The gut microbiota plays a significant role in human health, participating in several functions beneficial to the host (Patel and DuPont, 2015; Kristensen et al., 2016). It has been implicated in preventing pathogen colonization (Hand, 2016), shaping our immune system (Round and Mazmanian, 2009; Patel and DuPont, 2015; Macpherson et al., 2017), stimulating the production of gastrointestinal hormones (Saulnier et al., 2013), and regulating brain behavior (De Palma et al., 2014, 2017) through production of neuroactive substances (Steenbergen et al., 2015; Kristensen et al., 2016).

Additionally, the gut microbiota has been involved in the fermentation of non-digestible carbohydrates reaching the colon. This process leads to the production of short chain fatty acids (SCFAs), which elicit health benefits (den Besten et al., 2013). The human gut microbiota can be manipulated through either passive or active processes. Passive factors include hygiene, lifestyle, and diet. For instance, primary colonizers of the gut involved in the immune development are shifted by sanitary practices (Zhou, 2016). In addition, dietary constituents can promote phylogenetic variations in the microbiota (Graf et al., 2015). In this context, prebiotics are defined as “a substrate that is selectively utilized by host microorganisms conferring a health benefit” (Gibson et al., 2017). Prebiotics act as growth substrates (Patrascu et al., 2017) to enhance the activity of bacterial genera (Scott et al., 2015) such as bifidobacteria and butyrate-producing clostridia (Rivière et al., 2016). SCFA and vitamins resulting from the fermentation of these components are crucial for human health (Graf et al., 2015). In terms of lifestyle factors, physical activity is known to positively impact the diversity of gut microbiota. In fact, gut microbiota of athletes is more diverse than that of non-athletic subjects (Clarke et al., 2014). Amongst the active processes manipulating microbiota composition are antibiotics and probiotics. Antibiotic use has been linked to dysbiosis (Langdon et al., 2016), even leading to low diversity, evenness, and taxonomic richness (Dethlefsen and Relman, 2010; Francino, 2016). Moreover, presence and expression of microbial genes are altered following antibiotic therapy (Reijnders et al., 2016). These detrimental outcomes may lead to decreased SCFA, glycolysis, vitamin production, homeostasis of the immune system, and impaired protection against pathogens (Guarner and Malagelada, 2003). As a result, antibiotic associated diarrhea (AAD) and recurrent infectious diseases like Clostridium difficile infection (CDI) may occur (Francino, 2016).

On the other side of the spectrum are probiotics, which can affect the host either directly or through their products, or even influence the activity of resident bacteria in the host (Scott et al., 2015). Probiotics are defined as “live microorganisms which when administered in adequate amounts confer a health benefit on the host” (WHO/FAO, 2006; Hill et al., 2014). The effect of probiotics in preventing metabolic syndromes such as obesity, type 2 diabetes (Kasińska and Drzewoski, 2015), and dyslipidemia has been reported (Asemi et al., 2013). For instance, administration of Bifidobacterium (Yin, 2010; Chen et al., 2011; Plaza-Diaz et al., 2014; Reichold et al., 2014; Savcheniuk et al., 2014; Wang et al., 2014) and Lactobacillus species reduced body weight gain and adipose tissue in mice fed high-fat diet through stimulation of adiponectin production (Kim et al., 2013; Kobyliak et al., 2016). In addition, lactobacilli have been proven to have therapeutic effects in different pathologies (Di Cerbo et al., 2016). Moreover, probiotics regulate the mucosal immune response (Klaenhammer et al., 2012), improving the activity of macrophages (Sang, 2010) and changing the expression of the genes associated. Even though these outcomes depend on specific bacteria and strains, probiotics may interact with TLR and downregulate the expression of NF-κB and pro-inflammatory cytokines (Ng et al., 2009; Plaza-Diaz, 2014). For instance, peptides of microbial anti-inflammatory molecules (MAMs) that are found in the Faecalibacterium prausnitzii supernatant inhibit the NF-κB pathway in vitro and in vivo (Breyner et al., 2017), confirming the anti-inflammatory and therapeutic properties of F. prausnitzii (Martín et al., 2014). These properties and protective effects of F. prausnitzii were identified in different models such as dinitrobenzene sulfate (DNBS)-induced colitis model, dextran sodium sulfate (DSS)-induced colitis (Breyner et al., 2017), and 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced acute colitis in mice (Miquel et al., 2015). Additionally, levels of anti-inflammatory cytokines and immunoglobulins, immune cell proliferation, and production of proinflammatory cytokines produced by the T cells may be modulated following probiotic supplementation (Miettinen et al., 1996; Nazemian et al., 2016). Furthermore, probiotics can be alternative strategies for inflammatory disorders, as they upregulate the production of CD4+Foxp3+ regulatory T cells (T_regs) (Kwon et al., 2010; Yan and Polk, 2011).

