Alternative pathways for hydrogen disposal during fermentation in the human colon

Influence of menstrual cycle and oral contraception on taxonomic composition and gas production in the gut microbiome

Introduction. Oral contraceptives (OCs) are widely used for birth control and offer benefits such as menstrual cycle regulation and reduced menstrual pain. However, they have also been associated with an increased risk of cancer and reduced bone mass density.Gap Statement. While the gut microbiome is known to interact with endocrine factors, the impact of hormonal OCs on its composition and function remains underexplored. Additionally, we explore the relationship of OC use and the microbiome to gas production, which can cause symptoms and be indicative of poor health.Aim. This study investigates the effects of OCs on the diversity and composition of the gut microbiome and its association with breath hydrogen (H2) and methane (CH4) levels.Methodology. We utilized 16S rRNA gene sequencing to analyse faecal samples from 65 women, comparing OC users with non-users at two menstrual cycle time points. Breath tests measured hydrogen and CH4 production. Data were analysed for microbial diversity, community composition and correlation with gas production.Results. There were no differences in overall microbial diversity between OC users and non-users in samples collected on day 2 of the menstrual cycle. However, on day 21, we found a significant difference in microbial richness, suggesting a cycle-dependent effect of OCs on gut microbiota species richness but not composition. We found a strong correlation between H2 and CH4 concentrations and an interaction between OC use and the menstrual cycle on H2 and CH4 production. We also identified several taxa associated with both high levels of H2 and CH4 production and OC use.Conclusion. Our study highlights the intricate relationships among hormonal contraceptives, the gut microbiota and gas production and connects shifts in the microbiome composition to gastrointestinal symptoms (e.g. gas production) that can impact overall health. This underscores the need for further research on the long-term effects of OCs and for the development of precise therapeutic strategies to address potential adverse effects. Our findings offer new perspectives on the microbiome-hormone-gas production nexus, potentially broadening our understanding of the systemic implications of OCs.

Hyperimmune bovine colostrum containing lipopolysaccharide antibodies (IMM124-E) has a nondetrimental effect on gut microbial communities in unchallenged mice

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of bacterial diarrhea with the potential to cause long-term gastrointestinal (GI) dysfunction. Preventative treatments for ETEC-induced diarrhea exist, yet the effects of these treatments on GI commensals in healthy individuals are unclear. Whether administration of a prophylactic preventative treatment for ETEC-induced diarrhea causes specific shifts in gut microbial populations in controlled environments is also unknown. Here, we studied the effects of a hyperimmune bovine colostrum (IMM-124E) used in the manufacture of Travelan (AUST L 106709) on GI bacteria in healthy C57BL/6 mice. Using next-generation sequencing, we aimed to test the onset and magnitude of potential changes to the mouse gut microbiome in response to the antidiarrheagenic hyperimmune bovine colostrum product, rich in immunoglobulins against select ETEC strains (Travelan, Immuron Ltd). We show that in mice administered colostrum containing lipopolysaccharide (LPS) antibodies, there was an increased abundance of potentially gut-beneficial bacteria, such as Akkermansia and Desulfovibrio, without disrupting the underlying ecology of the GI tract. Compared to controls, there was no difference in overall weight gain, body or cecal weights, or small intestine length following LPS antibody colostrum supplementation. Overall, dietary supplementation with colostrum containing LPS antibodies produced subtle alterations in the gut bacterial composition of mice. Primarily, Travelan LPS antibody treatment decreased the ratio of Firmicutes/Bacteroidetes in gut microbial populations in unchallenged healthy mice. Further studies are required to examine the effect of Travelan LPS antibody treatment to engineer the microbiome in a diseased state and during recovery.

Role of Hydrogen Sulfide in Inflammatory Bowel Disease

Hydrogen sulfide (H2S), originally known as toxic gas, has now attracted attention as one of the gasotransmitters involved in many reactions in the human body. H2S has been assumed to play a role in the pathogenesis of many chronic diseases, of which the exact pathogenesis remains unknown. One of them is inflammatory bowel disease (IBD), a chronic intestinal disease subclassified as Crohn's disease (CD) and ulcerative colitis (UC). Any change in the amount of H2S seems to be linked to inflammation in this illness. These changes can be brought about by alterations in the microbiota, in the endogenous metabolism of H2S and in the diet. As both too little and too much H2S drive inflammation, a balanced level is needed for intestinal health. The aim of this review is to summarize the available literature published until June 2023 in order to provide an overview of the current knowledge of the connection between H2S and IBD.

Advancing human gut microbiota research by considering gut transit time

Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet-microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.

Interpreting tree ensemble machine learning models with endoR

Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.

Effect of oat or rice flour on pulse-induced gastrointestinal symptoms and breath hydrogen in subjects sensitive to pulses and controls - a randomised cross-over trial with two parallel groups

Pulses are healthy and sustainable but induce gut symptoms in people with a sensitive gut. Oats, on the contrary, have no fermentable oligo- di-, monosaccharides and polyols compounds and are known for the health effects of their fibres. This 4-day cross-over trial investigated the effects of oat and rice flour ingested with pulses on gut symptoms and exhaled gases (4th day only) in subjects with a sensitive gut or IBS (n 21) and controls (n 21). The sensitive group perceived more symptoms after both meals than controls (P = 0·001, P = 0·001). Frequency, intensity or quality of the symptoms did not differ between meals during the first 3 d in either group. More breath hydrogen was produced after an oat than rice containing meal in both groups (AUC, P = 0·001, P = 0·001). No between-group difference was seen in breath gases. During day 4, both sensitive and control groups perceived more symptoms after the oat flour meal (P = 0·001, P = 0·0104, respectively) as mainly mild flatulence. No difference in moderate or severe symptoms was detected. Increased hydrogen production correlated to a higher amount of perceived flatulence after the oat flour meal in both the sensitive and the control groups (P = 0·042, P = 0·003, respectively). In summary, ingestion of oat flour with pulses increases breath hydrogen levels compared with rice flour, but gastrointestinal symptoms of subjects sensitive to pulses were not explained by breath hydrogen levels. Additionally, consumer mindsets towards pulse consumption and pulse-related gut symptoms were assessed by an online survey, which implied that perceived gut symptoms hinder the use of pulses in sensitive subjects.

Aetiology, diagnosis and management of small intestinal bacterial overgrowth

Small intestinal bacterial overgrowth is a small bowel disorder characterised by excessive amounts of bacteria populating the small intestine leading to symptoms of abdominal pain, bloating and change in bowel habit. This creates some degree of diagnostic uncertainty due to the overlap of these symptoms with numerous other gastrointestinal conditions. Quantitative culture of jejunal aspirates is the gold standard diagnostic test but has largely been replaced by glucose and lactulose breath tests due to their relative ease and accessibility. The approach to treatment centres around reducing bacterial numbers through antibiotic therapy and managing any predisposing factors. Further research is required in order to define the optimum antibiotic choice and duration of therapy as well as the potential diagnostic utility of home breath testing and capsule-based technology.

