Human Colonic Microbiota Research Articles

Effects of digested flours from four different sweet potato (Ipomoea batatas L.) root varieties on the composition and metabolic activity of human colonic microbiota in vitro.

This study evaluated the effects of flours from four different sweet potato root (SPR) varieties, being two with white peel and two with purple peel, on the composition and metabolic activity of human colonic microbiota in vitro. The capability of these SPR flours (20g/L) to cause alterations in relative abundance of different bacterial groups found as part of human colonic microbiota, as well as in lactic acid and short-chain fatty acid production was evaluated during 48 hr of an in vitro colonic fermentation. The SPR flours were submitted to a simulated gastrointestinal digestion prior to use in experiments. The four SPR flours increased the relative abundance of Lactobacillus/Enterococcus (range: 0.49-4.48%) and Bifidobacterium (range: 0.32-3.27%) and decreased the relative abundance of Bacteroides/Prevotella (range: 0.29-7.49%), Clostridium histolyticum (range: 0.15-2.08%), and Eubacterium rectale/Clostridium coccoides (range: 0.28-3.86%) during the 48 hr of colonic fermentation. The four SPRF flours had positive prebiotic indexes (>0.38) after 24 and 48 hr of colonic fermentation, reinforcing the occurrence of selective stimulatory effects on colonic microbiota. An increased metabolic activity of human colonic microbiota was caused by tested SPR flours, which was evidenced by decreased pH (range: 3.20-3.83) and increased lactic acid and short chain fatty acid production during the 48 hr of colonic fermentation. The four examined SPR flours were capable of causing positive alterations in composition and driving the metabolic activity of human colonic microbiota during in vitro colonic fermentation, which should be linked to their prebiotic properties. PRACTICAL APPLICATION: The four examined sweet potato root flours (SPRF) caused beneficial alterations in composition besides of driving the metabolic activity of human colonic microbiota in vitro. These results characterize the examined SPRF as candidates for use as prebiotic ingredients by food industry for formulation of value-added functional foods or dietary supplements.

W27 IgA suppresses growth of Escherichia in an in vitro model of the human intestinal microbiota

W27 monoclonal immunoglobulin A (IgA) suppresses pathogenic Escherichia coli cell growth; however, its effect on the human intestine remains unclear. We aimed to determine how W27 IgA affects the human colonic microbiota using the in vitro microbiota model. This model was established using fecal samples collected from 12 healthy volunteers; after anaerobic cultivation, each model was found to retain the genera found in the original human fecal samples. After pre-incubating W27 IgA with the respective fecal sample under aerobic conditions, the mixture of W27 IgA (final concentration, 0.5 μg/mL) and each fecal sample was added to the in vitro microbiota model and cultured under anaerobic conditions. Next-generation sequencing of the bacterial 16S rRNA gene revealed that W27 IgA significantly decreased the relative abundance of bacteria related to the genus Escherichia in the model. Additionally, at a final concentration of 5 μg/mL, W27 IgA delayed growth in the pure culture of Escherichia coli isolated from human fecal samples. Our study thus revealed the suppressive effect of W27 IgA on the genus Escherichia at relatively low-concentrations and the usefulness of an in vitro microbiota model to evaluate the effect of IgA as a gut microbiota regulator.

Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris.

The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1-8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.

Impact of Cashew (Anacardium occidentale L.) by-Product on Composition and Metabolic Activity of Human Colonic Microbiota In Vitro Indicates Prebiotic Properties.

Cashew apple by-product (CAB) is an important agro-industrial waste still underutilized, although it has been characterized as source of a variety of nutrients and bioactive compounds. This study evaluated the capability of freeze-dried CAB (FCAB) submitted to a simulated gastrointestinal digestion of inducing changes in relative abundance of distinct microbial groups found as part of human colonic microbiota, as well as in pH and short-chain fatty acid production during a 24-h in vitro fermentation using a pooled human fecal inocula. FCAB increased the relative abundance of Bifidobacterium and Lactobacillus/Enterococcus during colonic fermentation, besides to decrease the relative abundance of Bacteroides/Prevotella, Eubacterium rectale/Clostridium coccoides, and Clostridium histolyticum. FCAB increased the counts of lactic acid bacteria and decreased the counts of Enterobacteriaceae during colonic fermentation. Furthermore, FCAB decreased pH and increased the production of short-chain fatty acids in colonic fermentation media. These effects could be linked to contents of dietary fibers and the presence of fructans and different phenolic compounds found in FCAB. These results showed that FCAB induced positive alterations in composition and metabolic activity of human colonic microbiota in vitro, which indicate prebiotic properties.