Different effects on the immune function may be species- and strain-related (Klaenhammer et al., 2012). It has been reported that probiotics have therapeutic effect on the central nervous system by reducing the intestinal inflammation. In this way, the regulation of HPA axis and the activity of the neurotransmitters may be improved (Wallace and Milev, 2017). Probiotics from Bifidobacterium and Lactobacillus genera are usually delivered through fermented products such as yogurts, milk, and cheeses, or they can be delivered as food supplements (Besseling-van der Vaart et al., 2016).

Probiotics have been categorized into monostrain or multistrain/multispecies products (Timmerman et al., 2004). Different studies have confirmed positive effects on health when multistrain probiotics are used, due to the symbiosis among strains (Timmerman et al., 2004). Strains in multispecies probiotics can be from different genera. For instance, the efficacy of the multispecies probiotic consortium VSL#3 (Streptococcus thermophilus, Eubacterium faecium, Bifidobacterium breve, Bifidobacterium infantis, Bifidobacterium longum, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus casei, and Lactobacillus delbrueckii subspecies bulgaricus) was proven for the treatment of ulcerative colitis (Venturi et al., 1999; Timmerman et al., 2004). Besides, VSL#3 supplementation in women with gestational diabetes mellitus (GDM) may help regulate inflammatory markers and positively influence glycemic control (Jafarnejad et al., 2016). In addition, Chapman et al. (2011) described that probiotic mixtures were more effective than single-strain probiotics in inhibiting pathogen growth and atopic dermatitis, suggesting further application on other diseases like IBD. Another multispecies probiotic called Ecologic^®Tolerance/Syngut^TM was developed using four different probiotic strains (Bifidobacterium lactis W51, L. acidophilus W22, L. plantarum W21, and Lactococcus lactis W19). Strains of this consortium have been proven to strengthen the gut barrier function, have beneficial effects on post-immunological induced stress, inhibit Th2, and stimulate IL-10 levels, thus providing beneficial effects in patients with food intolerance (Besseling-van der Vaart et al., 2016). Moreover, a multispecies probiotic consortium, Ecologic AAD (B. bifidum W23, B. lactis W18, B. longum W51, E. faecium W54, L. acidophilus W37 and W55, L. paracasei W72, L. plantarum W62, L. rhamnosus W71, and L. salivarius W24), reduced diarrhea-like bowel movements when administered in healthy volunteers taking amoxicillin (Koning et al., 2008). Multispecies probiotics also prevented rise in fasting plasma glucose (FPG), to decrease high sensitivity C-reactive protein (hs-CRP), and to increase plasma glutathione (GSH) in diabetic patients (Asemi et al., 2013). van Minnen et al. (2007) provided evidence that manipulation of the intestinal flora with multispecies probiotics reduced bacterial translocation, morbidity and mortality in a rat model of acute pancreatitis. Furthermore, multispecies probiotics rapidly relieved IBS symptoms and shifted the microbiota composition (Yoon et al., 2013). According to these results, combining specific probiotic effects from diverse strains can lead to an additive and more synergetic multispecies probiotic consortium (Timmerman et al., 2007).

