Contributions of the microbial hydrogen economy to colonic homeostasis

Regulation of Gut Microbiota and Metabolic Endotoxemia with Dietary Factors

Metabolic endotoxemia is a condition in which blood lipopolysaccharide (LPS) levels are elevated, regardless of the presence of obvious infection. It has been suggested to lead to chronic inflammation-related diseases such as obesity, type 2 diabetes mellitus, non-alcoholic fatty liver disease (NAFLD), pancreatitis, amyotrophic lateral sclerosis, and Alzheimer’s disease. In addition, it has attracted attention as a target for the prevention and treatment of these chronic diseases. As metabolic endotoxemia was first reported in mice that were fed a high-fat diet, research regarding its relationship with diets has been actively conducted in humans and animals. In this review, we summarize the relationship between fat intake and induction of metabolic endotoxemia, focusing on gut dysbiosis and the influx, kinetics, and metabolism of LPS. We also summarize the recent findings about dietary factors that attenuate metabolic endotoxemia, focusing on the regulation of gut microbiota. We hope that in the future, control of metabolic endotoxemia using dietary factors will help maintain human health.

Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data

The availability of large-scale metagenomic sequencing data can facilitate the understanding of microbial ecosystems in unprecedented detail. However, current computational methods for predicting ecological interactions are hampered by insufficient statistical resolution and limited computational scalability. They also do not integrate metadata, which can reduce the interpretability of predicted ecological patterns. Here, we present FlashWeave, a computational approach based on a flexible Probabilistic Graphical Model framework that integrates metadata and predicts direct microbial interactions from heterogeneous microbial abundance data sets with hundreds of thousands of samples. FlashWeave outperforms state-of-the-art methods on diverse benchmarking challenges in terms of runtime and accuracy. We use FlashWeave to analyze a cross-study data set of 69,818 publicly available human gut samples and produce, to the best of our knowledge, the largest and most diverse network of predicted, direct gastrointestinal microbial interactions to date. FlashWeave is freely available for download here: https://github.com/meringlab/FlashWeave.jl.

Small Intestinal Bacterial Overgrowth in Children: A State-Of-The-Art Review

Small intestinal bacterial overgrowth (SIBO) is a heterogenous and poorly understood entity characterised by an excessive growth of select microorganisms within the small intestine. This excessive bacterial biomass, in turn, disrupts host physiology in a myriad of ways, leading to gastrointestinal and non-gastrointestinal symptoms and complications. SIBO is a common cause of non-specific gastrointestinal symptoms in children, such as chronic abdominal pain, abdominal distention, diarrhoea, and flatulence, amongst others. In addition, it has recently been implicated in the pathophysiology of stunting, a disease that affects millions of children worldwide. Risk factors such as acid-suppressive therapies, alterations in gastrointestinal motility and anatomy, as well as impoverished conditions, have been shown to predispose children to SIBO. SIBO can be diagnosed via culture-dependant or culture-independent approaches. SIBO's epidemiology is limited due to the lack of uniformity and consensus of its diagnostic criteria, as well as the paucity of literature available. Antibiotics remain the first-line treatment option for SIBO, although emerging modalities such as probiotics and diet manipulation could also have a role. Herein, we present a state-of-the-art-review which aims to comprehensively outline the most current information on SIBO in children, with particular emphasis on the gut microbiota.

Micro/Nanomaterials-Augmented Hydrogen Therapy

Hydrogen therapy is an emerging and promising therapy strategy of using molecular hydrogen as a new type of safe and effective therapeutic agent, exhibiting remarkable therapeutic effects on many oxidative stress-/inflammation-related diseases owing to its bio-reductivity and homeostatic regulation ability. Different from other gaseous transmitters such as NO, CO, and H₂ S, hydrogen gas has no blood poisoning risk at high concentration because it does not affect the oxygen-carrying behavior of blood red cells. Hydrogen molecules also have low aqueous solubility and high but aimless diffusibility, causing limited therapy efficacy in many diseases. To realize the site-specific hydrogen delivery, controlled hydrogen release and combined therapy is significant but still challenging. Here, a concept of hydrogen nanomedicine to address the issues of hydrogen medicine by using functional micro/nanomaterials for augmented hydrogen therapy is proposed. In this review, various strategies of micro/nanomaterials-augmented hydrogen therapy, including micro/nanomaterials-mediated targeted hydrogen delivery, controlled hydrogen release, and nanocatalytic and multimodel enhancement of hydrogen therapy efficacy, are summarized, which can open a new window for treatment of inflammation-related diseases.

Hydrogen-producing milk to prevent reduction in tear stability in persons using visual display terminals

PURPOSE

To examine the effect of hydrogen (H₂)-producing milk, which induces H₂ production by intestinal microbiota, on the prevention of dry eye disease.

METHODS

A randomized, double-blind, placebo-controlled, parallel-group comparative study was conducted in humans. Of 118 candidates aged 20-60 years who were using visual display terminals daily, 54 subjects (mean age, 42.4 years) with mild-to-moderate dry eye symptoms, who were not dry eye patients based on the 2006 Japanese Diagnostic Criteria for Dry Eye, were included in the study. Subjects were assigned to the H₂-producing milk group or the placebo group. They were instructed to ingest the assigned test beverage once per day for three consecutive weeks. Breath H₂ concentration, fluorescein tear film breakup time (fTBUT), Schirmer's test, 8-OHdG concentration in tears, reported ocular symptoms using the dry eye-related QOL score questionnaire, and the visual analogue scale were assessed at weeks 0 and 3.