In vitro evaluation of the anti-pathogenic activity of Okoubaka aubrevillei on the human gastrointestinal tract.

Background Okoubaka aubrevillei is used in traditional West African medicine and in homeopathy for treatment and prevention of several gastrointestinal problems. The aim of this in vitro study was to evaluate the effect of repeated doses of two Okoubaka products (10 % ethanolic tincture, mother tincture (MT); 3 rd decimal potency, 3X) on the microbial activity of physiological human colon microbiota using a Simulator of the Human Intestinal Microbial Ecosystem (SHIME ® ) and to investigate any preventive effect against infections with diarrhea-causing pathogens. Methods Upon inoculation with fecal microbiota from a healthy donor, 4 parallel proximal colon compartments of the SHIME were treated either with Okoubaka MT, Okoubaka 3X, ethanol control or blank control for 7 days. Using the Okoubaka -adapted microbial community from SHIME, 48 h challenge tests were performed with enterotoxigenic Escherichia coli (ETEC) and Salmonella enteritidis in 4 different doses (10 3 –10 8 colony forming units as typical in vivo infectious doses). Pathogen concentrations, short-chain fatty acids (SCFAs) and branched SCFA production were measured in triplicate at 0, 24 and 48 h. Results In the challenge tests, both Okoubaka products were able to restrict the colonization of ETEC and Salmonella at 3 of the 4 pathogen doses (except the highest doses), with a stronger anti-pathogenic effect for MT, which included a reduction of 2.0 log-units of ETEC (p < 0.0001) and 1.1 log-units of Salmonella (p < 0.0001). Total SCFA levels remained unaffected, but butyrate increased during the first 24 h (p < 0.0001 for ETEC), accompanied by decreased acetate production. Conclusion We observed in vitro a systemic activating effect of Okoubaka on intestinal microbiome resistance, which resulted in an anti-pathogenic effect, especially against ETEC. We hypothesize that the mode of action in vivo is also based on systemic regulative effects.

The Kobe University Human Intestinal Microbiota Model for gut intervention studies.

The human gut harbors a complex microbial community that performs a range of metabolic, physiological, and immunological functions. The host and its inhabiting microorganisms are often referred to as a "superorganism." Dysbiosis of gut microflora has been associated with the pathogenesis of intestinal disorders including inflammatory bowel disease, colorectal cancer, and extra-intestinal disorders such as cardiovascular disease. Therefore, gut microbiome interventions are important for the prevention and treatment of diseases. However, ethical, economic, scientific, and time constraints limit the outcome of human intervention or animal studies targeting gut microbiota. We recently developed an in vitro batch fermentation model (the Kobe University Human Intestinal Microbiota Model, KUHIMM) that is capable of hosting a majority of gut microbial species in humans and also detects the metabolites produced by microorganisms in real time. In this mini review, we elucidated the characteristics of the KUHIMM and its applicability in analyzing the effect of diet, drugs, probiotics, and prebiotics on intestinal bacteria. In addition, we introduce as examples its application to disease models, such as ulcerative colitis, in which intestinal bacteria are intricately involved in the process of pathogenesis. We also discuss the potential of the KUHIMM in precision medicine. KEY POINTS: • In vitro gut fermentation model to simulate human colonic microbiota • Screening of potential prebiotics and probiotic candidates in healthy model • Construction of disease models of ulcerative colitis and coronary artery disease.

Growth stimulation of Bifidobacterium from human colon using daikenchuto in an in vitro model of human intestinal microbiota

Daikenchuto (DKT) is a Japanese traditional herbal (Kampo) medicine containing ginseng, processed ginger, and Japanese or Chinese pepper. We aimed to determine how DKT affects human colonic microbiota. An in vitro microbiota model was established using fecal inocula collected from nine healthy volunteers, and each model was found to retain operational taxonomic units similar to the ones in the original human fecal samples. DKT was added to the in vitro microbiota model culture at a concentration of 0.5% by weight. Next-generation sequencing of bacterial 16S rRNA gene revealed a significant increase in the relative abundance of bacteria related to the Bifidobacterium genus in the model after incubation with DKT. In pure cultures, DKT significantly promoted the growth of Bifidobacterium adolescentis, but not that of Fusobacterium nucleatum or Escherichia coli. Additionally, in pure cultures, B. adolescentis transformed ginsenoside Rc to Rd, which was then probably utilized for its growth. Our study reveals the in vitro bifidogenic effect of DKT that likely contributes to its beneficial effects on the human colon.

