia-Shigella</italic> involved in inflammatory response increased in the feces of AD&#x20;patients and there was a significant positive correlation between the expression of IL-6, cxcl2, and NLRP3 (<xref ref-type="bibr" rid="B6">Cattaneo et&#x20;al., 2017</xref>). Interestingly, both <italic>Ruminococcaceae_UCG_09</italic> and <italic>norank_f_Ruminococcaceae</italic> belong to the Ruminococcaceae family, although the two species are similar at the taxonomic level, they may perform distinct functions <italic>in vivo</italic> to influence disease progression (<xref ref-type="bibr" rid="B26">Liu H. et&#x20;al., 2019</xref>). One study reported that high salt diet induced an increase in the abundance of <italic>Ruminococcaceae_UCG_09</italic> in hypertensive mice, accompanied by increased intestinal permeability and inflammation in the small intestine and periphery (<xref ref-type="bibr" rid="B66">Zhang Z. et&#x20;al., 2019</xref>). The increased intestinal permeability led to intestinal bacterial translocation, and the A&#x3b2; peptides and LPS secreted by harmful bacteria further induced peripheral and neuronal inflammation, exacerbating cognitive impairment in AD (<xref ref-type="bibr" rid="B14">Friedland and Chapman, 2017</xref>). Taken together, our results suggested that there were highly dynamic changes and extensive interactions between the gut microbiota of Tg mice that exacerbated the disease phenotype over&#x20;time.</p>
<p>Changes in the composition and function of the gut microbiota can affect the overall effectiveness of the drug (<xref ref-type="bibr" rid="B58">Wu TR. et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B64">Zeng et&#x20;al., 2020</xref>). Meng Yu et&#x20;al. (<xref ref-type="bibr" rid="B62">Yu et&#x20;al., 2017</xref>) reported a reduced abundance of <italic>Marvinbryantia</italic> in the gut microbiota and fecal metabolites of rats in a depression model and a significant association existed in bile acid and tryptophan metabolism as well as 5-HT, DA, and NE in the brain. An observational study of AD patients indicated that bile acids may be a biomarker for the early diagnosis of AD (<xref ref-type="bibr" rid="B29">MahmoudianDehkordi et&#x20;al., 2019</xref>). Gut microbiota and the host co-regulate tryptophan metabolic pathways associated with several neurodegenerative diseases (<xref ref-type="bibr" rid="B40">Platten et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B9">Dong et&#x20;al., 2020</xref>). Gut microbiota has a regulatory effect on 5-HT production by intestinal enterochromaffin cells and affect the overall tryptophan metabolism and 5-HT levels in the colon and blood, which in turn affects the central concentration of the precursor substance of 5-HT, 5-HTP, and regulates neurotransmitter levels in the brain (<xref ref-type="bibr" rid="B24">Kwon et&#x20;al., 2019</xref>). Herein, rhubarb-responsive bacteria were screened by RT-PCR analysis. We found that the abundance of <italic>Marvinbryantia</italic> gradually decreased with increasing age in Tg mice and was correlated with various metabolites in feces as well as the 5-HT, DA, Glu, and GABA neurotransmitters in the brain. We also found that long-term intervention with rhubarb elevated the abundance of <italic>Marvinbryantia</italic>. Therefore, we hypothesized that <italic>Marvinbryantia</italic> might be an important microbiome target for rhubarb to alleviate AD cognitive impairment.</p>
