Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities.

Heating and cooking vegetables not only enhances their palatability but also modifies their chemical structure, which in turn might affect their fermentation by resident gut microbes. Three commonly consumed vegetables that are known to undergo chemical browning, also known as Maillard reaction, during cooking - eggplant, garlic, and onion - were each fried, grilled, or roasted. The cooked vegetables were then subjected to an in vitro digestion-fermentation process aimed to simulate the passage of food through the human oro-gastro-intestinal tract. In the last step, the undigested fractions of these foods were anaerobically fermented by the complex human gut microbiota. We assessed the structure of microbial communities maintained on each cooked vegetable by high-throughput 16S rRNA gene amplicon sequencing, measured the levels of furosine, a chemical marker of the Maillard browning reaction, by HPLC, and determined the antioxidant capacities in all samples with ABTS and FRAP methods. Overall, vegetable type had the largest, statistically significant, effect on the microbiota structure followed by the cooking method. Onion fermentation supported a more beneficial community including an expansion of Bifidobacterium members and inhibition of Enterobacteriaceae. Fermentation of cooked garlic promoted Faecalibacterium growth. Among cooking methods, roasting led to a much higher ratio of beneficial-to-detrimental microbes in comparison with grilling and frying, possibly due to the exclusion of any cooking oil in the cooking process.

Cultivar and Harvest Time of Almonds Affect Their Antioxidant and Nutritional Profile through Gut Microbiota Modifications.

Almonds are a rich source of beneficial compounds for human health. In this work, we assessed the influence of almond cultivars and harvest time on their morphological (length, width and thickness) and nutritional (ash, moisture, proteins) profiles. We also evaluated the impact of an in vitro digestion and fermentation process on almonds' antioxidant and phenolic content, as well as their support of gut microbiota community and functionality, including the production of short-chain fatty acids (SCFAs), lactic and succinic acids. The length, width, and thickness of almonds varied significantly among cultivars, with the latter two parameters also exhibiting significant changes over time. Moisture content decreased with maturity, while protein and ash increased significantly. Total antioxidant capacity released by almonds after digestion and fermentation had different trends depending on the antioxidant capacity method used. The fermentation step contributed more to the antioxidant capacity than the digestion step. Both cultivar and harvest time exerted a significant influence on the concentration of certain phenolic compounds, although the total content remained unaffected. Similarly, fecal microbiota modulation depended on the cultivar and maturity stage, with the Guara cultivar and late maturity showing the largest effects. Cultivar type also exerted a significant impact on the concentration of SCFAs, with the Guara cultivar displaying the highest total SCFAs concentration. Thus, we conclude that cultivar and harvest time are key factors in shaping the morphological and nutritional composition of almonds. In addition, taking into account all the results obtained, the Guara variety has the best nutritional profile.

Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota.

Melanoidins are the products of the Maillard reaction between carbonyl and amino groups of macromolecules and are readily formed in foods, especially during heat treatment. In this study we utilized the three-stage Human Gut Simulator system to assess the effect of providing melanoidins extracted from either biscuits or bread crust to the human gut microbiota. Addition of melanoidins to the growth medium led to statistically significant alterations in the microbial community composition, and it increased short-chain fatty acid and antioxidant production by the microbiota. The magnitude of these changes was much higher for cultures grown with biscuit melanoidins. Several lines of evidence indicate that such differences between these melanoidin sources might be due to the presence of lipid components in biscuit melanoidin structures. Because melanoidins are largely not degraded by human gastrointestinal enzymes, they provide an additional source of microbiota-accessible nutrients to our gut microbes.

Growth of Bifidobacterium species is inhibited by free fatty acids and bile salts but not by glycerides.

High-fat diets have been associated with lower gut and fecal abundances of genus Bifidobacterium. Here, we investigated whether commonly consumed dietary free fatty acids have any detrimental effect on the growth of B. adolescentis, B. bifidum, and B. longum. We found that the presence of free fatty acids in the medium inhibits the growth of Bifidobacterium species to a varying degree, with capric (C10:0), oleic (C18:1), and linoleic (C18:2) acids displaying the largest effect. In comparison, free fatty acids did not affect the growth of Escherichia coli. When fats were added as a mixture of mono- and diacylglycerols, the inhibitory effect on Bifidobacterium growth was abolished.