Archaeome in Colorectal Cancer: High Abundance of Methanogenic Archaea in Colorectal Cancer Patients

Background: The importance of microbiome in the progression and development of colorectal cancer (CRC) has been discussed in the last decade. Like colon bacteria, other intestinal microorganisms, including archaea, could also be involved in the CRC progression, so it's important to work out the archaeal microbiome (archaeome) composition among CRC patients. Objectives: The aim of this study was to determine the archaeome composition of CRC and healthy controls based on age and gender. Methods: Total bacterial DNA was extracted from 30 biopsy samples (17 CRC and 13 healthy controls). Archaeome communities were profiled by 16S rRNA high throughput sequencing, then compared to clinicopathological features, including CRC patients’ gender and age. Results: In the CRC patients, archaeal methanogens including Methanobrevibacter (86%) and Methanomassiliicoccus (8%) were overrepresented at the genus level. In contrast in the healthy controls, only two genera of haloarchaea including Natronococcus (58%) and Haloterrigena (42%) were presented. The results showed that the number of archaeal genera in men is higher than women in both the CRC and healthy controls. moreover, our results showed that the most genera of archaea are present in the CRC-32-50 group, six archaeal genera. The differential abundance taxa analysis results showed significant differences between healthy controls and CRC patients (P ≤ 0.05). Conclusions: The high abundance of methanogens in the colon archaeome of CRC patients compared to healthy controls suggests that methanogens may be involved in CRC development.

Carbohydrate Maldigestion and Intolerance

This review summarizes dietary carbohydrate intolerance conditions and recent advances on the possible role of carbohydrate maldigestion and dietary outcomes in patients with functional bowel disease. When malabsorbed carbohydrates reach the colon, they are fermented by colonic bacteria, with the production of short-chain fatty acids and gas lowering colonic pH. The appearance of diarrhoea or symptoms of flatulence depends in part on the balance between the production and elimination of these fermentation products. Different studies have shown that there are no differences in the frequency of sugar malabsorption between patients with irritable bowel disease (IBS) and healthy controls; however, the severity of symptoms after a sugar challenge is higher in patients than in controls. A diet low in 'Fermentable, Oligo-Di- and Monosaccharides and Polyols' (FODMAPs) is an effective treatment for global symptoms and abdominal pain in IBS, but its implementation should be supervised by a trained dietitian. A 'bottom-up' approach to the low-FODMAP diet has been suggested to avoid an alteration of gut microbiota and nutritional status. Two approaches have been suggested in this regard: starting with only certain subgroups of the low-FODMAP diet based on dietary history or with a gluten-free diet.

Microbial community in human gut: a therapeutic prospect and implication in health and diseases

The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.

How the North American Consensus Protocol Affects the Performance of Glucose Breath Testing for Bacterial Overgrowth Versus a Traditional Method

INTRODUCTION

The North American Consensus guidelines for glucose breath testing (GBT) for small intestinal bacterial overgrowth (SIBO) incorporated changes in glucose dosing and diagnostic cutoffs. We compared GBT positivity based on hydrogen and methane excretion and quantified symptoms during performance of the North American vs older modified Rome Consensus protocols.

METHODS

GBT was performed using the North American protocol (75 g glucose, cutoffs >20 parts per million [ppm] hydrogen increase after glucose and >10 ppm methane anytime) in 3,102 patients vs modified Rome protocol (50 g glucose, >12 ppm hydrogen and methane increases after glucose) in 3,193 patients with suspected SIBO.

RESULTS

Positive GBT were more common with the North American vs modified Rome protocol (39.5% vs 29.7%, P < 0.001). Overall percentages with GBT positivity using methane criteria were greater and hydrogen criteria lower with the North American protocol (P < 0.001). Peak methane levels were higher for the North American protocol (P < 0.001). Times to peak hydrogen and methane production were not different between protocols. With the North American protocol, gastrointestinal and extraintestinal symptoms were more prevalent after glucose with both positive and negative GBT (P < 0.04) and greater numbers of symptoms (P < 0.001) were reported.

DISCUSSION

GBT performed using the North American Consensus protocol was more often positive for SIBO vs the modified Rome protocol because of more prevalent positive methane excretion. Symptoms during testing were greater with the North American protocol. Implications of these observations on determining breath test positivity and antibiotic decisions for SIBO await future prospective testing.

Carbohydrate-induced gastrointestinal symptoms: development and validation of a test-specific symptom questionnaire for an adult population, the adult Carbohydrate Perception Questionnaire

OBJECTIVES

Carbohydrate intolerances may affect a majority of the worlds-population but there is no validated, test-specific assessment of carbohydrate-induced symptoms during breath tests. We aimed to develop and validate a questionnaire for evaluation and quantification of carbohydrate intolerance.

METHODS

A visual analog scale-questionnaire with five complaints (pain, nausea, bloating, flatulence, and diarrhea) was designed. The time frame of symptoms was 'current' (for baseline symptoms) and 'since filling out the last questionnaire'. Validity was determined in focus-group style interviews and during breath tests in an original (n = 342) and follow-up patient groups (n = 338).

RESULTS

The questionnaire had good face validity, content validity ratio according to Lawshe was 1. Intraclass correlation coefficients (n = 195; 30-min' interval) demonstrated excellent reliability (P < 0.001), Cohen's d (measure of effect size) was small (≤0.19 for each symptom). Convergent and discriminant validity were supported against patient interviews. Questionnaire-derived results highly correlated with a medical interview (P < 0.001; n = 338). Responsiveness to change was verified during breath tests despite small effect sizes (≤0.32). Additional cross-validation and external validation studies (follow-up in-house: n = 182; external: n = 156) demonstrated generalizability and identified relevant numbers of patients in whom there was no co-occurrence of carbohydrate malabsorption and intolerance.

CONCLUSIONS

The adult Carbohydrate Perception Questionnaire is a valid instrument for the assessment of gastrointestinal symptoms after carbohydrate ingestion with excellent psychometric properties. It allows standardized, test-specific diagnosis of carbohydrate intolerance and evaluation of the relation between malabsorption and intolerance. It shall be useful for future studies on treatment of carbohydrate intolerance.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

Breath Test Gas Patterns in Inflammatory Bowel Disease with Concomitant Irritable Bowel Syndrome-Like Symptoms: A Controlled Large-Scale Database Linkage Analysis

INTRODUCTION

Breath testing (BT) has gained interest for diagnosing small intestinal bacterial overgrowth (SIBO) in IBD patients with irritable bowel syndrome (IBS) overlap. We aim to characterize the rate of SIBO and BT gas patterns in IBD patients with IBS-like symptoms compared to non-IBD patients.