RESULTS

Change in fTBUT in the H₂-producing milk group was significantly greater than that in the placebo group. A significant decline in fTBUT was observed in the placebo group (p = 0.04), but not the H₂-producing group (p = 0.26). This phenomenon was strongly observed in females. We found a positive correlation between the change in fTBUT and net H₂ production, and a negative correlation between the change in 8-OHdG concentration and net H₂ production in young females.

CONCLUSIONS

H₂-producing milk appeared to retard the decline in tear stability and may prevent short fTBUT-type dry eye by decreasing oxidative stress in the lacrimal functional unit.

A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria

Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.

Are probiotics useful in the treatment of chronic idiopathic constipation in adults? A review of existing systematic reviews, meta-analyses, and recommendations

Chronic idiopathic constipation (CIC) has emerged as common problem for contemporary gastroenterology and is one of the most frequent complaints in primary care. Chronic idiopathic constipation significantly affects patients' quality of life and has an impact on global health and economy. Functional gastrointestinal disorders and bowel disorders, according to Rome IV criteria, result from inappropriate gut-brain interactions. The pathophysiology is complex and poorly understood, with evidence accumulating that gut microbiota can be implicated in the development and function of the enteric nervous system. Gut bacteria modulate gut barrier function, short chain fatty acid synthesis, and bile acid metabolism, factors which play roles in the gut peristalsis regulation. The high prevalence of CIC, with poor treatment outcomes, warrants searches for new forms of therapy, including probiotic therapies. Probiotics are often recommended by medical practitioners, but evidence-based utility in adults with CIC is uncertain. Recommendations/guidelines are often based on results from individual studies, rather than meta-analyses or umbrella reviews. Additionally, meta-analyses often indicate a group of probiotics rather than individual strains, and they create difficulty for physicians in making therapeutic choices. More CIC patient randomised clinical studies utilising well-defined strains, or combinations, are necessary.

Metabolism, bioenergetics and thermal physiology: influences of the human intestinal microbiota

The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, 'Are intestinal microbiota effects measurable and meaningful?' and 'What research methods and variables are influenced by intestinal microbiota effects?'. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.

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.

Formate hydrogenlyase: A group 4 [NiFe]-hydrogenase in tandem with a formate dehydrogenase

Hydrogenase enzymes are currently under the international research spotlight due to emphasis on biologically produced hydrogen as one potential energy carrier to relinquish the requirement for 'fossil fuel' derived energy. Three major classes of hydrogenase exist in microbes all able to catalyze the reversible oxidation of dihydrogen to protons and electrons. These classes are defined by their active site metal content: [NiFe]-; [FeFe]- and [Fe]-hydrogenases. Of these the [NiFe]-hydrogenases have links to ancient forms of metabolism, utilizing hydrogen as the original source of reductant on Earth. This review progresses to highlight the Group 4 [NiFe]-hydrogenase enzymes that preferentially generate hydrogen exploiting various partner enzymes or ferredoxin, while in some cases translocating ions across biological membranes. Specific focus is paid to Group 4A, the Formate hydrogenlyase complexes. These are the combination of a six or nine subunit [NiFe]-hydrogenase with a soluble formate dehydrogenase to derived electrons from formate oxidation for proton reduction. The incidence, physiology, structure and biotechnological application of these complexes will be explored with attention on Escherichia coli Formate Hydrogenlyase-1 (FHL-1).

Quantification of hydrogen production by intestinal bacteria that are specifically dysregulated in Parkinson's disease

Oral administration of hydrogen water ameliorates Parkinson’s disease (PD) in rats, mice, and humans. We previously reported that the number of putative hydrogen-producing bacteria in intestinal microbiota is low in PD compared to controls. We also reported that the amount of hydrogen produced by ingestion of lactulose is low in PD patients. The decreased hydrogen production by intestinal microbiota may be associated with the development and progression of PD. We measured the amount of hydrogen production using gas chromatography by seven bacterial strains, which represented seven major intestinal bacterial groups/genera/species. Blautia coccoides and Clostridium leptum produced the largest amount of hydrogen. Escherichia coli and Bacteroides fragilis constituted the second group that produced hydrogen 34- to 93-fold lower than B. coccoides. Bifidobacterium pseudocatenulatum and Atopobium parvulum constituted the third group that produced hydrogen 559- to 2164-fold lower than B. coccoides. Lactobacillus casei produced no detectable hydrogen. Assuming that taxonomically neighboring strains have similar hydrogen production, we simulated hydrogen production using intestinal microbiota that we previously reported, and found that PD patients produce a 2.2-fold lower amount of intestinal hydrogen compared to controls. The lower amount of intestinal hydrogen production in PD was also simulated in cohorts of two other countries. The number of hydrogen-producing intestinal bacteria may be associated with the development and progression of PD. Further studies are required to prove its beneficial effect.

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.