<p>Studies have indicated that microbial metabolites derived from intestinal bacteria may be important messengers for bidirectional cross-talk between the gut and brain. In food and the human body, choline mainly exists in the form of phosphatidylcholine (PC) (<xref ref-type="bibr" rid="B56">Wang et&#x20;al., 2011</xref>). Many intestinal bacteria that can utilize choline to convert PC into free choline, which is metabolized to trimethylamine (TMA) (<xref ref-type="bibr" rid="B7">Chittim et&#x20;al., 2019</xref>). Some studies have identified the involvement of phospholipase D in PC metabolism from gut microbiota, indicating that intestinal microorganisms are potential targets for phospholipid metabolism and TMA inhibition (<xref ref-type="bibr" rid="B7">Chittim et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B36">Orman et&#x20;al., 2019</xref>). Herein, drug-responsive microbial metabolites in Tg mice after rhubarb intervention for 30 and 60&#xa0;days with consistent trends were further screened by metabolomic analysis. Our study showed that PC (15:0/18:2(9Z,12Z)) was broadly correlated with gut microbiota. Rhubarb reversed the abnormal increase of PC (15:0/18:2(9Z,12Z)) in Tg mice, which suggested that choline metabolism disorders in gut microbiota were alleviated. Patients with inflammatory bowel disease (IBD) harbour a variety of clinically pathogenic bacteria that damaged the integrity of the intestinal barrier by reducing the level of intestinal lysophosphatide, leading to the destruction of the intestinal epithelial barrier and immune activation (<xref ref-type="bibr" rid="B69">Zou et&#x20;al., 2020</xref>). Our results showed that the lysophospholipid LysoPE (14:0/0:0) was associated with <italic>Escherichia-Shigella</italic>, <italic>Marvinbryantia,</italic> and IL-1&#x3b2;. Rhubarb significantly increased the LysoPE (14:0/0:0) level and decreased <italic>Marvinbryantia</italic> abundance in Tg mice. This suggested that rhubarb could affect the metabolism of lysophosphatidylcholine by regulating gut microbiota, thereby playing an important role in reducing inflammation, improving the intestinal barrier. 3-hydroxyundecanoyl carnitine belongs to the acyl carnitine family and structurally contains <italic>O</italic>-acyl carnitine. Our study showed that rhubarb reduced 3-hydroxyundecanoyl carnitine, which was positively correlated with IL-1&#x3b2;, IL-18, A&#x3b2;, and <italic>Erysipelatoclostridium</italic>, but negatively correlated with <italic>Bacteroides</italic>. A multi-omic study in the human microbiome program found that the imbalance of acyl carnitine compounds in the feces of patients with IBD with microbiome transcriptome and serum antibodies was accompanied by the reduction of obligatory anaerobes and the overgrowth of facultative anaerobes (<xref ref-type="bibr" rid="B18">Integrative, 2019</xref>). These results suggest that 3-hydroxyundecanoyl carnitine may be a key metabolic marker for rhubarb to improve the flora and indicators of AD. Pyroglutamic acid is a cyclized derivative of lactam formed from free amino cyclization of L-glutamic acid (<xref ref-type="bibr" rid="B41">Ponnusamy et&#x20;al., 2011</xref>). Our results showed that rhubarb could significantly increase the levels of glutamate and pyroglutamate in the feces of Tg mice, regulate the metabolism of neurotransmitters related to intestinal microbiota positively, and thus increase the content of neurotransmitters in the&#x20;brain.</p>
<p>As a biomarker for oxidative stress (<xref ref-type="bibr" rid="B19">Ipson and Fisher, 2016</xref>), <italic>o-</italic>tyr is affected by a variety of microorganisms and can bind abnormally to phenylalanine tRNA in cells, producing oxidative proteins that lead to intracellular protein degradation (<xref ref-type="bibr" rid="B4">Bertin et&#x20;al., 2007</xref>; <xref ref-type="bibr" rid="B23">Klipcan et&#x20;al., 2009</xref>), further reducing cellular activity and inhibiting cellular proliferation (<xref ref-type="bibr" rid="B1">Aronson and Wermus, 1965</xref>). In this study, we found that <italic>o-</italic>tyr, which continued to increase in the progression of AD, was significantly negatively correlated with a number of neurotransmitters and positively correlated with IL-18. In further <italic>in&#x20;vitro</italic> experiments, <italic>o-</italic>tyr was proved to increase ROS and NO in neuronal and BV-2 cells as well as to inhibit cellular activity. These results suggested that gut microbiota-derived <italic>o-</italic>tyr might contribute to oxidative stress and neuroinflammation, exacerbating pathological damage in&#x20;AD.</p>
