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Research on gut microbiota has generally focused on fecal samples, representing luminal content of the large intestine. However, nutrient uptake is restricted to the small intestine. Abundant immune cell populations at this anatomical site combined with diminished mucus secretion and looser junctions (partly to allow for more efficient fluid and nutrient absorption) also results in intimate host-microbe interactions despite more rapid transit. It is thus crucial to dissect key differences in both ecology and physiology between small and large intestine to better leverage the immense potential of human gut microbiota imprinting, including probiotic engraftment at biological sensible niches. Here, we provide a detailed review unfolding how the physiological and anatomical differences between the small and large intestine affect gut microbiota composition, function, and plasticity. This information is key to understanding how gut microbiota manipulation, including probiotic administration, may strain-dependently transform host-microbe interactions at defined locations., Competing Interests: Declaration of interests A.C.O., M.N., B.P., D.S., L.G.W.S., and P.V.D.A. work full time for IFF, ADM, Yakult, Novozymes, Caelus Health, and Cryptobiotix respectively. These companies were not involved in carrying out this research., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Modulation of the gut microbiota is a trending strategy to improve health. While butyrate has been identified as a key health-related microbial metabolite, managing its supply to the host remains challenging. Therefore, this study investigated the potential to manage butyrate supply via tributyrin oil supplementation (TB; glycerol with three butyrate molecules) using the ex vivo SIFR ® (Systemic Intestinal Fermentation Research) technology, a highly reproducible, in vivo predictive gut model that accurately preserves in vivo-derived microbiota and enables addressing interpersonal differences. Dosing 1 g TB/L significantly increased butyrate with 4.1 (±0.3) mM, corresponding with 83 ± 6% of the theoretical butyrate content of TB. Interestingly, co-administration of Limosilactobacillus reuteri ATCC 53608 (REU) and Lacticaseibacillus rhamnosus ATCC 53103 (LGG) markedly enhanced butyrate to levels that exceeded the theoretical butyrate content of TB (138 ± 11% for REU; 126 ± 8% for LGG). Both TB + REU and TB + LGG stimulated Coprococcus catus , a lactate-utilizing, butyrate-producing species. The stimulation of C. catus with TB + REU was remarkably consistent across the six human adults tested. It is hypothesized that LGG and REU ferment the glycerol backbone of TB to produce lactate, a precursor of butyrate. TB + REU also significantly stimulated the butyrate-producing Eubacterium rectale and Gemmiger formicilis and promoted microbial diversity. The more potent effects of REU could be due to its ability to convert glycerol to reuterin, an antimicrobial compound. Overall, both the direct butyrate release from TB and the additional butyrate production via REU/LGG-mediated cross-feeding were highly consistent. This contrasts with the large interpersonal differences in butyrate production that are often observed upon prebiotic treatment. Combining TB with LGG and especially REU is thus a promising strategy to consistently supply butyrate to the host, potentially resulting in more predictable health benefits.

The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae , and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.

MegaSporeBiotic™ is an oral, spore-based probiotic comprised of five Bacillus spp. (Bacillus indicus HU36, Bacillus subtilis HU58, Bacillus coagulans SC208, Bacillus licheniformis SL307, and Bacillus clausii SC109). The effects of MegaSporeBiotic™ on gut microbiota activity and community composition were evaluated for the first time using an in vitro model of the human gastrointestinal tract, the simulator of the human intestinal microbial ecosystem (SHIME®), under healthy conditions. Following a stabilization period and a control period (2 weeks each), the reactor feed was supplemented with daily MegaSporeBiotic™ for 3 weeks (treatment period). Changes in microbial community activity and composition between the control and treatment periods were evaluated for each colon compartment (ascending [AC], transverse [TC], and descending colon [DC]). Propionate levels increased significantly in the TC (week 2, P = 0.02; week 3, P = 0.0019) and DC (week 2, P = 0.03) with treatment while lactate levels significantly decreased in the TC (week 3, P = 0.03). Ammonium levels were significantly decreased during the final week of treatment (TC, P = 0.02; DC, P = 0.03). Overall, Akkermansia muciniphila, Bifidobacteria spp., and Firmicutes increased with treatment while Lactobacillus spp. and Bacteroidetes decreased. The Firmicutes:Bacteroidetes ratio increased with treatment in the AC compartment. MegaSporeProbiotic™ treatment resulted in changes in metabolism and increased bacterial diversity., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