Bioactivity of food melanoidins is mediated by gut microbiota.

Melanoidins are an important component of the human diet (average consumption 10 g/day), which escape gastrointestinal digestion and are fermented by the gut microbiota. In this study melanoidins from different food sources (coffee, bread, beer, balsamic vinegar, sweet wine, biscuit, chocolate, and breakfast cereals) were submitted to an in vitro digestion and fermentation process, and their bioactivity was assessed. Some melanoidins were extensively used by gut microbes, increasing production of short chain fatty acids (mainly acetate and lactate) and favoring growth of the beneficial genera Bifidobacterium (bread crust, pilsner and black beers, chocolate and sweet wine melanoidins) and Faecalibacterium (biscuit melanoidins). Quantification of individual phenolic compounds after in vitro fermentation allowed their identification as microbial metabolites or phenolics released from the melanoidins backbone (specially pyrogallol, 2-(3,4-dihydroxyphenyl)acetic and 3-(3,4-dihydroxyphenyl)propionic acids). Our results also showed that antioxidant capacity of melanoidins is affected by gut microbiota fermentation.

Differential MicroRNA Signatures in the Pathogenesis of Barrett's Esophagus.

OBJECTIVES: Barrett's esophagus (BE) is the precursor lesion and a major risk factor for esophageal adenocarcinoma (EAC). Although patients with BE undergo routine endoscopic surveillance, current screening methodologies have proven ineffective at identifying individuals at risk of EAC. Since microRNAs (miRNAs) have potential diagnostic and prognostic value as disease biomarkers, we sought to identify an miRNA signature of BE and EAC. METHODS: High-throughput sequencing of miRNAs was performed on serum and tissue biopsies from 31 patients identified either as normal, gastroesophageal reflux disease (GERD), BE, BE with low-grade dysplasia (LGD), or EAC. Logistic regression modeling of miRNA profiles with Lasso regularization was used to identify discriminating miRNA. Quantitative reverse transcription polymerase chain reaction was used to validate changes in miRNA expression using 46 formalin-fixed, paraffin-embedded specimens obtained from normal, GERD, BE, BE with LGD or HGD, and EAC subjects. RESULTS: A 3-class predictive model was able to classify tissue samples into normal, GERD/BE, or LGD/EAC classes with an accuracy of 80%. Sixteen miRNAs were identified that predicted 1 of the 3 classes. Our analysis confirmed previous reports indicating that miR-29c-3p and miR-193b-5p expressions are altered in BE and EAC and identified miR-4485-5p as a novel biomarker of esophageal dysplasia. Quantitative reverse transcription polymerase chain reaction validated 11 of 16 discriminating miRNAs. DISCUSSION: Our data provide an miRNA signature of normal, precancerous, and cancerous tissue that may stratify patients at risk of progressing to EAC. We found that serum miRNAs have a limited ability to distinguish between disease states, thus limiting their potential utility in early disease detection.

Titanium Dioxide Nanoparticles Elicit Lower Direct Inhibitory Effect on Human Gut Microbiota Than Silver Nanoparticles.

Due to continued technological development, people increasingly come in contact with engineered nanomaterials (ENMs) that are now used in foods and many industrial applications. Many ENMs have historically been shown to possess antimicrobial properties, which has sparked concern for how dietary nanomaterials impact gastrointestinal health via microbial dysbiosis. We employed an in vitro Human Gut Simulator system to examine interactions of dietary nano titanium dioxide (TiO2) with human gut microbiota. Electron microscopy indicated a close association of TiO2 particles with bacterial cells. Addition of TiO2 to microbial communities led to a modest reduction in community density but had no impact on community diversity and evenness. In contrast, administration of known antimicrobial silver nanoparticles (NPs) in a control experiment resulted in a drastic reduction of population density. In both cases, communities recovered once the addition of nanomaterials was ceased. Constrained ordination analysis of community profiles revealed that simulated colonic region was the primary determinant of microbiota composition. Accordingly, predicted community functional capacity and measured production of short-chain fatty acids were not changed significantly upon microbiota exposure to TiO2. We conclude that tested TiO2 NPs have limited direct effect on human gut microbiota.

Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota.

Coffee is one of the most consumed beverages and has been linked to health in different studies. However, green and roasted coffees have different chemical composition and therefore their health properties might differ as well. Here, we study the effect of in vitro digestion-fermentation on the antioxidant capacity, phenolic profile, production of short-chain fatty acids (SCFAs), and gut microbiota community structure of green and roasted coffee brews. Roasted coffees showed higher antioxidant capacity than green coffees, with the highest level achieved in fermented samples. Polyphenol profile was similar between green and roasted coffees in regular coffee brews and the digested fraction, but very different after fermentation. Production of SCFAs was higher after fermentation of green coffee brews. Fermentation of coffee brews by human gut microbiota led to different community structure between green and roasted coffees. All these data suggest that green and roasted coffees behave as different types of food.

Dietary Fatty Acids Sustain the Growth of the Human Gut Microbiota.

While a substantial amount of dietary fats escape absorption in the human small intestine and reach the colon, the ability of resident microbiota to utilize these dietary fats for growth has not been investigated in detail. In this study, we used an in vitro multivessel simulator system of the human colon to reveal that the human gut microbiota is able to utilize typically consumed dietary fatty acids to sustain growth. Gut microbiota adapted quickly to a macronutrient switch from a balanced Western diet-type medium to its variant lacking carbohydrates and proteins. We defined specific genera that increased in their abundances on the fats-only medium, including Alistipes, Bilophila, and several genera of the class Gammaproteobacteria In contrast, the abundances of well-known glycan and protein degraders, including Bacteroides, Clostridium, and Roseburia spp., were reduced under such conditions. The predicted prevalences of microbial genes coding for fatty acid degradation enzymes and anaerobic respiratory reductases were significantly increased in the fats-only environment, whereas the abundance of glycan degradation genes was diminished. These changes also resulted in lower microbial production of short-chain fatty acids and antioxidants. Our findings provide justification for the previously observed alterations in gut microbiota observed in human and animal studies of high-fat diets.IMPORTANCE Increased intake of fats in many developed countries has raised awareness of potentially harmful and beneficial effects of high fat consumption on human health. Some dietary fats escape digestion in the small intestine and reach the colon where they can be metabolized by gut microbiota. We show that human gut microbes are able to maintain a complex community when supplied with dietary fatty acids as the only nutrient and carbon sources. Such fatty acid-based growth leads to lower production of short-chain fatty acids and antioxidants by community members, which potentially have negative health consequences on the host.

Intestinal Epithelial Cells Regulate Gut Eotaxin Responses and Severity of Allergy.

Intestinal epithelial cells (IECs) are known to regulate allergic sensitization. We addressed the role of the intrinsic IKKß signaling in IECs in the effector phase of allergy following oral allergen challenge and its impact on the severity of responses is poorly. Upon orally sensitization by co-administration of ovalbumin with cholera toxin as adjuvant, wild-type and mice lacking IKKß in IECs (IKKßΔIEC mice) developed similar levels of serum IgE and allergen-specific secretory IgA in the gut. However, subsequent allergen challenges in the gut promoted allergic lower responses in KKßΔIEC mice. Analysis of cytokines and chemokines in serum and gut tissues after oral allergen challenge revealed impaired eotaxin responses in IKKßΔIEC mice, which correlated with lower frequencies of eosinophils in the gut lamina propria. We also determined that IECs were a major source of eotaxin and that impaired eotaxin production was due to the lack of IKKß signaling in IECs. Oral administration of CCL11 to IKKßΔIEC mice during oral allergen challenge enhanced allergic responses to levels in wild-type mice, confirming the role of IEC-derived eotaxin as regulator of the effector phase of allergy following allergen challenge. Our results identified targeting IEC-derived eotaxin as potential strategy to limit the severity of allergic responses to food antigens.