However, the phylogenetic origin of probiotics is currently limited to conventional formulations of Bifidobacterium, Lactobacillus species and other lactic acid bacteria (LAB) (Govender et al., 2013) or yeast strains. This may decrease the probiotic effectiveness in the prevention or therapy of diseases entailing severe dysbiosis. Hence, a functionally and phylogenetically diverse probiotic product may be desirable when alterations in the gut microbiota composition are present (Marotz and Zarrinpar, 2016). For instance, CDI and recurrent CDI are major medical conditions that need urgent treatment when conventional antibiotics fail. As a result, development of complex communities with targeted functions is needed.

Fecal microbiota transplant (FMT) or fecal bacteriotherapy is an alternative strategy successfully used for the treatment of CDI (Kelly, 2013). Severe antibiotic therapy and CDI trigger dysbiosis, reducing diversity and functionality of the gut endogenous microbiota (Brandt, 2012). In this case, C. difficile spores can germinate, colonize, and thrive in the gut. Treatment of CDI requires additional antibiotics, increasing the risk of recurrent CDI (rCDI) after cessation of treatment, as a result of the dysbiosis caused by antibiotic therapy (Becattini et al., 2016; Francino, 2016), due to infection with the original strain (Barbut et al., 2000; Marsh et al., 2012) or re-infection caused by a different strain (Johnson et al., 1989; Kelly, 2009; Figueroa et al., 2012).

Poor colonization resistance from the gut microbiota and the patient’s poor immune response further contribute to CDI risk (Pérez-Cobas et al., 2015). Recurrent CDI risk is 10–20% after initial CDI (Surawicz et al., 2013), and it increases to 45% after a first relapse, and to 60% for those with two or more recurrences (Bartlett, 1990). However, FMT can resolve both CDI and rCDI (Bakken, 2009), with a success rate of 90% when further antibiotic treatments fail (Youngster et al., 2014; Rao and Safdar, 2015). Given the success of FMT, it is now being considered as potential treatment for disorders such as ulcerative colitis (Shi et al., 2016), irritable bowel syndrome (Distrutti et al., 2016), and metabolic syndrome (Hartstra et al., 2015). For instance, FMT induced remission in patients with active ulcerative colitis (Moayyedi et al., 2015), potentially as a result of the introduction of normal flora and the subsequent correction of the imbalance in the microbiota caused by the disease (Bakken et al., 2011). The complexity of the fecal sample can be the key factor behind the positive shift in the microbiota composition generated by the FMT (Marotz and Zarrinpar, 2016). Thus, diversity of the donor microbiome may be crucial (Leszczyszyn et al., 2016). Indeed, some patients do not respond to FMT, probably because only specific bacterial phylotypes can be therapeutic when effectively transferred (Vermeire et al., 2015). Hence, FMT efficacy for treating gastrointestinal disorders is controversial (Sbahi and Di Palma, 2016). Adverse effects after FMT include nausea, vomit, fever, abdominal pain, and diarrhea (Vermeire et al., 2015; Pigneur and Sokol, 2016). Data for long-term effects of FMT is lacking, but theoretically, any disease phenotype from the donor can be transferred to the patient (Sbahi and Di Palma, 2016). This could be expected, as the uncharacterized nature of FMT may result in undetected or unmonitored risk factors such as viruses, pathogens or even allergens being passed to the FMT recipient, causing disease. To overcome this problem, Petrof et al. (2013) developed a synthetic bacteria cocktail with characterized nature to substitute FMT. Alternatively, a thorough pre-screening should be performed on the donor before the actual procedure of the FMT. Thus, the French Group of Fecal microbiota Transplantation (FGFT) was created to secure and evaluate the practice in this field (Sokol et al., 2016). Despite having experience treating CDI, FMT is not yet the top treatment choice of physicians (Zipursky et al., 2014). However, the majority of gastroenterologists and physicians in metropolitan areas were supportive to the idea of creating a fecal transplantation center, and a high percentage of the physicians would refer their patients to those centers (Jiang et al., 2013).