While a large set of in vitro models are available to study the effects of specific food ingredients (e.g. pre- and probiotics) on the human gut microbiome, the availability of such models for companion animals is limited. Since improving gut health of such animals is an emerging research field, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data. The current study presents a further improvement of this model by using an alternative method for feed preparation, i.e. by administering digestive enzymes to mimic upper gastro-intestinal digestion followed by a dialysis approach to mimic small intestinal absorption. As opposed to the previously implemented method, this resulted in a more optimal simulation of protein digestion and absorption. Further, upon entrance in the colon, increased production of the health-promoting butyrate and lower levels of Lactobacillus spp. and Bifidobacterium spp. were observed, which corresponded better with obtained in vivo data. A second model improvement consisted of the implementation of a mucosal environment to not only simulate luminal but also mucosal microbiota. In consistency with the human model for which this technology was previously validated, it was found that for all canine microbiota mucin beads were enriched with members of the Lachnospiraceae (~ Clostridium cluster XIVa), a family containing multiple well-known butyrate producers. The SCIME™ was thus upgraded to a so-called Mucosal SCIME™ (M-SCIME™). In conclusion, the current study presents improvements of the SCIME™, further increasing the relevance of obtained data with this in vitro model for dogs., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Symprove, a multi-strain probiotic, has been shown to exert a mild anti-inflammatory effect in patients with ulcerative colitis (UC). We examined stool samples from 3 patients with UC in order to create microbiotas in an in-vitro gut model. The effects of Symprove on bacterial diversity and metabolic activity in the microbiotas was evaluated over 48 h. In addition, the influence of probiotic dosing on epithelial tight-junction integrity, production of inflammatory markers and wound healing were evaluated in cell culture models. The relative proportions of the main bacterial phyla in UC patients differed from those of healthy subjects studied previously; levels of Firmicutes were lowered and levels of Bacteroidetes were raised. Addition of Symprove changed the bacterial composition in the microbiotas over a 48 h period. Several other factors generally implicated in good gut health changed after dosing with probiotic; production of short chain fatty acids (SCFAs) and lactate was stimulated, levels of anti-inflammatory cytokines (IL-6, IL-10) increased, levels of pro-inflammatory cytokines and chemokines (MCP-1 and IL-8) decreased, epithelial tight junction integrity improved and wound healing occurred faster than a control. The results imply it is not the simple addition of probiotic bacteria that improves gut health. Rather, the probiotic bacteria generate lactate, which then stimulates growth of commensal gut bacteria, raising SCFA levels (particularly butyrate). The increased butyrate concentration positively influences inflammation response and time of wound healing., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Background: This study evaluated the impact of Bifidobacterium animalis ssp. lactis CNCM I-3446, Bovine Milk-derived OligoSaccharides (BMOS) and their combination on infant gut microbiota in vitro. In addition, a novel strategy consisting of preculturing B. lactis with BMOS to further enhance their potential synbiotic effects was assessed., Method: Short-term fecal batch fermentations (48 h) were used to assess the microbial composition and activity modulated by BMOS alone, B. lactis grown on BMOS or dextrose alone, or their combinations on different three-month-old infant microbiota., Results: BMOS alone significantly induced acetate and lactate production (leading to pH decrease) and stimulated bifidobacterial growth in 10 donors. A further in-depth study on two different donors proved B. lactis ability to colonize the infant microbiota, regardless of the competitiveness of the environment. BMOS further enhanced this engraftment, suggesting a strong synbiotic effect. This was also observed at the microbiota activity level, especially in a donor containing low initial levels of bifidobacteria. In this donor, preculturing B. lactis with BMOS strengthened further the early modulation of microbiota activity observed after 6 h., Conclusion: This study demonstrated the strong synbiotic effect of BMOS and B. lactis on the infant gut microbiota, and suggests a strategy to improve its effectiveness in an otherwise low- Bifidobacterium microbiota.

Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Poorly formulated probiotic supplements intended for oral administration often fail to protect bacteria from the challenges of human digestion, meaning bacteria do not reach the small intestine in a viable state. As a result, the ability of probiotics to influence the human gut microbiota has not been proven. Here we show how (i) considered formulation of an aqueous probiotic suspension can facilitate delivery of viable probiotic bacteria to the gut and (ii) quantitate the effect of colonisation and proliferation of specific probiotic species on the human gut microbiota, using an in-vitro gut model. Our data revealed immediate colonisation and growth of three probiotic species in the luminal and mucosal compartments of the proximal and distal colon, and growth of a fourth species in the luminal proximal colon, leading to higher proximal and distal colonic lactate concentrations. The lactate stimulated growth of lactate-consuming bacteria, altering the bacterial diversity of the microbiota and resulting in increased short-chain fatty acid production, especially butyrate. Additionally, an immunomodulatory effect of the probiotics was seen; production of anti-inflammatory cytokines (IL-6 and IL-10) was increased and production of inflammatory chemokines (MCP-1, CXCL 10 and IL-8.) was reduced. The results indicate that the probiotic species alone do not result in a clinical effect; rather, they facilitate modulation of the gut microbiota composition and metabolic activity thereby influencing the immune response., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Butyrate-producing bacteria are promising probiotic candidates to target microbial dysbiosis in gastrointestinal disorders like inflammatory bowel diseases. Butyricicoccus pullicaecorum 25-3(T), a butyrate-producing clostridial cluster IV strain, is such a candidate. Little is known about its abundance in the colon microbiota and its butyrogenic properties. We used the M-SHIME(®), an in vitro simulator for the human intestinal microbial ecosystem, to study the effect of supplementing a single dose of B. pullicaecorum 25-3(T) on lumen- and mucus-associated microbiota of eight individuals. Butyricicoccus pullicaecorum was more abundant in mucus-associated microbiota compared with lumen microbiota. Supplementation with a single dose of B. pullicaecorum 25-3(T) resulted in a temporary increase in B. pullicaecorum bacteria in lumen compartment of all individuals. In two cases, the responders, an increased butyrate production was observed as compared with the control. 16S rRNA gene amplicon sequencing revealed the microbiota of responders to be different as compared to non-responder microbiota. We can conclude that B. pullicaecorum 25-3(T) is a mucus-associated bacterium whose potency to stimulate butyrate production is characterized by a large interindividual variability in terms of composition of the receiving microbial community., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The objective of the study was to examine the influence of encapsulated Lactobacillus casei 01 combining with two types of pressurized-purple-rice drinks on colonizing the colon using a simulator of the human intestinal microbial ecosystem. Subsequently, the metabolic products of colon bacteria and various microflora were determined. The finding revealed that acetate which was the predominant short-chain fatty acid (SCFA) was found in both proximal and distal colons, while the combination of encapsulated L. casei 01 and germinated-purple-rice drinks gave rise to highest formation of SCFA. Significant impact of rice drinks could be observed on reducing ammonia production. The quantitative polymerase chain reaction analysis demonstrated that encapsulated L. casei 01 and encapsulated L. casei 01 plus rice drinks markedly increased concentration of colon lactobacilli and bifidobacteria by 2 and 1 log 16S rRNA gene copies/mL, respectively. On the contrary, undesirable bacteria such as clostridia and coliforms were significantly reduced with the influence of encapsulated L. casei 01 plus purple-rice drinks.

Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2–THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella—a critical factor in Salmonella pathogenesis—was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks. [ABSTRACT FROM AUTHOR]

Benefits associated with probiotic use have been reported; however, the mechanisms behind these benefits are poorly understood. The effects of a probiotic formulation (MegaDuo™) containing Bacillus coagulans SC208 and Bacillus subtilis HU58 on intestinal permeability and immune markers was assessed using a combination of the in vitro gut model, the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME®), and an in vitro inflammatory bowel disease-like Caco-2/THP1 co-culture model in both healthy and antibiotic-induced dysbiosis conditions. Established M-SHIME® proximal colon vessels were treated with/without clindamycin (1 week) and then with/without daily MegaDuo™ treatment (2 weeks). The mucosal and luminal microbial communities were sampled weekly. Suspensions were removed from the proximal colon vessels after 1 and 2 weeks of MegaDuo™ treatment and added to the co-culture system. Transepithelial resistance (membrane barrier function), cytokine/chemokine release, and NFκB activity were then measured. Under conditions of antibiotic-induced dysbiosis, suspensions from MegaDuo™ treated vessels showed reduced gut membrane barrier damage and decreased levels of TNFα and IL-6 compared with suspensions from untreated vessels; no appreciable differences were observed under healthy conditions. MegaDuo™ treatment had no effect on NFκB activity of THP1-Blue™ cells. The potential benefits of MegaDuo™ treatment appeared most evident after 2 weeks of treatment. [ABSTRACT FROM AUTHOR]