METHODS

A database of 14,847 consecutive lactulose BTs was developed from patients with IBS-like symptoms between November 2005 and October 2013. BTs were classified as normal, H₂ predominant, CH₄ predominant, and flatline based on criteria established from the literature. BT data linkage with electronic health records and chart review identified IBD patients along with disease phenotype, location, severity, and antibiotic response. Poisson loglinear model evaluated differences in gas patterns between the two groups.

RESULTS

After excluding patients with repeat breath tests, we identified 486 IBD and 10,505 non-IBD patients with at least one BT. Positive BT was present in 57% (n = 264) of IBD patients. Crohn's disease (odds ratio (OR) 0.21, [95% confidence interval (CI) 0.11-0.38]) and ulcerative colitis (OR 0.39, [95% CI 0.22-0.70]) patients were less likely to produce excess CH₄. IBD patients were more likely to have flatline BT (OR 1.82, [95% CI 1.20-2.77]). In IBD patients with SIBO, 57% improved symptomatically with antibiotics.

CONCLUSION

In a cohort of IBD patients with IBS-like symptoms, a high rate of patients had positive BT and symptomatic improvement with antibiotics. In IBD, methanogenesis is suppressed and flatline BT is more frequent, suggesting excess hydrogenotrophic bacteria. These findings suggest methanogenic and hydrogenotrophic microorganisms as potential targets for microbiome-driven biomarkers and therapies.

Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture

Understanding the metabolic dynamics of the human gastrointestinal tract (GIT) microbiota is of growing importance as research continues to link the microbiome to host health status. Microbial strains that metabolize hydrogen have been associated with a variety of both positive and negative host nutritional and health outcomes, but limited data exists for their competition in the GIT. To enable greater insight into the behaviour of these microbes, a mathematical model was developed for the metabolism and growth of the three major hydrogenotrophic groups: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens. In batch culture simulations with abundant sulphate and hydrogen, the SRB outcompeted the methanogen for hydrogen due to having a half-saturation constant 10⁶ times lower than that of the methanogen. The acetogen, with a high model threshold for hydrogen uptake of around 70 mM, was the least competitive. Under high lactate and zero sulphate conditions, hydrogen exchange between the SRB and the methanogen was the dominant interaction. The methanogen grew at 70% the rate of the SRB, with negligible acetogen growth. In continuous culture simulations, both the SRB and the methanogen were washed out at dilution rates above 0.15 h⁻¹ regardless of substrate availability, whereas the acetogen could survive under abundant hydrogen conditions. Specific combinations of conditions were required for survival of more than one hydrogenotroph in continuous culture, and survival of all three was not possible. The stringency of these requirements and the inability of the model to simulate survival of all three hydrogenotrophs in continuous culture demonstrates that factors outside of those modelled are vital to allow hydrogenotroph coexistence in the GIT.

Prebiotics Inhibit Proteolysis by Gut Bacteria in a Host Diet-Dependent Manner: a Three-Stage Continuous In Vitro Gut Model Experiment

Dietary protein residue can result in microbial generation of various toxic metabolites in the gut, such as ammonia. A prebiotic is "a substrate that is selectively utilised by host microorganisms conferring a health benefit" (G. R. Gibson, R. Hutkins, M. E. Sanders, S. L. Prescott, et al., Nat Rev Gastroenterol Hepatol 14:491-502, 2017, https://doi.org/10.1038/nrgastro.2017.75). Prebiotics are carbohydrates that may have the potential to reverse the harmful effects of gut bacterial protein fermentation. Three-stage continuous colonic model systems were inoculated with fecal samples from omnivore and vegetarian volunteers. Casein (equivalent to 105 g protein consumption per day) was used within the systems as a protein source. Two different doses of inulin-type fructans (Synergy1) were later added (equivalent to 10 g per day in vivo and 15 g per day) to assess whether this influenced protein fermentation. Bacteria were enumerated by fluorescence in situ hybridization with flow cytometry. Metabolites from bacterial fermentation (short-chain fatty acid [SCFA], ammonia, phenol, indole, and p-cresol) were monitored to further analyze proteolysis and the prebiotic effect. A significantly higher number of bifidobacteria was observed with the addition of inulin together with reduction of Desulfovibrio spp. Furthermore, metabolites from protein fermentation, such as branched-chain fatty acids (BCFA) and ammonia, were significantly lowered with Synergy1. Production of p-cresol varied among donors, as we recognized four high producing models and two low producing models. Prebiotic addition reduced its production only in vegetarian high p-cresol producers.IMPORTANCE Dietary protein levels are generally higher in Western populations than in the world average. We challenged three-stage continuous colonic model systems containing high protein levels and confirmed the production of potentially harmful metabolites from proteolysis, especially replicates of the transverse and distal colon. Fermentations of proteins with a prebiotic supplementation resulted in a change in the human gut microbiota and inhibited the production of some proteolytic metabolites. Moreover, we observed both bacterial and metabolic differences between fecal bacteria from omnivore donors and vegetarian donors. Proteins with prebiotic supplementation showed higher Bacteroides spp. and inhibited Clostridium cluster IX in omnivore models, while in vegetarian modes, Clostridium cluster IX was higher and Bacteroides spp. lower with high protein plus prebiotic supplementation. Synergy1 addition inhibited p-cresol production in vegetarian high p-cresol-producing models while the inhibitory effect was not seen in omnivore models.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

Altered Gut Microbial Fermentation and Colonization with Methanobrevibacter smithii in Renal Transplant Recipients

Renal transplant recipients (RTRs) often suffer from posttransplant diarrhea. The observed dysbiosis in RTR may influence the fermentation processes in the gut. In this study, we aimed to investigate whether fermentation differs between RTRs and healthy controls (HCs), by measuring breath H₂ and CH₄ concentrations. Additionally, we determined the fecal presence of the methanogen Methanobrevibacter smithii (M. smithii), which plays a main role in the process of methanogenesis. Data from the TransplantLines Biobank and Cohort Study (NCT03272841) was used. A total of 142 RTRs and 77 HCs were included. Breath H₂ concentrations in RTRs were not significantly different from HCs. Breath CH₄ concentrations in RTRs were significantly lower compared with HCs (median [interquartile range (IQR)] 7.5 [3.9–10.6] ppm vs. 16.0 [8.0–45.5] ppm, p < 0.001). M. smithii was less frequently present in the feces of RTRs compared to HCs (28.6% vs. 86.4% resp., p < 0.001). Our findings regarding the altered methanogenesis in the gut of RTRs show similarities with previous results in inflammatory bowel disease patients. These findings provide novel insight into the alterations of fermentation after renal transplantation, which may contribute to understanding the occurrence of posttransplant diarrhea.