The human archaeome: methodological pitfalls and knowledge gaps

Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite a long time that methanogenic archaea are substantial components of the human gastrointestinal tract (GIT) and the oral cavity, the knowledge on the human archaeome is very limited. Various methodological problems contribute to the invisibility of the human archaeome, resulting in severe knowledge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT landscape, (iii) a mixed skin/GIT landscape in nose, and (iv) a woesearchaeal lung landscape, including numerous unknown archaeal clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal a wide diversity and high quantity of archaeal signatures in various human tissues, with up to 1 : 1 ratios of bacteria and archaea in appendix and nose samples. The archaeome interacts closely with the bacteriome and the human body cells, whereas the roles of the human-associated archaea with respect to human health are only sparsely described. Methanogenic archaea and methane production were correlated with many health issues, including constipation, periodontitis and multiple sclerosis. However, one of the most burning questions - do archaeal pathogens exist? - still remains obscure to date.

Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health

Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.

Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice

Real time in vivo methods are needed to better understand the interplay between diet and the gastrointestinal microbiota. Therefore, a rodent indirect calorimetry system was equipped with hydrogen (H2) and methane (CH4) sensors. H2 production was readily detected in C57BL/6J mice and followed a circadian rhythm. H2 production was increased within 12 hours after first exposure to a lowly-digestible starch diet (LDD) compared to a highly-digestible starch diet (HDD). Marked differences were observed in the faecal microbiota of animals fed the LDD and HDD diets. H2 was identified as a key variable explaining the variation in microbial communities, with specific taxa (including Bacteroides and Parasutterella) correlating with H2 production upon LDD-feeding. CH4 production was undetectable which was in line with absence of CH4 producers in the gut. We conclude that real-time in vivo monitoring of gases provides a non-invasive time-resolved system to explore the interplay between nutrition and gut microbes in a mouse model, and demonstrates potential for translation to other animal models and human studies.

The Digestive Health among Participants of the Woodstock Rock Festival in Poland-A Cross-Sectional Survey

Alterations of gut microbiota, intestinal barrier and the gut-brain axis may be involved in pathophysiology of functional gastrointestinal disorders. Our aim was to assess the prevalence of digestive tract symptoms and identify common variables potentially disrupting the gut-brain axis among participants of the Woodstock Festival Poland, 2017. In total 428 people filled in a questionnaire assessing health of their digestive tract. The investigator collected answers on an electronic device, while the study participant responded using a paper version of the same questionnaire. Liver and gallbladder related symptoms were the most prevalent among our study group (n = 266, 62%), however symptoms related to altered intestinal permeability were found to be the most intensive complaints. In females the intensity of gastrointestinal complaints was higher compared to men (p < 0.05), as well as the incidence of factors with the potential to alter gut-brain axis (p < 0.0001). Chronic psychological distress, intake of non-steroidal anti-inflammatory drugs (NSAIDs) and antibiotics, were the most common associations with gastrointestinal symptoms, which were the most prevalent in females. Further attention should be focused on stress as one of the main factors negatively influencing public health.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

The safety and sensitivity of a telemetric capsule to monitor gastrointestinal hydrogen production in vivo in healthy subjects: a pilot trial comparison to concurrent breath analysis

BACKGROUND

Intestinal gases are currently used for the diagnosis of disorders including small intestinal bacterial overgrowth and carbohydrate malabsorption.

AIM

To compare the performance of measuring hydrogen production within the gut directly with the telemetric gas-sensing capsule with that of indirect measurement through breath testing.

METHODS

Using standard breath testing protocols, the capsules and breath tests were simultaneously evaluated in a single-blinded trial in 12 healthy subjects. Eight received a single dose of 1.25-40 g inulin and four 20 or 40 g glucose. Safety and reliability of the capsules were also assessed.

RESULTS

There were no reported adverse events. All capsules were retrieved and operated without failure. Capsule measurements were in agreement with breath test measurements in magnitude but not in timing; minimal hydrogen production was observed after glucose ingestion and capsule measurements correlated with breath hydrogen after ingestion of 40 g inulin. A dose-dependent increase in concentration of hydrogen was observed from the capsule following ingestion of inulin as low as 1.25 g compared with >10 g for breath measurements. Specifically, the capsule measured >3000 times higher concentrations of hydrogen compared to breath tests, resulting in a signal-to-noise ratio of 23.4 for the capsule compared to 4.2 for the breath test.

CONCLUSIONS

The capsule showed high sensitivity and signal-to-noise ratio in measuring luminal hydrogen concentrations, provided information on the site of intestinal gas production, and demonstrated safety and reliability. The capsule has potential for improving diagnostic precision for disorders such as small intestinal bacterial overgrowth.

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Background

In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.

Results

Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla - Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation.

Conclusions

Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4959-4) contains supplementary material, which is available to authorized users.

Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression

The human gastrointestinal tract is inhabited by trillions of commensal bacteria collectively known as the gut microbiota. Our recognition of the significance of the complex interaction between the microbiota, and its host has grown dramatically over the past years. A balanced microbial community is a key regulator of the immune response, and metabolism of dietary components, which in turn, modulates several brain processes impacting mood and behavior. Consequently, it is likely that disruptions within the composition of the microbiota would remotely affect the mental state of the host. Here, we discuss how intestinal bacteria and their metabolites can orchestrate gut-associated neuroimmune mechanisms that influence mood and behavior leading to depression. In particular, we focus on microbiota-triggered gut inflammation and its implications in shifting the tryptophan metabolism towards kynurenine biosynthesis while disrupting the serotonergic signaling. We further investigate the gaps to be bridged in this exciting field of research in order to clarify our understanding of the multifaceted crosstalk in the microbiota–gut–brain interphase, bringing about novel, microbiota-targeted therapeutics for mental illnesses.

Microbial markers in colorectal cancer detection and/or prognosis

Colorectal cancer (CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbial-based test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, and the potential use of microbial variation markers for non-invasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.

Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243T

Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E. lenta bile acid metabolism are further metabolized by other members of the gut microbiota. We characterized a novel human fecal isolate identified as E. lenta strain C592. The complete genome of E. lenta strain C592 was sequenced and comparative genomics with the type strain (DSM 2243) revealed high conservation, but some notable differences. E. lenta strain C592 falls into group III, possessing 3α, 3β, 7α, and 12α-hydroxysteroid dehydrogenase (HSDH) activity, as determined by mass spectrometry of thin layer chromatography (TLC) separated metabolites of primary and secondary bile acids. Incubation of E. lenta oxo-bile acid and iso-bile acid metabolites with whole-cells of the high-activity bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI 12708, resulted in minimal conversion of oxo-derivatives to lithocholic acid (LCA). Further, Iso-chenodeoxycholic acid (iso-CDCA; 3β,7α-dihydroxy-5β-cholan-24-oic acid) was not metabolized by C. scindens. We then located a gene encoding a novel 12α-HSDH in E. lenta DSM 2243, also encoded by strain C592, and the recombinant purified enzyme was characterized and substrate-specificity determined. Genomic analysis revealed genes encoding an Rnf complex (rnfABCDEG), an energy conserving hydrogenase (echABCDEF) complex, as well as what appears to be a complete Wood-Ljungdahl pathway. Our prediction that by changing the gas atmosphere from nitrogen to hydrogen, bile acid oxidation would be inhibited, was confirmed. These results suggest that E. lenta is an important bile acid metabolizing gut microbe and that the gas atmosphere may be an important and overlooked regulator of bile acid metabolism in the gut.

Biomarkers for monitoring intestinal health in poultry: present status and future perspectives

Intestinal health is determined by host (immunity, mucosal barrier), nutritional, microbial and environmental factors. Deficiencies in intestinal health are associated with shifts in the composition of the intestinal microbiome (dysbiosis), leakage of the mucosal barrier and/or inflammation. Since the ban on growth promoting antimicrobials in animal feed, these dysbiosis-related problems have become a major issue, especially in intensive animal farming. The economical and animal welfare consequences are considerable. Consequently, there is a need for continuous monitoring of the intestinal health status, particularly in intensively reared animals, where the intestinal function is often pushed to the limit. In the current review, the recent advances in the field of intestinal health biomarkers, both in human and veterinary medicine are discussed, trying to identify present and future markers of intestinal health in poultry. The most promising new biomarkers will be stable molecules ending up in the feces and litter that can be quantified, preferably using rapid and simple pen-side tests. It is unlikely, however, that a single biomarker will be sufficient to follow up all aspects of intestinal health. Combinations of multiple biomarkers and/or metabarcoding, metagenomic, metatranscriptomic, metaproteomic and metabolomic approaches will be the way to go in the future. Candidate biomarkers currently are being investigated by many research groups, but the validation will be a major challenge, due to the complexity of intestinal health in the field.

Metabolism of hydrogen gases and bile acids in the gut microbiome

The human gut microbiome refers to a highly diverse microbial ecosystem, which has a symbiotic relationship with the host. Molecular hydrogen (H₂ ) and carbon dioxide (CO₂ ) are generated by fermentative metabolism in anaerobic ecosystems. H₂ generation and oxidation coupled to CO₂ reduction to methane or acetate help maintain the structure of the gut microbiome. Bile acids are synthesized by hepatocytes from cholesterol in the liver and are important regulators of host metabolism. In this Review, we discuss how gut bacteria metabolize hydrogen gases and bile acids in the intestinal tract and the consequences on host physiology. Finally, we focus on bile acid metabolism by the Actinobacterium Eggerthella lenta. Eggerthella lenta appears to couple hydroxyl group oxidations to reductive acetogenesis under a CO₂ or N₂ atmosphere, but not under H₂ . Hence, at low H₂ levels, E. lenta is proposed to use NADH from bile acid hydroxyl group oxidations to reduce CO₂ to acetate.

Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition

Mitochondrial dysfunction is prevalent in the aging gastrointestinal tract. We investigated whether mitochondrial function in aging colonic crypts and exercise influences microbial gut communities in mice. Twelve PolgAmut/mut mice were randomly divided into a sedentary and exercise group at 4 months. Seven-aged matched PolgA+/+ mice remained sedentary throughout. Stool samples were collected at 4, 7, and 11 months, and bacterial profiling was achieved through 16S rRNA sequencing profiling. Mitochondrial enzyme activity was assessed in colonic epithelial crypts at 11 months for PolgAmut/mut and PolgA+/+ mice. Sedentary and exercised PolgAmut/mut mice had significantly higher levels of mitochondrial dysfunction than PolgA+/+ mice (78%, 77%, and 1% of crypts, respectively). Bacterial profiles of sedentary PolgAmut/mut mice were significantly different from the sedentary PolgA+/+ mice, with increases in Lactobacillus and Mycoplasma, and decreases in Alistipes, Odoribacter, Anaeroplasma, Rikenella, Parabacteroides, and Allobaculum in the PolgAmut/mut mice. Exercise did not have any impact upon gut mitochondrial dysfunction; however, exercise did increase gut microbiota diversity and significantly increased bacterial genera Mucispirillum and Desulfovibrio. Mitochondrial dysfunction is associated with changes in the gut microbiota. Endurance exercise moderated some of these changes, establishing that environmental factors can influence gut microbiota, despite mitochondrial dysfunction.