Additional microbiome therapeutics using characterized microbial communities of selected fecal bacteria could be developed to replace FMT, and yield the desired outcome (Sbahi and Di Palma, 2016). For instance, Petrof et al. (2013) described a stool substitute constituted by 33 different purified intestinal bacteria isolated from a healthy donor (Table 1), to treat rCDI. In this study, the synthetic bacterial mixture was infused through the colon of the infected patient causing a change in the stool microbial profile. Major shifts reflecting the isolates of the synthetic mixture were still detectable 6 months after treatment. Thus, the concept of “RePOOPulate” the gut microbiome was coined. Authors of the study suggested that using a synthetic stool substitute may be an effective method to replace the use of FMT for treating rCDI. Although further validation is needed, complete resolution of the infection was achieved. Several advantages of this synthetic stool substitute can be highlighted. The composition of the administered bacterial cocktail is accurately characterized, facilitating registration. Further, assembly of the synthetic bacterial cocktail is highly reproducible enabling standardization and upscaling. In addition, patient safety can be guaranteed, because the bacterial mixture can be rendered pathogen- and virus-free (Petrof et al., 2013). These data suggest that a multi-species community such as that in the RePOOPulate study, can be more effective than single-strain probiotics or mixed cultures of probiotic species. This can be because the RePOOPulate community preserved its structure and thus successfully colonized a new environment (Petrof et al., 2013). Moreover, RePOOPulate consisted of a more phylogenetically diverse community including strains with beneficial health effects that can be candidates for next generation probiotics.

Looking at its internationally recognized definition, probiotics are live microorganisms that, when administered in adequate numbers, confer health benefits on the host. Probiotics are usually isolated from our commensal gut bacteria, but cannot be given the definition of probiotics until their stability, content, and health effect are characterized (Sanders, 2008). Probiotics are thought to improve the balance in the host, prevent disturbances, and decrease the risk of pathogen colonization (Goldenberg et al., 2013). They have been referred to as functional foods or beneficial bacteria, and they have been considered for the prevention and treatment of C. difficile-associated diarrhea (CDAD) (Goldenberg et al., 2013). Probiotics can be found as capsules or food supplements in health food stores and supermarkets (Goldenberg et al., 2013). Pattani et al. (2013) reported that Lactobacillus-based formulations combined with antibiotics reduced the risk of AAD and CDI. They however, suggested that larger studies are needed to decide on the use of probiotic/antibiotic combination as a therapy over the single species probiotic (Pattani et al., 2013). Furthermore, findings from randomized control trials (RCTs) and meta analyses suggest that there is moderate evidence on the ability of probiotics to prevent primary CDI (people at risk of CDI), but there is no enough evidence suggesting the probiotics can prevent secondary CDI (recurrent CDI) (Evans and Johnson, 2015). There are still some evidence gaps for the use of probiotics in the prevention of CDI such as the interaction between specific classes of antibiotics with the probiotics used on CDI risk, the bacterial taxa that provides the best efficacy in the prevention of CDI, and the use of probiotics in immunocompromised or critically ill patients (Rao and Young, 2017). Hence, future RCT should consider these different concerns (Rao and Young, 2017). Besides, probiotics impact the gut-brain axis.

For example, Bifidobacterium longum NC3001 had beneficial effects on psychiatric comorbidities, which in turn could temporarily improve the quality of life in IBS patients, indicating that this probiotic reduces limbic reactivity (Pinto-Sanchez et al., 2017).