The alga Euglena gracilis stimulates Faecalibacterium in the gut and contributes to increased defecation

The alga Euglena gracilis (E. gracilis) has recently gained attention as a health food, but its effects on human gut microbiota remain unknown. This study aimed to determine the effect of E. gracilis on gut microbiota and defecation due to modulation of microbiota composition in vitro and in vivo. The in vitro model simulating human colonic microbiota revealed that E. gracilis addition stimulated the growth of commensal Faecalibacterium. Further, E. gracilis addition enhanced butyrate production by Faecalibacterium prausnitzii. Paramylon, an insoluble dietary fibre that accumulates in E. gracilis and is the main component of E. gracilis, did not stimulate Faecalibacterium growth in vitro. Daily ingestion of 2 g of E. gracilis for 30 days increased bowel movement frequency as well as stool volume in 28 human participants. Collectively, these findings indicate that E. gracilis components other than paramylon, stimulate the growth of Faecalibacterium to improve digestive health as well as promote defecation by increasing butyrate production.

Examination of hydrogen cross-feeders using a colonic microbiota model

BackgroundHydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.ResultsAn existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.ConclusionsAlthough the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.

Diesel exhaust particle role on gut microbiome and onset of Alzheimer disease neuroinflammation

AbstractBackgroundRecent evidence has emerged to show that diesel exhaust particulate (DEP) pollution can double the risk of getting dementia. Evidence suggest that exposure to high levels of air pollution are significantly more likely to develop dementia‐related diseases including Alzheimer’s disease. DEP is primarily composed of polycyclic aromatic hydrocarbons (PAHs) and nitro‐substituted polycyclic aromatic hydrocarbons (n‐PAHs). PAHs have previously been shown to undergo biotransformation through interactions with human colonic microbiota. The goal of the present study is to determine if DEP may influence selective gut microbiota. We will eventually identify gut‐brain‐axis mechanisms associated with DEP mediated neuroinflammatory mechanisms through microbiota dysbiosis.MethodUsing an in vitro model of the human gastrointestinal tract, EBIOME, we are exploring the human gut bacteria exposed to various concentrations of diesel exhaust particulate matter. Bacterial species were quantified over an extended time‐course to monitor log‐scale changes in colony survival and growth. In order to obtain higher resolution of gut microbiome species meta‐genomic analysis will be also conducted.ResultThe current studies have identified concentration dependent changes in microbiome biodiversity. Through ongoing analysis, it is anticipated that altered biodiversity will lead to decreases in the production of brain penetrant metabolites, such as short‐chain fatty acids including butyrate, acetate, and propionate.ConclusionOur studies provide novel information regarding the role of the gut‐brain‐axis in neuroinflammation in Alzheimer’s disease and other forms of dementia.

In vitro catabolism of 3′,4′-dihydroxycinnamic acid by human colonic microbiota

3′,4′-Dihydroxycinnamic acid (aka caffeic acid) is a common dietary component found in a variety of plant-derived food products either in a free form or esterified as in chlorogenic acids such as 5-O-caffeoylquinic acid. The dihydroxycinnamate is produced principally by hydrolysis in the colon of 5-O-caffeoylquinic acid and other caffeoylquinic acid esters, and is catabolised by the resident microbiota prior to absorption. In the present study 3′,4′-dihydroxycinnamic acid was incubated in vitro, with or without glucose, under anaerobic conditions with faecal slurries obtained from five volunteers. The main resultant catabolites to accumulate were 3-(3′,4′-dihydroxyphenyl)propanoic acid (aka dihydrocaffeic acid), 3-(3′-hydroxyphenyl)propanoic acid and phenylacetic acid. Both the rate of degradation of the hydroxycinnamate substrate and the catabolite profile varied between the faecal samples from the individual volunteers. Overall there was no clear cut effect when glucose was added to incubation medium.