Methane Production and Bioactivity-A Link to Oxido-Reductive Stress

Biological methane formation is associated with anoxic environments and the activity of anaerobic prokaryotes (Archaea). However, recent studies have confirmed methane release from eukaryotes, including plants, fungi, and animals, even in the absence of microbes and in the presence of oxygen. Furthermore, it was found that aerobic methane emission in plants is stimulated by a variety of environmental stress factors, leading to reactive oxygen species (ROS) generation. Further research presented evidence that molecules with sulfur and nitrogen bonded methyl groups such as methionine or choline are carbon precursors of aerobic methane formation. Once generated, methane is widely considered to be physiologically inert in eukaryotes, but several studies have found association between mammalian methanogenesis and gastrointestinal (GI) motility changes. In addition, a number of recent reports demonstrated anti-inflammatory potential for exogenous methane-based approaches in model anoxia-reoxygenation experiments. It has also been convincingly demonstrated that methane can influence the downstream effectors of transiently increased ROS levels, including mitochondria-related pro-apoptotic pathways during ischemia-reperfusion (IR) conditions. Besides, exogenous methane can modify the outcome of gasotransmitter-mediated events in plants, and it appears that similar mechanism might be active in mammals as well. This review summarizes the relevant literature on methane-producing processes in eukaryotes, and the available results that underscore its bioactivity. The current evidences suggest that methane liberation and biological effectiveness are both linked to cellular redox regulation. The data collectively imply that exogenous methane influences the regulatory mechanisms and signaling pathways involved in oxidative and nitrosative stress responses, which suggests a modulator role for methane in hypoxia-linked pathologies.

Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis

The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H₂S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H₂S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H₂S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria

High-protein diets may be linked to gut inflammation due to increased production of hydrogen sulfide (H₂S), a potential toxin, as an end product of microbial fermentation in the colon by sulfidogenic sulfate-reducing bacteria (SRB). We hypothesized that dietary content of sulfur-containing amino acids (SAA) leads to variation in the relative abundances of intestinal SRB, which include Desulfovibrio and Bilophila taxa. To test this hypothesis we performed a pilot crossover study in four healthy volunteers, who consumed two interventional diets for 10-14 days, containing high or low SAA content. The total energy intake was similar between the two dietary extremes. Microbial communities were characterized by 16S rRNA gene amplicon and shotgun next-generation DNA sequencing. While the relative abundance of Desulfovibrio differed among participants (ANOVA P= 0.001), we could not detect a change with dietary treatments. Similarly, no differences in Bilophila abundance were observed among individuals or dietary arms. Inter-personal differences in microbial community composition and functional gene categories differed between subjects and these differences were maintained over the course of the study. These observations are consistent with re-analysis of two previously published dietary intervention studies. Finally, we found that inter-personal differences in the taxonomic composition of fecal microbiota, including the relative abundances of SRB, were maintained over time in 19 healthy individuals in our stool donor program. These results suggest that the use of dietary interventions alone may be insufficient for rapid therapeutic targeting of SRB. Nevertheless, these pilot data provide a foundation to inform future, statistically powered, studies.

Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins

Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with ³⁵SO₄^2- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H₂S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu²⁺(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.

Methanogenesis in animals with foregut and hindgut fermentation: a review

Methane is the main greenhouse-gas contributor to global warming in the livestock sector; it is generated by anaerobic fermentation in the different sections of the gut, and the methane concentration differs significantly among species. Methane is produced only by certain types of microorganisms called methanogens. The species composition of methanogenic archaea population is largely affected by the diet, geographical location, host and the section of the gut. Consequently, methane production, either measured as total grams emitted per day or per bodyweight mass, differs greatly among animal species. The main difference in methanogenic activity among different gut sections and animal species is the substrate fermented and the metabolic pathway to complete anaerobic fermentation of plant material. The three main substrates used by methanogens are CO2, acetate and compounds containing methyl groups. The three dominant orders of methanogens in gut environments are Methanomicrobiales, Methanobacteriales and Methanosarcinales. They normally are present in low numbers (below 3% of total microbiome). The present review will describe the main metabolic pathways and methanogens involved in CH4 production in the gut of different host-animal species, as well as discuss general trends that influence such emissions, such as geographical distribution, feed composition, section of the gut, host age and diurnal and season variation. Finally, the review will describe animal species (large and small domestic ruminants, wild ruminants, camelids, pigs, rabbits, horses, macropods, termites and humans) specificities in the methanogen diversity and their effects on methane emission.

Hydrogen cross-feeders of the human gastrointestinal tract

Hydrogen plays a key role in many microbial metabolic pathways in the human gastrointestinal tract (GIT) that have an impact on human nutrition, health and wellbeing. Hydrogen is produced by many members of the GIT microbiota, and may be subsequently utilized by cross-feeding microbes for growth and in the production of larger molecules. Hydrogenotrophic microbes fall into three functional groups: sulfate-reducing bacteria, methanogenic archaea and acetogenic bacteria, which can convert hydrogen into hydrogen sulfide, methane and acetate, respectively. Despite different energy yields per molecule of hydrogen used between the functional groups, all three can coexist in the human GIT. The factors affecting the numerical balance of hydrogenotrophs in the GIT remain unconfirmed. There is increasing evidence linking both hydrogen sulfide and methane to GIT diseases such as irritable bowel syndrome, and strategies for the mitigation of such health problems through targeting of hydrogenotrophs constitute an important field for further investigation.

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production

The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber. pH in the sheep rumen was more than 1 unit higher than that in the rabbit cecum. The acetate to propionate ratio in the rabbit cecum was more than threefold greater than that in the sheep rumen. Comparative analysis of 16S rRNA gene amplicon libraries revealed distinct microbiota between the rumen of sheep and the cecum of rabbits. Hydrogen-producing fibrolytic bacteria, especially Butyrivibrio, Succiniclastium, Mogibacterium, Prevotella, and Christensenellaceae, were more predominant in the sheep rumen, whereas non-hydrogen producing fibrolytic bacteria, such as Bacteroides, were more predominant in the rabbit cecum. The rabbit cecum had a greater predominance of acetogens, such as those in the genus Blautia, order Clostridiales, and family Ruminococcaceae. The differences in the occurrence of hydrogen-metabolizing bacteria probably explain much of the differential methane outputs from the rumen and the cecum. Future research using metatranscriptomics and metabolomics shall help confirm this premise and understand the factors that shape the differential microbiota between the two digestive organs. Furthermore, our present study strongly suggests the presence of new fibrolytic bacteria in the rabbit cecum, which may explain the stronger fibrolytic activities therein.