Overall, classical probiotics show limited effects on the human gut microbiota seeking the need for a better selection and formulation of bacterial strains (Neef and Sanz, 2013). Results from previous studies show promising outcomes in the treatment or prevention of diverse metabolic and inflammatory diseases by specific bacteria (Neef and Sanz, 2013). Those probiotics encompass species different from Lactobacillus and Bifidobacterium (Cani and Van Hul, 2015; Patel and DuPont, 2015). Nevertheless, the gut microbiome is a complex community, which makes it difficult to define the host–microbe interaction.

The United Nations Food and Agriculture organization (FAO) definition of probiotics is broad, allowing flexibility in terms of the phylogenetic origin of probiotics. Information generated from previous studies assisted in the selection of next generation probiotics, which include members from Clostridium clusters IV, XIVa and XVIII, F. prausnitzii, Akkermansia muciniphila, Bacteroides uniformis (Neef and Sanz, 2013; Patel and DuPont, 2015), Bacteroides fragilis (Round et al., 2011), and Eubacterium hallii (Udayappan et al., 2016). These next generation probiotics were evaluated in preclinical trials and yielded positive outcomes for inflammatory and metabolic disorders (Neef and Sanz, 2013; Patel and DuPont, 2015). In addition, new techniques are required for the development of new probiotic products containing strains from human origin. This is to say, these strains must come from the major groups of the intestinal microbiota, they have to be defined to have a safe status and proven to have potential beneficial effects (Martín et al., 2017). In the following sections, we will discuss some of the most promising bacterial species that are currently under consideration for being used as next-generation probiotics.

As previously described, T_regs can regulate immune homeostasis and serve as a therapeutic target for different gut inflammatory disorders. Induction of the colonic T_regs is dependent on special properties of our commensal bacteria. Clostridium spp. belonging to clusters IV and XIVa (also known as Clostridium leptum and coccoides groups, respectively) are exceptional inducers of T_regs in the colon and can be considered as therapeutic options for IBD and allergies (Atarashi et al., 2011). Previous work indicated that a cocktail of strains isolated for the human gut microbiota can be more effective than a single strain in preventing or treating disease. Thus, Atarashi et al. (2013) isolated 17 strains belonging to Clostridia clusters XIVa, IV, and XVIII from a human fecal sample, which were effective in T_reg cell differentiation and accumulation in mouse colon. Authors proposed that the SCFAs produced by this community influenced the expression of Foxp3, a key gene controlling T_reg cell development (Atarashi et al., 2013). Incidentally, Clostridia clusters XIVa and IV are decreased in fecal samples from patients with inflammatory bowel disease (IBD), and thus the cocktail of the 17 strains could potentially reverse this dysbiosis (Atarashi et al., 2013).

FMT may be replaced with a characterized multispecies bacterial mixture that can be safer, free of allergens or viruses, and capable of treating CDI. With the current in vitro and in vivo data, next generation probiotics hold promise to treat diverse medical conditions, and they can be more effective than single or multi strains of the commercial probiotics. Moreover, several different strains with proven health benefits can also be considered candidates for next generation probiotics and other microbiota-based drugs. However, additional research is required for an increased understanding of the interactions among those strains, aiming at producing a successful therapeutic formulation. Research should be conducted to demonstrate whether these probiotics can be applicable to humans, as safety assessments have only been completed in animals. Effective carriage of bacterial strains in food matrices is critical for survival. Thus, optimisation of the growing conditions, and even encapsulation must be considered to promote delivery and release of the live product in the colon. The development of next generation probiotics and MMPs hold promise for innovation in both the food/feed sector and the pharmaceutical industry. A close interaction between academia, industry and regulatory agencies is essential for developing safe and health-promoting products, as both prophylactic and therapeutic strategies.

Conceived and designed the review: REH, EH-S, and TVW. Funding acquisition: TVW. Wrote the paper: REH. Reviewed the manuscript: REH, EH-S, and TVW.

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.