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo

Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.

A timeline of hydrogen sulfide (H2S) research: From environmental toxin to biological mediator

The history of H2S - as an environmental toxin - dates back to 1700, to the observations of the Italian physician Bernardino Ramazzini, whose book "De Morbis Artificum Diatriba" described the painful eye irritation and inflammation of "sewer gas" in sewer workers. The gas has subsequently been identified as hydrogen sulfide (H2S), and opened three centuries of research into the biological roles of H2S. The current article highlights the key discoveries in the field of H2S research, including (a) the toxicological studies, which characterized H2S as an environmental toxin, and identified some of its modes of action, including the inhibition of mitochondrial respiration; (b) work in the field of bacteriology, which, starting in the early 1900s, identified H2S as a bacterial product - with subsequently defined roles in the regulation of periodontal disease (oral bacterial flora), intestinal epithelial cell function (enteral bacterial flora) as well as in the regulation of bacterial resistance to antibiotics; and (c), work in diverse fields of mammalian biology, which, starting in the 1940s, identified H2S as an endogenous mammalian enzymatic product, the functions of which - among others, in the cardiovascular and nervous system - have become subjects of intensive investigation for the last decade. The current review not only enumerates the key discoveries related to H2S made over the last three centuries, but also compiles the most frequently cited papers in the field which have been published over the last decade and highlights some of the current 'hot topics' in the field of H2S biology.

Transplantation of High Hydrogen-Producing Microbiota Leads to Generation of Large Amounts of Colonic Hydrogen in Recipient Rats Fed High Amylose Maize Starch

The hydrogen molecule (H₂), which has low redox potential, is produced by colonic fermentation. We examined whether increased H₂ concentration in the portal vein in rats fed high amylose maize starch (HAS) helped alleviate oxidative stress, and whether the transplantation of rat colonic microbiota with high H₂ production can shift low H₂-generating rats (LG) to high H₂-generating rats (HG). Rats were fed a 20% HAS diet for 10 days and 13 days in experiments 1 and 2, respectively. After 10 days (experiment 1), rats underwent a hepatic ischemia–reperfusion (IR) operation. Rats were then categorized into quintiles of portal H₂ concentration. Plasma alanine aminotransferase activity and hepatic oxidized glutathione concentration were significantly lower as portal H₂ concentration increased. In experiment 2, microbiota derived from HG (the transplantation group) or saline (the control group) were orally inoculated into LG on days 3 and 4. On day 13, portal H₂ concentration in the transplantation group was significantly higher compared with the control group, and positively correlated with genera Bifidobacterium, Allobaculum, and Parabacteroides, and negatively correlated with genera Bacteroides, Ruminococcus, and Escherichia. In conclusion, the transplantation of microbiota derived from HG leads to stable, high H₂ production in LG, with the resultant high production of H₂ contributing to the alleviation of oxidative stress.

Hydrogen excretion in pediatric lactose malabsorbers: relation to symptoms and the dose of lactose

INTRODUCTION

Lactose malabsorption arises from lactase deficiency and may lead to lactose intolerance - gastrointestinal symptoms after lactose ingestion. Occurrence and severity of the symptoms are influenced by many factors, including the dose of lactose and the intensity of its colonic fermentation to short chain fatty acids and gases.

MATERIAL AND METHODS

The hydrogen breath test (HBT) after 30 g or 50 g of lactose was performed in 387 children. Further analysis included children who had a positive HBT result. The HBT parameters were net hydrogen concentration in each breath and total net hydrogen concentration during the HBT. The time of the first hydrogen rise was also calculated. HBT parameters were analyzed according to symptoms occurrence (lack or present), symptoms severity (lack, moderate or severe) and the dose of lactose (30 g or 50 g).

RESULTS

One hundred and six children (12.1 years, 46 boys) had a positive HBT result. Symptoms occurrence was positively related to net hydrogen concentration at 30 min, 60 min and 90 min (p < 0.001 at each time point), as well as to the total net hydrogen concentration (p < 0.001). There were no differences in hydrogen excretion between subjects with moderate and severe symptoms after lactose ingestion. Symptoms were more frequent in subjects given 50 g of lactose than in those given 30 g of lactose (79% vs. 47%, p = 0.003). In both dose groups symptoms occurrence was related to hydrogen excretion.

CONCLUSIONS

Symptoms occurrence is closely related to hydrogen excretion and to the dose of ingested lactose.

Interactions between species introduce spurious associations in microbiome studies

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.

Triterpenoid herbal saponins enhance beneficial bacteria, decrease sulfate-reducing bacteria, modulate inflammatory intestinal microenvironment and exert cancer preventive effects in ApcMin/+ mice