Dietary pea fibre alters the microbial community and fermentation with increase in fibre degradation-associated bacterial groups in the colon of pigs

This study was attempted to investigate the influence of dietary pea fibre (PF) on the community and quantity of colonic bacteria of piglets and finisher pigs using pyrosequencing data and real-time PCR. The concentration of acetate in colonic digesta from PF-fed piglets was significantly higher than that from control (p < .05). Feeding PF diet to finisher pigs increased the ratio of acetate to total volatile fatty acids (VFAs) but decreased the ratio of butyrate, as compared with the control pigs (p < .05 in both cases). The lower ratio of butyrate in samples from finisher pigs receiving PF suggested that this dietary fibre did not favour butyrate production in the hindgut. Supplementation of PF to piglets reduced abundance of Bacteroidetes, as compared with control animals. However, PF had opposite effects in finisher pigs, higher abundance of Bacteroidetes but lower of Firmicutes. Lactobacillus and Prevotella were found as the predominant genera in PF piglets. Prevotella accounted for nearly half of the total bacteria in the colon of finisher pigs in the PF group, but only one-third in the control animals. Quantitative PCR showed that Firmicutes/Bacteroidetes were significantly increased in the colon of PF piglets (p < .05) as compared with control animals, but decreased in PF finisher pigs. Bacteroidetes-Prevotella-Porphyromonas and Desulfovibrio desulfuricans which are involved in degradation of dietary fibres were more abundant in the PF finisher pigs than in the controls (p < .05), suggesting mutualism between host and its gut microbes.

Hydrogen Sulfide and Sulfate Prebiotic Stimulates the Secretion of GLP-1 and Improves Glycemia in Male Mice

Recently, the gastrointestinal microbiome, and its metabolites, has emerged as a potential regulator of host metabolism. However, to date little is known on the precise mechanisms of how this regulation occurs. Hydrogen sulfide (H2S) is abundantly produced in the colon by sulfate-reducing bacteria (SRB). H2S is a bioactive gas that plays regulatory roles in many systems, including metabolic hormone regulation. This gas metabolite is produced in close proximity to the glucagonlike peptide-1 (GLP-1)-secreting cells in the gut epithelium. GLP-1 is a peptide hormone that plays pivotal roles in both glucose homeostasis and appetite regulation. We hypothesized that H2S can directly regulate GLP-1 secretion. We demonstrated that H2S donors (NaHS and GYY4137) directly stimulate GLP-1 secretion in murine L-cells (GLUTag) and that this occurs through p38 mitogen-activated protein kinase without affecting cell viability. We then increased SRB in mice by supplementing the diet with a prebiotic chondroitin sulfate for 4 weeks. Mice treated with chondroitin sulfate had elevated Desulfovibrio piger levels in the feces and increased colonic and fecal H2S concentration. These animals also had enhanced GLP-1 and insulin secretion, improved oral glucose tolerance, and reduced food consumption. These results indicate that H2S plays a stimulatory role in GLP-1 secretion and that sulfate prebiotics can enhance GLP-1 release and its downstream metabolic actions.

The effects and mechanism of action of methane on ileal motor function

BACKGROUND

Methane has been associated with constipation-predominant irritable bowel syndrome, slowing intestinal transit time by augmenting contractile activity. However, the precise mechanism underlying this effect remains unclear. Therefore, we investigated the mechanisms underlying the effect of methane on contractile activity, and whether such effects are mediated by nerve impulses or muscular contraction.

METHODS

We connected guinea pig ileal muscle strips to a force/tension transducer and measured amplitudes of contraction in response to electrical field stimulation (EFS; 1, 2, 8, 16 Hz) following methane infusion in the presence of tetradotoxin (TTX), atropine, guanethidine, or GR 113808. We then performed calcium imaging using Oregon Green 488 BAPTA-1 AM in order to visualize changes in calcium fluorescence in response to EFS following methane infusion in the presence of TTX, atropine, or a high K⁺ solution.

KEY RESULTS

Methane significantly increased amplitudes of contraction (P<.05), while treatment with TTX abolished such contraction. Methane-induced increases in amplitude were inhibited when lower-frequency (1, 2 Hz) EFS was applied following atropine infusion (P<.05). Neither guanethidine nor GR 113808 significantly altered contraction amplitudes. Methane significantly increased calcium fluorescence, while this increase was attenuated following atropine infusion (P<.05). Although calcium fluorescence was increased by the high K⁺ solution under pretreatment with TTX, the intensity of fluorescence remained unchanged after methane infusion.

CONCLUSIONS AND INFERENCES

The actions of methane on the intestine are influenced by the cholinergic pathway of the enteric nervous system. Our findings support the classification of methane as a gasotransmitter.

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning

Homoacetogenic bacteria have received attention as a hydrogenotrophic population that offers a significant energetic advantage to the host animal. Reductive acetogenesis is likely an important hydrogen disposal mechanism in the cecum of rabbits. However, molecular ecology information about cecal acetogen candidates has rarely been reported. To better understand the effect of host selection in the rabbit cecal acetogen community with respect to growth, rabbits at four different age stages (30, 60, 120 and 180 days) with the same diet were studied. Although the abundance of potential acetogens and methanogens was high in the cecum of rabbits undergoing growth, many novel potential acetogen populations were observed in the cecum of rabbits across all age groups. Young and adult rabbits had their own distinct acetogen community although they received the same diet, which suggests that as the rabbit ages, acetogens in the cecum undergo developmental changes because of host selection that are independent of diet, and perhaps the different acetogen communities result in different hydrogenotrophic characteristics. The within-group similarity increased with age, indicating that the acetogen community converges to a more homogeneous and stable arrangement with aging.

Hydrogen sulphide in exhaled breath: a potential biomarker for small intestinal bacterial overgrowth in IBS

There is a pressing need to develop a novel early-detection strategy for the precise evolution of small intestinal bacterial overgrowth (SIBO) in irritable bowel syndrome (IBS) patients. The current method based on a hydrogen breath test (HBT) for the detection of SIBO is highly controversial. HBT has many limitations and drawbacks. It often fails to indentify SIBO when IBS individuals have 'non-hydrogen-producing' colonic bacteria. Here, we show that hydrogen sulphide (H2S) in exhaled breath is distinctly altered for diarrhea-predominant IBS individuals with positive and negative SIBO by the activity of intestinal sulphate-reducing bacteria. Subsequently, by analyzing the excretion kinetics of breath H2S, we found a missing link between breath H2S and SIBO when HBT often fails to diagnose SIBO. Moreover, breath H2S can track the precise evolution of SIBO, even after the eradication of bacterial overgrowth. Our findings suggest that the changes in H2S in the bacterial environment may contribute to the pathogenesis of SIBO and the breath H2S as a potential biomarker for non-invasive, rapid and precise assessment of SIBO without the endoscopy-based microbial culture of jejunal aspirates, and thus may open new perspectives into the pathophysiology of SIBO in IBS subjects.