Prebiotic effects of yeast mannan, which selectively promotes Bacteroides thetaiotaomicron and Bacteroides ovatus in a human colonic microbiota model

Yeast mannan (YM) is an indigestible water-soluble polysaccharide of the yeast cell wall, with a notable prebiotic effect on the intestinal microbiota. We previously reported that YM increased Bacteroides thetaiotaomicron abundance in in vitro rat faeces fermentation, concluding that its effects on human colonic microbiota should be investigated. In this study, we show the effects of YM on human colonic microbiota and its metabolites using an in vitro human faeces fermentation system. Bacterial 16S rRNA gene sequence analysis showed that YM administration did not change the microbial diversity or composition. Quantitative real-time PCR analysis revealed that YM administration significantly increased the relative abundance of Bacteroides ovatus and B. thetaiotaomicron. Moreover, a positive correlation was observed between the relative ratio (with or without YM administration) of B. thetaiotaomicron and B. ovatus (r = 0.92), suggesting that these bacteria utilise YM in a coordinated manner. In addition, YM administration increased the production of acetate, propionate, and total short-chain fatty acids. These results demonstrate the potential of YM as a novel prebiotic that selectively increases B. thetaiotaomicron and B. ovatus and improves the intestinal environment. The findings also provide insights that might be useful for the development of novel functional foods.

Acerola (Malpighia glabra L.) and guava (Psidium guayaba L.) industrial processing by-products stimulate probiotic Lactobacillus and Bifidobacterium growth and induce beneficial changes in colonic microbiota.

This study evaluated whether by-products from industrial processing of acerola (Malpighia glabra L.; AB) and guava (Psidium guajava L.; GB) fruit may stimulate the growth and metabolism of probiotic Lactobacillus and Bifidobacterium and induce changes in human colonic microbiota. The ability of non-digested and digested AB or GB to stimulate the growth ad metabolism of Lactobacillus acidophilus LA-05, Lactobacillus casei L-26 and Bifidobacterium animalis subsp. lactis BB-12 was evaluated. Changes in populations of distinct bacterial groups of human colonic microbiota induced by digested AB and GB were evaluated using an in vitro colonic fermentation system. Non-digested and digested AB and GB favoured probiotic growth. No difference among counts of probiotics in media with glucose, fructooligosaccharides and non-digested and digested AB and GB was found during a 48-h cultivation. Cultivation of probiotics in media with non-digested and digested AB and GB resulted in decreased pH, increased organic acid production and sugar consumption over time. Digested AB and GB caused overall beneficial changes in abundance of Bifidobacterium spp., Lactobacillus-Enterococcus, Eubacterium rectall-Clostridium coccoides and Bacteroides-Provotella populations, besides to decrease the pH and increase the short-chain fatty acid production during a 24-h in vitro colonic fermentation. AB and GB could be novel prebiotic ingredients because they can stimulate the growth and metabolism of probiotics and induce overall beneficial changes in human colonic microbiota. AB and GB stimulated the growth and metabolism of probiotics, in addition to induce beneficial alterations in human colonic microbiota composition and increase short-chain fatty acid production. These results characterize AB and GB as potential prebiotic ingredients and fruit processing by-products as sources of added-value compounds.

Fermentation of prebiotics by human colonic microbiota in vitro and short-chain fatty acids production: a critical review.

Prebiotics are known for their health benefits to man, including reducing cardiovascular disease and improving gut health. This review takes a critical assessment of the impact of dietary fibres and prebiotics on the gastrointestinal microbiota in vitro. The roles of colonic organisms, slow fermentation of prebiotics, production of high butyric and propionic acids and positive modulation of the host health were taken into cognizance. Also, the short-chain fatty acids (SCFAs) molecular signalling mechanisms associated with their prebiotic substrate structural conformations and the phenotypic responses related to the gut microbes composition were discussed. Furthermore, common dietary fibres such as resistant starch, pectin, hemicelluloses, β-glucan and fructan in context of their prebiotic potentials for human health were also explained. Finally, the in vitro human colonic fermentation depends on prebiotic type and its physicochemical characteristics, which will then affect the rate of fermentation, selectivity of micro-organisms to multiply, and SCFAs concentrations and compositions.