Saponins derived from medicinal plants have raised considerable interest for their preventive roles in various diseases. Here, we investigated the impacts of triterpenoid saponins isolated from Gynostemma pentaphyllum (GpS) on gut microbiome, mucosal environment, and the preventive effect on tumor growth. Six-week old ApcMin/+ mice and their wild-type littermates were fed either with vehicle or GpS daily for the duration of 8 weeks. The fecal microbiome was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and 16S rRNA gene pyrosequencing. Study showed that GpS treatment significantly reduced the number of intestinal polyps in a preventive mode. More importantly, GpS feeding strikingly reduced the sulfate-reducing bacteria lineage, which are known to produce hydrogen sulfide and contribute to damage the intestinal epithelium or even promote cancer progression. Meanwhile, GpS also boosted the beneficial microbes. In the gut barrier of the ApcMin/+ mice, GpS treatment increased Paneth and goblet cells, up-regulated E-cadherin and down-regulated N-cadherin. In addition, GpS decreased the pro-oncogenic β-catenin, p-Src and the p-STAT3. Furthermore, GpS might also improve the inflamed gut epithelium of the ApcMin/+ mice by upregulating the anti-inflammatory cytokine IL-4, while downregulating pro-inflammatory cytokines TNF-α, IL-1β and IL-18. Intriguingly, GpS markedly stimulated M2 and suppressed M1 macrophage markers, indicating that GpS altered mucosal cytokine profile in favor of the M1 to M2 macrophages switching, facilitating intestinal tissue repair. In conclusion, GpS might reverse the host's inflammatory phenotype by increasing beneficial bacteria, decreasing sulfate-reducing bacteria, and alleviating intestinal inflammatory gut environment, which might contribute to its cancer preventive effects.

Repeated Oral Exposure to N ε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice

BACKGROUND

Diet is suggested to participate in the etiology of inflammatory bowel diseases (IBD). Repeated exposure to Maillard reaction products (MRPs), molecules resulting from reduction reactions between amino acids and sugars during food heating, has been reported to be either potentially detrimental or beneficial to health.

AIMS

The aim of this study is to determine the effect of repeated oral ingestion of N ^ε-carboxymethyllysine (CML), an advanced MRP, on the onset of two models of experimental IBD and on the gut microbiota composition of mice.

METHODS

Mice received either saline (control) or N ^ε-carboxymethyllysine daily for 21 days. For the last week of treatment, each group was split into subgroups, receiving dextran sulfate sodium salt (DSS) or trinitrobenzenesulfonic acid (TNBS) to induce colitis. Intensity of inflammation was quantified, and cecal microbiota characterized by bacterial 16S ribosomal RNA (rRNA) amplicon sequencing.

RESULTS

Daily oral administration of N ^ε-carboxymethyllysine did not induce intestinal inflammation and had limited impact on gut microbiota composition (Bacteroidaceae increase, Lachnospiraceae decrease). DSS and TNBS administration resulted in expected moderate experimental colitis with a shift of Bacteroidetes/Firmicutes ratio and a significant Proteobacteria increase but with distinct profiles: different Proteobacteria taxa for DSS, but mainly Enterobacteriaceae for TNBS. While N ^ε-carboxymethyllysine exposure failed to prevent the inflammatory response, it allowed maintenance of healthy gut microbiota profiles in mice treated with DSS (but not TNBS).

CONCLUSIONS

Repeated oral exposure to CML limits dysbiosis in experimental colitis. IBD patients may modulate their microbiota profile by regulating the level and type of dietary MRP consumption.

Tart Cherries and health: Current knowledge and need for a better understanding of the fate of phytochemicals in the human gastrointestinal tract

Tart cherries are increasingly popular due to purported health benefits. This Prunus cesarus species is cultivated worldwide, and its market has increased significantly in the last two decades due to improvements in agricultural practices and food processing technology. Tart cherries are rich in polyphenols, with a very specific profile combining anthocyanins and flavonols (berries-like) and chlorogenic acid (coffee-like). Tart cherries have been suggested to exert several potentially beneficial health effects including: lowering blood pressure, modulating blood glucose, enhancing cognitive function, protecting against oxidative stress and reducing inflammation. Studies focusing on tart cherry consumption have demonstrated particular benefits in recovery from exercise-induced muscle damage and diabetes associated parameters. However, the bioconversion of tart cherry polyphenols by resident colonic microbiota has never been considered, considerably reducing the impact of in vitro studies that have relied on fruit polyphenol extracts. In vitro and in vivo gut microbiota and metabolome studies are necessary to reinforce health claims linked to tart cherries consumption.

Assessing the colonic microbiome, hydrogenogenic and hydrogenotrophic genes, transit and breath methane in constipation

BACKGROUND

Differences in the gut microbiota and breath methane production have been observed in chronic constipation, but the relationship between colonic microbiota, transit, and breath tests remains unclear.

METHODS

In 25 healthy and 25 constipated females we evaluated the sigmoid colonic mucosal and fecal microbiota using 16S rRNA gene sequencing, abundance of hydrogenogenic FeFe (FeFe-hydA) and hydrogenotrophic (methyl coenzyme M reductase A [mrcA] and dissimilatory sulfite reductase A [dsrA]) genes with real-time qPCR assays, breath hydrogen and methane levels after oral lactulose, and colonic transit with scintigraphy.

KEY RESULTS

Breath hydrogen and methane were not correlated with constipation, slow colon transit, or with abundance of corresponding genes. After adjusting for colonic transit, the abundance of FeFehydA, dsrA, and mcrA were greater (P<.005) in colonic mucosa, but not stool, of constipated patients. The abundance of the selected functional gene targets also correlated with that of selected taxa. The colonic mucosal abundance of FeFe-hydA, but not mcrA, correlated positively (P<.05) with breath methane production, slow colonic transit, and overall microbiome composition. In the colonic mucosa and feces, the abundance of hydrogenogenic and hydrogenotrophic genes were positively correlated (P<.05). Breath methane production was not associated with constipation or colonic transit.