H2 metabolism is widespread and diverse among human colonic microbes

Microbial molecular hydrogen (H2) cycling is central to metabolic homeostasis and microbial composition in the human gastrointestinal tract. Molecular H2 is produced as an endproduct of carbohydrate fermentation and is reoxidised primarily by sulfate-reduction, acetogenesis, and methanogenesis. However, the enzymatic basis for these processes is incompletely understood and the hydrogenases responsible have not been investigated. In this work, we surveyed the genomic and metagenomic distribution of hydrogenase-encoding genes in the human colon to infer dominant mechanisms of H2 cycling. The data demonstrate that 70% of gastrointestinal microbial species listed in the Human Microbiome Project encode the genetic capacity to metabolise H2. A wide variety of anaerobically-adapted hydrogenases were present, with [FeFe]-hydrogenases predominant. We subsequently analyzed the hydrogenase gene content of stools from 20 healthy human subjects. The hydrogenase gene content of all samples was overwhelmingly dominated by fermentative and electron-bifurcating [FeFe]-hydrogenases emerging from the Bacteroidetes and Firmicutes. This study supports that H2 metabolism in the human gut is driven by fermentative H2 production and interspecies H2 transfer. However, it suggests that electron-bifurcation rather than respiration is the dominant mechanism of H2 reoxidation in the human colon, generating reduced ferredoxin to sustain carbon-fixation (e.g. acetogenesis) and respiration (via the Rnf complex). This work provides the first comprehensive bioinformatic insight into the mechanisms of H2 metabolism in the human colon.

Obesity and the microbiome

Obesity constitutes a significant and rapidly increasing public health challenge and is associated with significant co-morbidities and healthcare costs. Although undoubtedly multifactorial, research over the last decade has demonstrated that the microbes that colonize the human gut may contribute to the development of obesity through roles in polysaccharide breakdown, nutrient absorption, inflammatory responses and gut permeability. Studies have consistently shown that the Firmicutes to Bacteroidetes ratio, in particular, is increased in obesity and reduces with weight loss. In addition, we and others have shown that the methanogenic Archaea may also contribute to altered metabolism and weight gain in the host. However, much remains to be learned about the roles of different gut microbial populations in weight gain and obesity and the underlying mechanisms before we can begin to approach targeted treatments.

Metabolic effects of eradicating breath methane using antibiotics in prediabetic subjects with obesity

OBJECTIVE

Methanogens colonizing the human gut produce methane and influence host metabolism. This study examined metabolic parameters in methane-producing subjects before and after antibiotic treatment.

METHODS

Eleven prediabetic methane-positive subjects (9F, 2M) with obesity (BMI 35.17 ± 7.71 kg/m(2) ) aged 47 ± 9 years were recruited. Subjects underwent breath testing, symptom questionnaire, oral glucose tolerance test (OGTT), lipid profile, and stool Methanobrevibacter smithii levels, gastric transit, and energy utilization analyses. After a 10-day antibiotic therapy (neomycin 500 mg bid/rifaximin 550 mg tid), all testing was repeated.

RESULTS

Baseline stool M. smithii levels correlated with breath methane (R = 0.7, P = 0.05). Eight subjects (73%) eradicated breath methane and showed reduced stool M. smithii (P = 0.16). After therapy, methane-eradicated subjects showed significant improvements in low-density lipoprotein (LDL) (P = 0.028), total cholesterol (P = 0.01), and insulin levels on OGTT (P = 0.05 at 120 minutes), lower blood glucose levels on OGTT (P = 0.054 at 90 minutes), significant reductions in bloating (P = 0.018) and straining (P = 0.059), and a trend toward lower stool dry weight. No changes were detected in gastric emptying time or energy harvest.

CONCLUSIONS

Breath methane eradication and M. smithii reduction are associated with significant improvements in total cholesterol, LDL, and insulin levels and with lower glucose levels in prediabetic subjects with obesity. The underlying mechanisms require further elucidation.

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation

BACKGROUND & AIMS

In fecal samples from patients with chronic constipation, the microbiota differs from that of healthy subjects. However, the profiles of fecal microbiota only partially replicate those of the mucosal microbiota. It is not clear whether these differences are caused by variations in diet or colonic transit, or are associated with methane production (measured by breath tests). We compared the colonic mucosal and fecal microbiota in patients with chronic constipation and in healthy subjects to investigate the relationships between microbiota and other parameters.

METHODS

Sigmoid colonic mucosal and fecal microbiota samples were collected from 25 healthy women (controls) and 25 women with chronic constipation and evaluated by 16S ribosomal RNA gene sequencing (average, 49,186 reads/sample). We assessed associations between microbiota (overall composition and operational taxonomic units) and demographic variables, diet, constipation status, colonic transit, and methane production (measured in breath samples after oral lactulose intake).

RESULTS

Fourteen patients with chronic constipation had slow colonic transit. The profile of the colonic mucosal microbiota differed between constipated patients and controls (P < .05). The overall composition of the colonic mucosal microbiota was associated with constipation, independent of colonic transit (P < .05), and discriminated between patients with constipation and controls with 94% accuracy. Genera from Bacteroidetes were more abundant in the colonic mucosal microbiota of patients with constipation. The profile of the fecal microbiota was associated with colonic transit before adjusting for constipation, age, body mass index, and diet; genera from Firmicutes (Faecalibacterium, Lactococcus, and Roseburia) correlated with faster colonic transit. Methane production was associated with the composition of the fecal microbiota, but not with constipation or colonic transit.

CONCLUSIONS

After adjusting for diet and colonic transit, the profile of the microbiota in the colonic mucosa could discriminate patients with constipation from healthy individuals. The profile of the fecal microbiota was associated with colonic transit and methane production (measured in breath), but not constipation.

Gut microbiota and non-alcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a common disorder with poorly understood pathogenesis. Beyond environmental and genetic factors, cumulative data support the causative role of gut microbiota in disease development and progression.

DATA SOURCE

We performed a PubMed literature search with the following key words: "non-alcoholic fatty liver disease", "non-alcoholic steatohepatitis", "fatty liver", "gut microbiota" and "microbiome", to review the data implicating gut microbiota in NAFLD development and progression.