Alcohol use alters the colonic mucosa–associated gut microbiota in humans

Alcohol misuse is a risk factor for many adverse health outcomes. Alcohol misuse has been associated with an imbalance of gut microbiota in preclinical models and alcoholic diseases. We hypothesized that daily alcohol use would change the community composition and structure of the human colonic gut microbiota. Thirty-four polyp-free individuals donated 97 snap-frozen colonic biopsies. Microbial DNA was sequenced for the 16S ribosomal RNA gene hypervariable region 4. The SILVA database was used for operational taxonomic unit classification. Alcohol use was assessed using a food frequency questionnaire. We compared the biodiversity and relative abundance of the taxa among never drinkers (ND, n = 9), former drinkers (FD, n = 10), current light drinkers (LD, <2 drinks daily, n = 9), and current heavy drinkers (HD, ≥2 drinks daily, n = 6). False discovery rate–adjusted P values (q values) < .05 indicated statistical significance. HD had the lowest α diversity (Shannon index q value < 0.001), and HD's microbial composition differed the most from the other groups (P value = .002). LD had the highest relative abundance of Akkermansia (q values < 0.001). HD had the lowest relative abundance of Subdoligranulum, Roseburia, and Lachnospiraceaeunc91005 but the highest relative abundance of Lachnospiraceaeunc8895 (all q values < 0.05). The multivariable negative binomial regression model supported these observations. ND and FD had a similar microbial profile. Heavy alcohol use was associated with impaired gut microbiota that may partially mediate its effect on health outcomes.

Glycosidic Linkage Structures Influence Dietary Fiber Fermentability and Propionate Production by Human Colonic Microbiota In Vitro.

Some dietary fibers can be produced by starch modification; however, information regarding the relationships between glycosidic linkages and dietary fiber fermentability or the production of short-chain fatty acids is limited. Thus, these relationships are investigated using an in vitro model of human colonic microbiota, which approximates the bacterial species richness and diversity in inoculated fecal samples. Six dietary fibers with various glycosidic linkage contents are prepared. Each dietary fiber (final concentration: 1.0 wt%) is administered in vitro to human microbiota models 18 h after fecal samples are inoculated. The contents of (1 → 2) plus (1 → 3) linkages and β-linkages in the six dietary fibers negatively correlate with the fermentation speed and fermentation ratio of the indigestible parts of the dietary fibers (R2 = 0.8126 or 0.8306 and R2 = 0.9106 or 0.9673, respectively) 24 h after administering each dietary fiber. Further, the concentrations of propionate produced in vitro by human microbiota positively correlate with the fermentation speed and fermentation ratio (R2 = 0.9149 and 0.9581, respectively). The in vitro assay reveals that (1 → 2) plus (1 → 3) linkages and β-linkages in dietary fiber affect resistance to fermentation and propionate production by the human colonic microbiota.

Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem.

Lactate can be produced by many gut bacteria, but in adults its accumulation in the colon is often an indicator of microbiota perturbation. Using continuous culture anaerobic fermentor systems, we found that lactate concentrations remained low in communities of human colonic bacteria maintained at pH 6.5, even when dl-lactate was infused at 10 or 20 mM. In contrast, lower pH (5.5) led to periodic lactate accumulation following lactate infusion in three fecal microbial communities examined. Lactate accumulation was concomitant with greatly reduced butyrate and propionate production and major shifts in microbiota composition, with Bacteroidetes and anaerobic Firmicutes being replaced by Actinobacteria, lactobacilli, and Proteobacteria Pure-culture experiments confirmed that Bacteroides and Firmicutes isolates were susceptible to growth inhibition by relevant concentrations of lactate and acetate, whereas the lactate-producer Bifidobacterium adolescentis was resistant. To investigate system behavior further, we used a mathematical model (microPop) based on 10 microbial functional groups. By incorporating differential growth inhibition, our model reproduced the chaotic behavior of the system, including the potential for lactate infusion both to promote and to rescue the perturbed system. The modeling revealed that system behavior is critically dependent on the proportion of the community able to convert lactate into butyrate or propionate. Communities with low numbers of lactate-utilizing bacteria are inherently less stable and more prone to lactate-induced perturbations. These findings can help us to understand the consequences of interindividual microbiota variation for dietary responses and microbiota changes associated with disease states.IMPORTANCE Lactate is formed by many species of colonic bacteria, and can accumulate to high levels in the colons of inflammatory bowel disease subjects. Conversely, in healthy colons lactate is metabolized by lactate-utilizing species to the short-chain fatty acids butyrate and propionate, which are beneficial for the host. Here, we investigated the impact of continuous lactate infusions (up to 20 mM) at two pH values (6.5 and 5.5) on human colonic microbiota responsiveness and metabolic outputs. At pH 5.5 in particular, lactate tended to accumulate in tandem with decreases in butyrate and propionate and with corresponding changes in microbial composition. Moreover, microbial communities with low numbers of lactate-utilizing bacteria were inherently less stable and therefore more prone to lactate-induced perturbations. These investigations provide clear evidence of the important role these lactate utilizers may play in health maintenance. These should therefore be considered as potential new therapeutic probiotics to combat microbiota perturbations.