CONCLUSIONS & INFERENCES

Corroborating our earlier findings with 16S rRNA genes, colonic mucosal but not fecal hydrogenogenic and hydrogenotrophic genes were more abundant in constipated vs. healthy subjects independent of colonic transit. Breath gases do not directly reflect the abundance of target genes contributing to their production.

Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants

The aetiology of colic, a functional gastrointestinal disorder in infants, is not yet resolved. Different mechanisms have been suggested involving the gut microbiota and intermediate metabolites such as lactate. Lactate can be metabolized by lactate-utilizing bacteria (LUB) to form different end-products. Using a functional approach, we hypothesized that H₂ production and accumulation by LUB is associated with the development of colic. The LUB communities in the feces of forty infants, including eight colicky infants, were characterized using a combination of culture- and molecular-based methods, and metabolite concentrations were measured by HPLC. Interactions among LUB strains isolated from feces were investigated with pure and mixed cultures using anaerobic techniques. We emphasized high prevalence of crying, flatulence, colic and positive correlations thereof in the first 3 months of life. Crying infants showed significantly higher ratio of LUB non-sulfate-reducing bacteria (LUB non-SRB) (H₂-producer), to LUB SRB (H₂-utilizer) at 3 months. Colicky infants had significantly higher number of H₂-producing Eubacterium hallii at 2 weeks compared to non-colicky infants. We revealed the function of Desulfovibrio piger and Eubacterium limosum to reduce H₂ accumulation in co-cultures with H₂-producing Veillonella ratti. Our data suggest that the balance between H₂-producing and H₂-utilizing LUB might contribute to colic symptoms.

Diet, Gut Microbiota, and Colorectal Cancer Prevention: A Review of Potential Mechanisms and Promising Targets for Future Research

Diet plays an important role in the development of colorectal cancer. Emerging data have implicated the gut microbiota in colorectal cancer. Diet is a major determinant for the gut microbial structure and function. Therefore, it has been hypothesized that alterations in gut microbes and their metabolites may contribute to the influence of diet on the development of colorectal cancer. We review several major dietary factors that have been linked to gut microbiota and colorectal cancer, including major dietary patterns, fiber, red meat and sulfur, and obesity. Most of the epidemiologic evidence derives from cross-sectional or short-term, highly controlled feeding studies that are limited in size. Therefore, high-quality large-scale prospective studies with dietary data collected over the life course and comprehensive gut microbial composition and function assessed well prior to neoplastic occurrence are critically needed to identify microbiome-based interventions that may complement or optimize current diet-based strategies for colorectal cancer prevention and management.

Inflammatory bowel disease and patterns of volatile organic compounds in the exhaled breath of children: A case-control study using Ion Molecule Reaction-Mass Spectrometry

Inflammatory bowel diseases (IBD) profoundly affect quality of life and have been gradually increasing in incidence, prevalence and severity in many areas of the world, and in children in particular. Patients with suspected IBD require careful history and clinical examination, while definitive diagnosis relies on endoscopic and histological findings. The aim of the present study was to investigate whether the alveolar air of pediatric patients with IBD presents a specific volatile organic compounds’ (VOCs) pattern when compared to controls. Patients 10–17 years of age, were divided into four groups: Crohn’s disease (CD), ulcerative colitis (UC), controls with gastrointestinal symptomatology, and surgical controls with no evidence of gastrointestinal problems. Alveolar breath was analyzed by ion molecule reaction mass spectrometry. Four models were built starting from 81 molecules plus the age of subjects as independent variables, adopting a penalizing LASSO logistic regression approach: 1) IBDs vs. controls, finally based on 18 VOCs plus age (sensitivity = 95%, specificity = 69%, AUC = 0.925); 2) CD vs. UC, finally based on 13 VOCs plus age (sensitivity = 94%, specificity = 76%, AUC = 0.934); 3) IBDs vs. gastroenterological controls, finally based on 15 VOCs plus age (sensitivity = 94%, specificity = 65%, AUC = 0.918); 4) IBDs vs. controls, built starting from the 21 directly or indirectly calibrated molecules only, and finally based on 12 VOCs plus age (sensitivity = 94%, specificity = 71%, AUC = 0.888). The molecules identified by the models were carefully studied in relation to the concerned outcomes. This study, with the creation of models based on VOCs profiles, precise instrumentation and advanced statistical methods, can contribute to the development of new non–invasive, fast and relatively inexpensive diagnostic tools, with high sensitivity and specificity. It also represents a crucial step towards gaining further insights on the etiology of IBD through the analysis of specific molecules which are the expression of the particular metabolism that characterizes these patients.

Serotonin Transporter Genotype Modulates the Gut Microbiota Composition in Young Rats, an Effect Augmented by Early Life Stress