RESULTS

Recent metagenomic studies revealed differences in the phylum and genus levels between patients with fatty liver and healthy controls. While bacteroidetes and firmicutes remain the dominant phyla among NAFLD patients, their proportional abundance and genera detection vary among different studies. New techniques indicate a correlation between the methanogenic archaeon (methanobrevibacter smithii) and obesity, while the bacterium akkermanshia municiphila protects against metabolic syndrome. Among NAFLD patients, small intestinal bacterial overgrowth detected by breath tests might induce gut microbiota and host interactions, facilitating disease development.

CONCLUSIONS

There is evidence that gut microbiota participates in NAFLD development through, among others, obesity induction, endogenous ethanol production, inflammatory response triggering and alterations in choline metabolism. Further studies with emerging techniques are needed to further elucidate the microbiome and host crosstalk in NAFLD pathogenesis.

Role of the Gut Microbiome in Obesity and Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) and obesity represent two of the biggest global health challenges of this century and are associated with significant comorbidities and healthcare costs. Although multiple factors undoubtedly contribute to the development and progression of DM and obesity, research over the last decade has demonstrated that the microbes that colonize the human gut may play key contributory roles. Gut microbes are now known to codevelop with the human host and are strongly influenced by mode of birth and early diet and nutrition, as well as environmental and other factors including antibiotic exposure. Gut microbes contribute to human health through roles in polysaccharide breakdown, nutrient absorption, inflammatory responses, gut permeability, and bile acid modification. Numerous studies have suggested that disruptions in the relative proportions of gut microbial populations may contribute to weight gain and insulin resistance, including alterations in Gammaproteobacteria and Verrucomicrobia and the ratios of Firmicutes to Bacteroidetes in weight gain and possible alterations in butyrate-producing bacteria such as Faecalibacterium prausnitzii in DM. In addition, it has been shown that the methanogenic Archaea may contribute to altered metabolism and weight gain in the host. However, the majority of studies are performed with stool or colonic samples and may not be representative of the metabolically active small intestine. Studies predominantly in rodent models are beginning to elucidate the mechanisms by which gut microbes contribute to DM and obesity, but much remains to be learned before we can begin to approach targeted treatments.

Breath methane in functional constipation: response to treatment with Ispaghula husk

BACKGROUND

Colonic fermentation produces hydrogen (H2 ), and also produces methane (CH4 ) in subjects with methanogenic flora (M+). Methane production has been associated with chronic constipation (CC) and with changes in gut motility. To determine CH4 production in CC compared to controls, and to assess whether the therapeutic response to Ispaghula husk in CC differs between CH4 -producers and non-producers.

METHODS

Forty-eight patients with functional constipation or irritable bowel syndrome-constipation and 19 healthy age-and-sex-matched volunteers (HV) filled in a 1-week symptom diary and a dietary questionnaire. They then underwent a lactulose breath test (LBT) to measure H2 and CH4 production (peak and area under the time-concentration curve, AUC-) and a colonic transit time (CTT) assessment. In patients, measurements were repeated after a 4-week treatment with Ispaghula husk.

KEY RESULTS

Prevalence of M+ in patients was 60.5% vs 52.6% in HV (p = 0.37). Patients had significantly longer CTT and greater production of both H2 and CH4 during LBT. There was a significant correlation between CH4 production and CTT (r = 0.51; p = 0.07). Treatment response rate was similar for M+ and M- patients (58.3% vs 52.9%; p = 0.76) as were the increases in bowel movements and Bristol score, changes in abdominal discomfort and bloating. In M+, treatment reduced CTT (-10 ± 35 h; p = 0.029 vs baseline) and CH4 levels: peak CH4 (-13 ± 24 ppm; p = 0.014) and CH4 -AUC (-817 ± 3100 ppm/min; p = 0.04).

CONCLUSIONS & INFERENCES

Although CH4 production has been associated with CC pathophysiology, we found that CH4 status did not negatively affect the response to Ispaghula husk treatment. The measurement of CH4 levels as a biomarker tool for CC requires further appraisal.

In vitro study and comparison of caecal methanogenesis and fermentation pattern in the brown hare (Lepus europaeus) and domestic rabbit (Oryctolagus cuniculus)

The brown hare and the domestic rabbit are mid-sized herbivorous mammals and hindgut fermenters, though their digestive physiologies differ in some traits. The objective of this study was to estimate and compare the caecal microbial activity in hares and rabbits via an analysis of the following end-products of in vitro caecal fermentation: methane, total gas production, short chain fatty acids and ammonia concentration. Hare caecal methanogenesis occurred at a much lower level (0.25 mmol/kg for samples incubated without substrate and 0.22 mmol/kg for samples incubated with substrate) than that of the rabbit (15.49 and 11.73 mmol/kg, respectively) (P<0.001). The impact of the substrate’s presence on caecal methanogenesis was not significant, though its presence increased the total gas production during fermentation (P<0.001). Hare caecal microflora produced a lower short chain fatty acids concentration than did rabbit microorganisms (P<0.05). In unincubated hare samples, the short chain fatty acids concentration was 28.4 mmol/kg, whereas in unincubated rabbit samples, the short chain fatty acids concentration was 51.8 mmol/kg. The caecal fermentation pattern of the hare was characterised by higher propionate and isobutyrate molar proportions compared with those observed in rabbit caecum (P<0.01). No significant changes in the ammonia concentration in either rabbit or hare caecum were found. The results obtained indicate some differences in the activity of the microbial populations colonising the hare and rabbit caecum, particularly in regards to methanogenic Archaea.

Examination of the Anaerobic Growth of Campylobacter concisus Strains

Campylobacter concisus is an oral bacterium that is associated with intestinal diseases. C. concisus was previously described as a bacterium that requires H2-enriched microaerobic conditions for growth. The level of H2 in the oral cavity is extremely low, suggesting that C. concisus is unlikely to have a microaerobic growth there. In this study, the anaerobic growth of C. concisus was investigated. The growth of fifty-seven oral C. concisus strains and six enteric C. concisus strains under various atmospheric conditions including anaerobic conditions with and without H2 was examined. The atmospheric conditions were generated using commercially available gas-generation systems. C. concisus putative virulence proteins were identified using mass spectrometry analysis. Under anaerobic conditions, 92% of the oral C. concisus strains (52/57) and all six enteric strains grew without the presence of H2 and the presence of H2 greatly increased C. concisus growth. An oral C. concisus strain was found to express a number of putative virulence proteins and the expression levels of these proteins were not affected by H2. The levels of H2 appeared to affect the optimal growth of C. concisus. This study provides useful information in understanding the natural colonization site and pathogenicity of C. concisus.