Effects of oral Akkermansia muciniphila supplementation in healthy dogs following antimicrobial administration.

OBJECTIVE To measure effects of oral Akkermansia muciniphila administration on systemic markers of gastrointestinal permeability and epithelial damage following antimicrobial administration in dogs. ANIMALS 8 healthy adult dogs. PROCEDURES Dogs were randomly assigned to receive either A muciniphila (109 cells/kg; n = 4) or vehicle (PBS solution; 4) for 6 days following metronidazole administration (12.5 mg/kg, PO, q 12 h for 7 d). After a 20-day washout period, the same dogs received the alternate treatment. After another washout period, experiments were repeated with amoxicillin-clavulanate (13.5 mg/kg, PO, q 12 h) instead of metronidazole. Fecal consistency was scored, a quantitative real-time PCR assay for A muciniphila in feces was performed, and plasma concentrations of cytokeratin-18, lipopolysaccharide, and glucagon-like peptides were measured by ELISA before (T0) and after (T1) antimicrobial administration and after administration of A muciniphila or vehicle (T2). RESULTS A muciniphila was detected in feces in 7 of 8 dogs after A muciniphila treatment at T2 (3/4 experiments) but not at T0 or T1. After metronidazole administration, mean change in plasma cytokeratin-18 concentration from T1 to T2 was significantly lower with vehicle than with A muciniphila treatment (-0.27 vs 2.4 ng/mL). Mean cytokeratin-18 concentration was lower at T1 than at T0 with amoxicillin-clavulanate. No other significant biomarker concentration changes were detected. Probiotic administration was not associated with changes in fecal scores. No adverse effects were attributed to A muciniphila treatment. CONCLUSIONS AND CLINICAL RELEVANCE Detection of A muciniphila in feces suggested successful gastrointestinal transit following oral supplementation in dogs. Plasma cytokeratin-18 alterations suggested an effect on gastrointestinal epithelium. Further study is needed to investigate effects in dogs with naturally occurring gastrointestinal disease.

Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline.

Advances in high-throughput sequencing have enabled profiling of microRNAs (miRNAs), however, a consensus pipeline for sequencing of small RNAs has not been established. We built and optimized an analysis pipeline using Partek Flow, circumventing the need for analyzing data via scripting languages. Our analysis assessed the effect of alignment reference, normalization method, and statistical model choice on biological data. The pipeline was evaluated using sequencing data from HaCaT cells transfected with either a non-silencing control or siRNA against ΔNp63α, a p53 family member protein which is highly expressed in non-melanoma skin cancer and shown to regulate a number of miRNAs. We posit that 1) alignment and quantification to the miRBase reference provides the most robust quantitation of miRNAs, 2) normalizing sample reads via Trimmed Mean of M-values is the most robust method for accurate downstream analyses, and 3) use of the lognormal with shrinkage statistical model effectively identifies differentially expressed miRNAs. Using our pipeline, we identified previously unrecognized regulation of miRs-149-5p, 18a-5p, 19b-1-5p, 20a-5p, 590-5p, 744-5p and 93-5p by ΔNp63α. Regulation of these miRNAs was validated by RT-qPCR, substantiating our small RNA-Seq pipeline. Further analysis of these miRNAs may provide insight into ΔNp63α's role in cancer progression. By defining the optimal alignment reference, normalization method, and statistical model for analysis of miRNA sequencing data, we have established an analysis pipeline that may be carried out in Partek Flow or at the command line. In this manner, our pipeline circumvents some of the major hurdles encountered during small RNA-Seq analysis.

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome.