<p>As the largest endocrine organ in the body, the gut microbial system can produce a wide range of small biologically active metabolites that enter the circulation and affect the brain (<xref ref-type="bibr" rid="B52">Vogt et&#x20;al., 2017</xref>). As AD is a progressive neurodegenerative disease, the gut microbiota and their metabolites accumulate over time as the disease progresses and may exacerbate the process. However, the identified gut microbiota by 16S rRNA sequencing can be highly variable across studies, even yielding completely opposite results regarding a single genus in different studies with the same disease model [6]. Thus, there would be many false positives in screened microbial metabolites by 16S rRNA sequencing-based co-network analysis and presents difficulties for the development of bacteria-targeted drugs for AD. In this study, an improved co-network analysis consisting of RT-PCR and different metabolites combined with pathological indicators provided a more accurate view to uncover the therapeutic mechanisms of rhubarb for AD from the point of gut microbiota. At the very beginning, we explored the microbiota and metabolites that changed with age and correlated with disease indicators. Four bacterial genera were discovered as the drug-responsive bacteria in the process of rhubarb treatment for AD, which were validated using RT-PCR. Then, based on the above identification results, the accuracy of identification for microbial metabolites associated with drug-responsive bacteria was immensely improved by co-network analysis. After that, <italic>o</italic>-tyr was identified and validated its role in promotion of AD pathology by gut-brain transmission. Finally, it demonstrated that rhubarb ameliorated cognitive impairment in Tg mice through decreasing the abundance of <italic>o</italic>-tyr in the gut owing to the regulation of rhubarb-responsive bacteria.</p>
<p>In conclusion (<xref ref-type="fig" rid="F9">Figure&#x20;9</xref>), our results demonstrated that with the progression of AD, dynamic changes occur in gut microbiota and their corresponding metabolites. Most importantly, a more accurate co-network analysis employed here demonstrated that the therapeutic effects of rhubarb for AD relies on certain bacteria and metabolites correlated with pathological indicators. Reducing the accumulation of metabolites produced by microbiota <italic>in vivo</italic> would help to intervene the progression of AD. The current findings provide a novel perspective on the accurate identification of drug-responsive gut microbes and metabolites to elaborate therapeutic mechanisms of bacteria-targeted drugs for&#x20;AD.</p>
<fig id="F9" position="float">
<label>FIGURE 9</label>
<caption>
<p>Rhubarb alleviates cognitive impairment in APP/PS1 mice by regulating drug-responsive bacteria and their corresponding microbial metabolites.</p>
</caption>
<graphic xlink:href="fphar-12-766120-g009.tif"/>
</fig>
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</body>
<back>
<sec id="s5">
<title>Data Availability Statement</title>
<p>The original contributions presented in the study are publicly available. This data can be found here: <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/bioproject/">https://www.ncbi.nlm.nih.gov/bioproject/</ext-link>, PRJNA779704. 210917.</p>
</sec>
<sec id="s6">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by the Ethics Committee for Animal Care and Treatment at Beijing University of Chinese Medicine.</p>