The neurotransmitter serotonin (5-HT) plays a vital regulatory role in both the brain and gut. 5-HT is crucial for regulating mood in the brain as well as gastrointestinal motility and secretion peripherally. Alterations in 5-HT transmission have been linked to pathological symptoms in both intestinal and psychiatric disorders and selective 5-HT transporter (5-HTT) inhibitors, affecting the 5-HT system by blocking the 5-HT transporter (5-HTT) have been successfully used to treat CNS- and intestinal disorders. Humans that carry the short allele of the 5-HTT-linked polymorphic region (5-HTTLPR) are more vulnerable to adverse environmental stressors, in particular early life stress. Although, early life stress has been shown to alter the composition of the gut microbiota, it is not known whether a lower 5-HTT expression is also associated with an altered microbiome composition. To investigate this, male and female wild type (5-HTT^+/+), heterozygous (5-HTT^+/-), and knockout (5-HTT^-/-) 5-HT transporter rats were maternally separated for 6 h a day from postnatal day 2 till 15. On postnatal day 21, fecal samples were collected and the impact of 5-HTT genotype and maternal separation (MS) on the microbiome was analyzed using high-throughput sequencing of the bacterial 16S rRNA gene. MS showed a shift in the ratio between the two main bacterial phyla characterized by a decrease in Bacteroidetes and an increase in Firmicutes. Interestingly, the 5-HTT genotype caused a greater microbal dysbiosis (microbial imbalance) compared with MS. A significant difference in microbiota composition was found segregating 5-HTT^-/- apart from 5-HTT^+/- and 5-HTT^+/+ rats. Moreover, exposure of rats with 5-HTT diminished expression to MS swayed the balance of their microbiota away from homeostasis to 'inflammatory' type microbiota characterized by higher abundance of members of the gut microbiome including Desulfovibrio, Mucispirillum, and Fusobacterium, all of which are previously reported to be associated with a state of intestinal inflammation, including inflammation associated with MS and brain disorders like multiple depressive disorders. Overall, our data show for the first time that altered expression of 5-HTT induces disruptions in male and female rat gut microbes and these 5-HTT genotype-related disruptions are augmented when combined with early life stress.

Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR

Delivery mode (natural vs. cesarean) and feeding type (breast vs. formula feeding) are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB), acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1-6 months by means of quantitative PCR (qPCR) targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE). qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian). DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.

BioSIMP: Using Software Testing Techniques for Sampling and Inference in Biological Organisms

Years of research in software engineering has given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we reverse the direction and present BioSIMP, a process that models and predicts the behavior of biological organisms to aid in the emerging field of systems biology. It utilizes techniques from testing and modeling of highly-configurable software systems. Using both experimental and simulation data we show that BioSIMP can find important environmental factors in two microbial organisms. However, we learn that in order to fully reason about the complexity of biological systems, we will need to extend existing or create new software engineering techniques.

Stress during pregnancy alters temporal and spatial dynamics of the maternal and offspring microbiome in a sex-specific manner

The microbiome is a regulator of host immunity, metabolism, neurodevelopment, and behavior. During early life, bacterial communities within maternal gut and vaginal compartments can have an impact on directing these processes. Maternal stress experience during pregnancy may impact offspring development by altering the temporal and spatial dynamics of the maternal microbiome during pregnancy. To examine the hypothesis that maternal stress disrupts gut and vaginal microbial dynamics during critical prenatal and postnatal windows, we used high-resolution 16S rRNA marker gene sequencing to examine outcomes in our mouse model of early prenatal stress. Consistent with predictions, maternal fecal communities shift across pregnancy, a process that is disrupted by stress. Vaginal bacterial community structure and composition exhibit lasting disruption following stress exposure. Comparison of maternal and offspring microbiota revealed that similarities in bacterial community composition was predicted by a complex interaction between maternal body niche and offspring age and sex. Importantly, early prenatal stress influenced offspring bacterial community assembly in a temporal and sex-specific manner. Taken together, our results demonstrate that early prenatal stress may influence offspring development through converging modifications to gut microbial composition during pregnancy and transmission of dysbiotic vaginal microbiome at birth.

Sufficient intake of high amylose cornstarch maintains high colonic hydrogen production for 24 h in rats

Colonic hydrogen (H2) can suppress oxidative stress and damage in the body. We examined the minimum requirement of high amylose cornstarch (HAS) to maintain high colonic H2 production for 24 h. Ileorectostomized and sham-operated rats were fed a control diet supplemented with or without 20% HAS for 7 days. Colonic starch utilization was determined. Next, rats were fed the control diet with or without 10% or 20% HAS for 14 or 28 days, respectively. Breath and flatus H2 excretion for 24 h was measured. 1.04 g of resistant fraction in HAS was utilized for 24 h by colonic bacteria. High H2 excretion was not maintained for 24 h in rats fed the 10% HAS diet, from which only 0.89 g of resistant starch was estimated to be delivered. High colonic H2 production for 24 h would be maintained by delivering more HAS to the large intestine than is utilized.

Gut Bacteria and Hydrogen Sulfide: The New Old Players in Circulatory System Homeostasis

Accumulating evidence suggests that gut bacteria play a role in homeostasis of the circulatory system in mammals. First, gut bacteria may affect the nervous control of the circulatory system via the sensory fibres of the enteric nervous system. Second, gut bacteria-derived metabolites may cross the gut-blood barrier and target blood vessels, the heart and other organs involved in the regulation of the circulatory system. A number of studies have shown that hydrogen sulfide (H₂S) is an important biological mediator in the circulatory system. Thus far, research has focused on the effects of H₂S enzymatically produced by cardiovascular tissues. However, some recent evidence indicates that H₂S released in the colon may also contribute to the control of arterial blood pressure. Incidentally, sulfate-reducing bacteria are ubiquitous in mammalian colon, and H₂S is just one among a number of molecules produced by the gut flora. Other gut bacteria-derived compounds that may affect the circulatory system include methane, nitric oxide, carbon monoxide, trimethylamine or indole. In this paper, we review studies that imply a role of gut microbiota and their metabolites, such as H₂S, in circulatory system homeostasis.