Progestogens Are Metabolized by the Gut Microbiota: Implications for Colonic Drug Delivery.

Following oral administration, the bioavailability of progestogens is very low and highly variable, in part due to metabolism by cytochrome P450 enzymes found in the mucosa of the small intestine. Conversely, the mucosa in the colon contains much lower levels of cytochrome P450 enzymes, thus, colonic delivery of progestogens may be beneficial. Microbiota in the colon are known to metabolize a great number of drugs, therefore, it is important to understand the stability of these hormones in the presence of colonic flora before developing formulations. The aim of this study was to investigate the stability of three progestogens: progesterone, and its two synthetic analogues, medroxyprogesterone acetate (MPA) and levonorgestrel (LNG), in the presence of human colonic microbiota. Progesterone, MPA, and LNG were incubated in mixed fecal inoculum (simulated human colonic fluid) under anerobic conditions. Progesterone was completely degraded after 2 h, whereas levels of MPA and LNG were still detectable after 24 h. The half-lives of progesterone, MPA, and LNG in fecal inoculum were 28, 644, and 240 min, respectively. This study describes the kinetics of colonic microbial metabolism of these hormones for the first time. MPA and LNG show promise for delivery to the colon, potentially improving pharmacokinetics over current oral delivery methods.

Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture

The gut microbiome plays an important role in human health and disease. Gnotobiotic animal and in vitro cell-based models provide some informative insights into mechanistic crosstalk. However, there is no existing system for a long-term co-culture of a human colonic mucosal barrier with super oxygen-sensitive commensal microbes, hindering the study of human-microbe interactions in a controlled manner. Here, we investigated the effects of an abundant super oxygen-sensitive commensal anaerobe, Faecalibacterium prausnitzii, on a primary human mucosal barrier using a Gut-MIcrobiome (GuMI) physiome platform that we designed and fabricated. Long-term continuous co-culture of F. prausnitzii for two days with colon epithelia, enabled by continuous flow of completely anoxic apical media and aerobic basal media, resulted in a strictly anaerobic apical environment fostering growth of and butyrate production by F. prausnitzii, while maintaining a stable colon epithelial barrier. We identified elevated differentiation and hypoxia-responsive genes and pathways in the platform compared with conventional aerobic static culture of the colon epithelia, attributable to a combination of anaerobic environment and continuous medium replenishment. Furthermore, we demonstrated anti-inflammatory effects of F. prausnitzii through HDAC and the TLR-NFKB axis. Finally, we identified that butyrate largely contributes to the anti-inflammatory effects by downregulating TLR3 and TLR4. Our results are consistent with some clinical observations regarding F. prausnitzii, thus motivating further studies employing this platform with more complex engineered colon tissues for understanding the interaction between the human colonic mucosal barrier and microbiota, pathogens, or engineered bacteria.

In vitro human colonic microbiota utilises D-\u03b2-hydroxybutyrate to increase butyrogenesis

The ketone body D-β-hydroxybutyrate (DBHB) has gained attention owing to its cellular signalling function; however, its effect on the human colonic microbiota remains unclear. Here, DBHB dynamics in the human colon were investigated using an in vitro colonic microbiota model, which maintained most of the operational taxonomic units detected in the original faeces. Over 54% of 0.41% (w/v) DBHB was metabolised by microbiota models originating from seven faecal samples after 30 h of fermentation (regarded as DBHB utilisers); however, <19% of DBHB was metabolised by microbiota models from five faecal samples (regarded as non-utilisers of DBHB). In utilisers, DBHB administration increased the relative abundance of the genus Coprococcus, correlated with increased butyrogenesis. Increased butyrogenesis was not observed in DBHB non-utilisers. Based on PICRUSt analysis, the relative abundance of β-hydroxybutyrate dehydrogenase was maintained in microbiota models from DBHB utilisers following DBHB administration; however, it decreased in microbiota models from non-utilisers. After 21 h of fermentation, the intracellular glutamate concentration, which is indicative of growth, showed a positive correlation with DBHB utilisation (R2 = 0.70). Human colonic microbiotas with high growth activity demonstrate efficient utilisation of DBHB for increased butyrate production, which affords health benefits.