</sec>
<sec id="s7">
<title>Author Contributions</title>
<p>GL, YW, and XG contributed to study conception and design; DG and HZ conducted the experiments, analyzed and interpreted the data, and wrote the manuscript. ZY and CH collected the samples and performed the analysis of samples. All authors critically reviewed the manuscript and approved the final version for submission.</p>
</sec>
<sec id="s8">
<title>Funding</title>
<p>This work was supported by the National Natural Science Foundation of China (81973467/H2803) and the Fundamental Research Funds for the Central Universities (2020-JYB-ZDGG-033).</p>
</sec>
<sec sec-type="COI-statement" id="s9">
<title>Conflict of Interest</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>
<sec sec-type="disclaimer" id="s10">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s11">
<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/fphar.2021.766120/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fphar.2021.766120/full&#x23;supplementary-material</ext-link>
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</ref-list>
<sec id="s12">
<title>Glossary</title>
<def-list>
<def-item>
<term id="G1-fphar.2021.766120">
<bold>5-HT</bold>
</term>
<def>
<p>serotonin</p>
</def>
</def-item>
<def-item>
<term id="G2-fphar.2021.766120">
<bold>A&#x3b2;</bold>
</term>
<def>
<p>amyloid-&#x3b2;</p>
</def>
</def-item>
<def-item>
<term id="G3-fphar.2021.766120">
<bold>Ach</bold>
</term>
<def>
<p>acetylcholine</p>
</def>
</def-item>
<def-item>
<term id="G4-fphar.2021.766120">
<bold>AD</bold>
</term>
<def>
<p>Alzheimer&#x2019;s disease</p>
</def>
</def-item>
<def-item>
<term id="G5-fphar.2021.766120">
<bold>ANOVA</bold>
</term>
<def>
<p>the analysis of variance</p>
</def>
</def-item>
<def-item>
<term id="G6-fphar.2021.766120">
<bold>BBB</bold>
</term>
<def>
<p>blood brain barrier</p>
</def>
</def-item>
<def-item>
<term id="G7-fphar.2021.766120">
<bold>BPIs</bold>
</term>
<def>
<p>Representative base peak ion chromatograms</p>
</def>
</def-item>
<def-item>
<term id="G8-fphar.2021.766120">
<bold>CV</bold>
</term>
<def>
<p>coefficient of variation</p>
</def>
</def-item>
<def-item>
<term id="G9-fphar.2021.766120">
<bold>DA</bold>
</term>
<def>
<p>dopamine</p>
</def>
</def-item>
<def-item>
<term id="G10-fphar.2021.766120">
<bold>DAF-FM DA</bold>
</term>
<def>
<p>3-amino,4-aminomethyl-2&#x2032;,7&#x2032;-difluorofluorescein diacetate</p>
</def>
</def-item>
<def-item>
<term id="G11-fphar.2021.766120">
<bold>DCFH-DA</bold>
</term>
<def>
<p>2&#x2032;,7&#x2032;-dichlorodihydrofluorescein diacetate</p>
</def>
</def-item>
<def-item>
<term id="G12-fphar.2021.766120">
<bold>DMEM</bold>
</term>
<def>
<p>Dulbecco&#x2019;s modified Eagle&#x2019;s medium</p>
</def>
</def-item>
<def-item>
<term id="G13-fphar.2021.766120">
<bold>DMSO</bold>
</term>
<def>
<p>dimethyl sulfoxide</p>
</def>
</def-item>
<def-item>
<term id="G14-fphar.2021.766120">
<bold>dNTP</bold>
</term>
<def>
<p>deoxynucleoside triphosphate</p>
</def>
</def-item>
<def-item>
<term id="G15-fphar.2021.766120">
<bold>ELISA</bold>
</term>
<def>
<p>enzyme-linked immunosorbent&#x20;assay</p>
</def>
</def-item>
<def-item>
<term id="G16-fphar.2021.766120">
<bold>FBS</bold>
</term>
<def>
<p>fetal bovine&#x20;serum</p>
</def>
</def-item>
<def-item>
<term id="G17-fphar.2021.766120">
<bold>FDR</bold>
</term>
<def>
<p>false discovery&#x20;rate</p>
</def>
</def-item>
<def-item>
<term id="G18-fphar.2021.766120">
<bold>GABA</bold>
</term>
<def>
<p>&#x3b3;-aminobutyric&#x20;acid</p>
</def>
</def-item>
<def-item>
<term id="G19-fphar.2021.766120">
<bold>Glu</bold>
</term>
<def>
<p>glutamate</p>
</def>
</def-item>
<def-item>
<term id="G20-fphar.2021.766120">
<bold>HE</bold>
</term>
<def>
<p>hematoxylin and&#x20;eosin</p>
</def>
</def-item>
<def-item>
<term id="G21-fphar.2021.766120">