BACKGROUND: We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy age-matched controls. Here we explored whether observed fecal microbiota and metabolite differences between these two adolescent populations can be used to discriminate between IBS and health. FINDINGS: We constructed individual microbiota- and metabolite-based sample classification models based on the partial least squares multivariate analysis and then applied a Bayesian approach to integrate individual models into a single classifier. The resulting combined classification achieved 84 % accuracy of correct sample group assignment and 86 % prediction for IBS-D in cross-validation tests. The performance of the cumulative classification model was further validated by the de novo analysis of stool samples from a small independent IBS-D cohort. CONCLUSION: High-throughput microbial and metabolite profiling of subject stool samples can be used to facilitate IBS diagnosis.

Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease.

Obesity is becoming the new pediatric epidemic. Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity and has become the most common cause of pediatric liver disease. The gut microbiome is the major metabolic organ and determines how calories are processed, serving as a caloric gate and contributing towards the pathogenesis of NAFLD. The goal of this study is to examine gut microbial profiles in children with NAFLD using phylogenetic, metabolomic, metagenomic and proteomic approaches. Fecal samples were obtained from obese children with or without NAFLD and healthy lean children. Stool specimens were subjected to 16S rRNA gene microarray, shotgun sequencing, mass spectroscopy for proteomics and NMR spectroscopy for metabolite analysis. Children with NAFLD had more abundant Gammaproteobacteria and Prevotella and significantly higher levels of ethanol, with differential effects on short chain fatty acids. This group also had increased genomic and protein abundance for energy production with a reduction in carbohydrate and amino acid metabolism and urea cycle and urea transport systems. The metaproteome and metagenome showed similar findings. The gut microbiome in pediatric NAFLD is distinct from lean healthy children with more alcohol production and pathways allocated to energy metabolism over carbohydrate and amino acid metabolism, which would contribute to development of disease.

The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome.

The goal of this study was to determine if fecal metabolite and microbiota profiles can serve as biomarkers of human intestinal diseases, and to uncover possible gut microbe-metabolite associations. We employed proton nuclear magnetic resonance to measure fecal metabolites of healthy children and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS-D). Metabolite levels were associated with fecal microbial abundances. Using several ordination techniques, healthy and irritable bowel syndrome (IBS) samples could be distinguished based on the metabolite profiles of fecal samples, and such partitioning was congruent with the microbiota-based sample separation. Measurements of individual metabolites indicated that the intestinal environment in IBS-D was characterized by increased proteolysis, incomplete anaerobic fermentation and possible change in methane production. By correlating metabolite levels with abundances of microbial genera, a number of statistically significant metabolite-genus associations were detected in stools of healthy children. No such associations were evident for IBS children. This finding complemented the previously observed reduction in the number of microbe-microbe associations in the distal gut of the same cohort of IBS-D children.

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation.

BACKGROUND: Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, particularly recurrent form of CDI, is through transplantation of fecal microbiota from a healthy donor to the infected patient. In this study we investigated the distal gut microbial communities of three CDI patients before and after fecal microbiota transplantation, and we compared these communities to the composition of the donor's fecal microbiota. We utilized phylogenetic Microbiota Array, high-throughput Illumina sequencing, and fluorescent in situ hybridization to profile microbiota composition down to the genus and species level resolution. RESULTS: The original patients' microbiota had low diversity, was dominated by members of Gammaproteobacteria and Bacilli, and had low numbers of Clostridia and Bacteroidia. At the genus level, fecal samples of CDI patients were rich in members of the Lactobacillus, Streptococcus, and Enterobacter genera. In comparison, the donor community was dominated by Clostridia and had significantly higher diversity and evenness. The patients' distal gut communities were completely transformed within 3 days following fecal transplantation, and these communities remained stable in each patient for at least 4 months. Despite compositional differences among recipients' pre-treatment gut microbiota, the transplanted gut communities were highly similar among recipients post-transplantation, were indistinguishable from that of the donor, and were rich in members of Blautia, Coprococcus, and Faecalibacterium. In each case, the gut microbiota restoration led to a complete patient recovery and symptom alleviation. CONCLUSION: We conclude that C. difficile infection can be successfully treated by fecal microbiota transplantation and that this leads to stable transformation of the distal gut microbial community from the one abundant in aerotolerant species to that dominated by members of the Clostridia.