Cobalt and Nickel

Cobalt and nickel play key roles in biological systems as cofactors in a small number of important enzymes. The majority of these are found in microbes. Evidence for direct roles for Ni(II) and Co(II) enzymes in higher organisms is limited, with the exception of the well-known requirement for the cobalt-containing vitamin B12 cofactor and the Ni-dependent urease in plants. Nonetheless, nickel in particular plays a key role in human health because of its essential role in microbes that inhabit various growth niches within the body. These roles can be beneficial, as can be seen with the anaerobic production and consumption of H2 in the digestive tract by bacteria and archaea that results in increased yields of short-chain fatty acids. In other cases, nickel has an established role in the establishment of pathogenic infection (Helicobacter pylori urease and colonization of the stomach). The synthesis of Co- and Ni-containing enzymes requires metal import from the extracellular milieu followed by the targeting of these metals to the appropriate protein and enzymes involved in metallocluster or cofactor biosynthesis. These metals are toxic in excess so their levels must be regulated carefully. This complex pathway of metalloenzyme synthesis and intracellular homeostasis requires proteins that can specifically recognize these metals in a hierarchical manner. This chapter focuses on quantitative and structural details of the cobalt and nickel binding sites in transport, trafficking and regulatory proteins involved in cobalt and nickel metabolism in microbes.

Gas and the microbiome

Humans are host to trillions of microbial colonizers that contribute significantly to human health and disease. Advances in sequencing and other technologies have facilitated dramatic advances in our knowledge of the types and number of organisms colonizing different areas of the body, and while our knowledge of the roles played by the different bacteria, fungi, and archaea has increased dramatically, there remains much to uncover. The microbes that colonize the human gut contribute to vitamin biosynthesis, immune modulation, and the breakdown of otherwise indigestible foods for nutrient harvest. Bacteria and archaea produce various gases as by-products of fermentation, and it is becoming increasingly understood that these gases have both direct and indirect effects on the gut, and may also be used as diagnostic markers, e.g., hydrogen production as measured by breath testing can be used to diagnose bacterial overgrowth. In this article, we review the roles and effects of hydrogen (H2), methane (CH4) and hydrogen sulfide (H2S) in the human gut.

Lactulose increases equol production and improves liver antioxidant status in barrows treated with Daidzein

Equol, one of the intestinal microflora metabolites of daidzein, has gained much attention for having greater bioactivity than its precursor (daidzein and daidzin) and seeming to be promoted by hydrogen gas. The effects of lactulose on the equol-producing capacity and liver antioxidant status of barrows treated with daidzein were investigated in this study. Male castrated piglets (barrows) of Landrace × Duroc, aged 40 days, were randomly divided into the following three groups: control group (C, n = 12, fed an isoflavones-free basic diet), daidzein group (D, n = 12, fed an isoflavones-free basic diet with 50 mg/kg of daidzein supplementation) and daidzein+lactulose group (D+L, n = 12, fed an isoflavones-free basic diet with 1% of lactulose and 50 mg/kg of daidzein supplementation). After 20 days, the profile of short-chain fatty acids in the colon digesta showed that lactulose significantly increased the fermented capacity in the gastrointestinal tract of the barrows. First-void urinary equol concentrations were significantly higher in the D+L group than in the D group (3.13 ± 0.93 compared to 2.11 ± 0.82 μg/ml, respectively). Furthermore, fecal equol levels were also significantly higher in the D+L group than in the D group (12.00 ± 2.68 compared to 10.00 ± 2.26 μg/g, respectively). The population of bacteroidetes and the percentage of bacteroidetes to bacteria in feces were higher in the D+L group than in the D group. The DGGE profiles results indicate that lactulose might shift the pathways of hydrogen utilization, and changing the profiles of SRB in feces. Moreover, the D+L group had weak enhancement of T-SOD and CuZn-SOD activities in the livers of barrows treated with daidzein.

Gastrointestinal tolerance and utilization of agave inulin by healthy adults

Little clinical research exists on agave inulin as a fiber source. Due to differences in botanical origin and chemical structure compared to other inulin-type fibers, research is needed to assess gastrointestinal (GI) tolerance following consumption. This study aimed to evaluate GI tolerance and utilization of 5.0 and 7.5 g per day of agave inulin in healthy adults (n = 29) using a randomized, double-blind, placebo-controlled crossover trial consisting of three 21 day periods with 1 week washouts among periods. GI tolerance was assessed via daily and weekly questionnaires, three fecal samples were collected on days 16-20 of each period, and breath hydrogen testing was completed on the final day of each treatment period. Survey data were compared using a generalized linear mixed model. All other outcomes were analyzed using a mixed linear model with a repeated measures procedure. Composite GI intolerance scores for 5.0 and 7.5 g treatments were both greater (P < 0.05) than control, however, scores were low, with means of 0.4, 1.9, and 2.3 on a 0-12 point composite scale for 0, 5.0, and 7.5 g treatments, respectively. There were slight increases (P < 0.05) in bloating, flatulence, and rumbling frequency with 5.0 and 7.5 g agave inulin. Abdominal pain and rumbling intensity were marginally greater (P < 0.05) with 7.5 g. Bloating and flatulence intensity increased (P < 0.05) with 5.0 g and 7.5 g. Agave inulin did not affect diarrhea (P > 0.05). Number of bowel movements per day increased, stools were softer, and stool dry matter percentage was lower with 7.5 g (P < 0.05). Breath hydrogen concentrations increased (P < 0.001) from 5-8 hour postprandial when participants consumed agave inulin compared to control. These data demonstrate that doses up to 7.5 g per day of agave inulin led to minimal GI upset, do not increase diarrhea, and improve laxation in healthy young adults.

Recent progress in engineering human-associated microbiomes

Recent progress in molecular biology and genetics opens up the possibility of engineering a variety of biological systems, from single-cellular to multicellular organisms. The consortia of microbes that reside on the human body, the human-associated microbiota, are particularly interesting as targets for forward engineering and manipulation due to their relevance in health and disease. New technologies in analysis and perturbation of the human microbiota will lead to better diagnostic and therapeutic strategies against diseases of microbial origin or pathogenesis. Here, we discuss recent advances that are bringing us closer to realizing the true potential of an engineered human-associated microbial community.

Emerging aspects of food and nutrition on gut microbiota

The human gastrointestinal tract contains a highly complex ecosystem that harbors various microorganisms, which together create a unique environment within each individual. There is growing awareness that dietary habits are one of the essential factors contributing to the microbial diversity and community configuration that ultimately affects human health. From an evolutionary perspective, human dietary history can be viewed as a central factor in the selection of the gut microbial community and stabilization of the mutualistic host-microbial interaction, that together drive host phenotype. Herein, current knowledge concerning the influence of major dietary macrostructure and individual food ingredients is presented. This knowledge will provide perspectives for personalized gut microbiota management and, ultimately, movement toward an era of personalized nutrition and medicine.