<bold>IBD</bold>
</term>
<def>
<p>inflammatory bowel disease</p>
</def>
</def-item>
<def-item>
<term id="G22-fphar.2021.766120">
<bold>IL</bold>
</term>
<def>
<p>interleukin</p>
</def>
</def-item>
<def-item>
<term id="G23-fphar.2021.766120">
<bold>LC-MS</bold>
</term>
<def>
<p>Liquid chromatography&#x2013;mass spectrometry</p>
</def>
</def-item>
<def-item>
<term id="G24-fphar.2021.766120">
<bold>LPS</bold>
</term>
<def>
<p>lipopolysaccharides</p>
</def>
</def-item>
<def-item>
<term id="G25-fphar.2021.766120">
<bold>MRM</bold>
</term>
<def>
<p>multiple reaction monitoring</p>
</def>
</def-item>
<def-item>
<term id="G26-fphar.2021.766120">
<bold>MS</bold>
</term>
<def>
<p>mass spectrometry</p>
</def>
</def-item>
<def-item>
<term id="G27-fphar.2021.766120">
<bold>NE</bold>
</term>
<def>
<p>norepinephrine</p>
</def>
</def-item>
<def-item>
<term id="G28-fphar.2021.766120">
<bold>NO</bold>
</term>
<def>
<p>Nitric oxide</p>
</def>
</def-item>
<def-item>
<term id="G29-fphar.2021.766120">
<italic>
<bold>o</bold>
</italic>
<bold>-tyr</bold>
</term>
<def>
<p>
<italic>o</italic>-tyrosine</p>
</def>
</def-item>
<def-item>
<term id="G30-fphar.2021.766120">
<bold>OTUs</bold>
</term>
<def>
<p>operational taxonomic&#x20;units</p>
</def>
</def-item>
<def-item>
<term id="G31-fphar.2021.766120">
<bold>PBS</bold>
</term>
<def>
<p>phosphate-buffered saline</p>
</def>
</def-item>
<def-item>
<term id="G32-fphar.2021.766120">
<bold>PC</bold>
</term>
<def>
<p>phosphatidylcholine</p>
</def>
</def-item>
<def-item>
<term id="G33-fphar.2021.766120">
<bold>PCA</bold>
</term>
<def>
<p>principal component analysis</p>
</def>
</def-item>
<def-item>
<term id="G34-fphar.2021.766120">
<bold>PLS-DA</bold>
</term>
<def>
<p>partial least-squares discriminant analysis</p>
</def>
</def-item>
<def-item>
<term id="G35-fphar.2021.766120">
<bold>QC</bold>
</term>
<def>
<p>quality control</p>
</def>
</def-item>
<def-item>
<term id="G36-fphar.2021.766120">
<bold>RT-PCR</bold>
</term>
<def>
<p>real-time polymerase chain reaction</p>
</def>
</def-item>
<def-item>
<term id="G37-fphar.2021.766120">
<bold>ROS</bold>
</term>
<def>
<p>reactive oxygen species</p>
</def>
</def-item>
<def-item>
<term id="G38-fphar.2021.766120">
<bold>SD</bold>
</term>
<def>
<p>Sprague-Dawley</p>
</def>
</def-item>
<def-item>
<term id="G39-fphar.2021.766120">
<bold>TCM</bold>
</term>
<def>
<p>Traditional Chinese medicine</p>
</def>
</def-item>
<def-item>
<term id="G40-fphar.2021.766120">
<bold>Tg</bold>
</term>
<def>
<p>transgenic</p>
</def>
</def-item>
<def-item>
<term id="G41-fphar.2021.766120">
<bold>TgP</bold>
</term>
<def>
<p>positive drug&#x20;group</p>
</def>
</def-item>
<def-item>
<term id="G42-fphar.2021.766120">
<bold>TgR</bold>
</term>
<def>
<p>rhubarb administration&#x20;group</p>
</def>
</def-item>
<def-item>
<term id="G43-fphar.2021.766120">
<bold>TMA</bold>
</term>
<def>
<p>trimethylamine</p>
</def>
</def-item>
<def-item>
<term id="G44-fphar.2021.766120">
<bold>TNF</bold>
</term>
<def>
<p>tumour necrosis factor</p>
</def>
</def-item>
<def-item>
<term id="G45-fphar.2021.766120">
<bold>UPLC</bold>
</term>
<def>
<p>ultra-performance liquid chromatography</p>
</def>
</def-item>
<def-item>
<term id="G46-fphar.2021.766120">
<bold>UPLC-Q-TOF/MS</bold>
</term>
<def>
<p>Ultra-Performance Liquid Chromatography-quadrupole time-of-flight mass spectrometry</p>
</def>
</def-item>
<def-item>
<term id="G47-fphar.2021.766120">
<bold>UPLC-TQ/MS</bold>
</term>
<def>
<p>Ultra-Performance Liquid Chromatography-Triple Quadruple Mass Spectrometry</p>
</def>
</def-item>
<def-item>
<term id="G48-fphar.2021.766120">
<bold>VIP</bold>
</term>
<def>
<p>variable importance of projection</p>
</def>
</def-item>
<def-item>
<term id="G49-fphar.2021.766120">
<bold>WT</bold>
</term>
<def>
<p>wild type control&#x20;group</p>
</def>
</def-item>
</def-list>
</sec>
</back>
</article>