Excess body weight during pregnancy and offspring obesity: potential mechanisms.

The rates of child and adult obesity have increased in most developed countries over the past several decades. The health consequences of obesity affect both physical and mental health, and the excess body weight can be linked to an elevated risk for developing type 2 diabetes, cardiovascular problems, and depression. Among the factors that can influence the development of obesity are higher infant weights and increased weight gain, which are associated with higher risk for excess body weight later in life. In turn, mother's excess body weight during and after pregnancy can be linked to the risk for offspring overweight and obesity through dietary habits, mode of delivery and feeding, breast milk composition, and through the influence on infant gut microbiota. This review considers current knowledge of these potential mechanisms that threaten to create an intergenerational cycle of obesity.

Do gut microbial communities differ in pediatric IBS and health?

Human gastrointestinal microbial communities are recognized as important determinants of the host health and disease status. We have recently examined the distal gut microbiota of two groups of children: healthy adolescents and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS). We have revealed the common core of phylotypes shared among all children, identified genera differentially abundant between two groups and surveyed possible relationships among intestinal microbial genera and phylotypes. In this article we explored the use of supervised and unsupervised ordination and classification methods to separate and classify child fecal samples based on their quantitative microbial profile. We observed sample separation according to the participant health status, and this separation could often be attributed to the abundance levels of several specific microbial genera. We also extended our original correlation network analysis of the relative abundances of bacterial genera across samples and determined possible association networks separately for healthy and IBS groups. Interestingly, the number of significant genus abundance associations was drastically lower among the IBS samples, which can potentially be attributed to the existence of multiple routes to microbiota disbalance in IBS or to the loss of microbial interactions during IBS development.

Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea.

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections in humans. The majority of urinary infections develop via ascending route through the urethra, where bacterial cells come in contact with human urine prior to reaching the bladder or kidneys. Since urine contains significant amounts of inorganic ions and urea, it imposes osmotic and denaturing stresses on bacterial cells. In this study, we determined the transcriptional adaptive responses of UPEC strain CFT073 to the presence of 0.3 M NaCl or 0.6 M urea in the growth medium. The cell responses to these two osmolytes were drastically different. Although most of the genes of the osmotically inducible regulon were overexpressed in medium with salt, urea failed to stimulate osmotic stress response. At the same time, UPEC colonization genes encoding type 1 and F1C fimbriae and capsule biosynthesis were transcriptionally induced in the presence of urea but did not respond to increased salt concentration. We speculate that urea can potentially be sensed by uropathogenic bacteria to initiate infection program. In addition, several molecular chaperone genes were overexpressed in the presence of urea, whereas adding NaCl to the medium led to an upregulation of a number of anaerobic metabolism pathways.

Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome.

OBJECTIVES: Human intestinal microbiota has a number of important roles in human health and is also implicated in several gastrointestinal disorders. The goal of this study was to determine the gut microbiota in two groups of pre- and adolescent children: healthy volunteers and children diagnosed with diarrhea predominant irritable bowel syndrome (IBS-D). METHODS: Phylogenetic Microbiota Array was used to obtain quantitative measurements of bacterial presence and abundance in subjects ' fecal samples. We utilized high-throughput DNA sequencing, quantitative PCR, and fluorescent in situ hybridization to confirm microarray findings. RESULTS: Both sample groups were dominated by the phyla Firmicutes, Bacteroidetes, and Actinobacteria, which cumulatively constituted 91 % of overall sample composition on average. A core microbiome shared among analyzed samples encompassed 55 bacterial phylotypes dominated by genus Ruminococcus ; members of genera Clostridium , Faecalibacterium, Roseburia, Streptococcus , and Bacteroides were also present. Several genera were found to be differentially abundant in the gut of healthy and IBS groups: levels of Veillonella , Prevotella , Lactobacillus , and Parasporo bacterium were increased in children diagnosed with IBS, whereas members of Bifidobacterium and Verrucomicrobium were less abundant in those individuals. By calculating a nonparametric correlation matrix among abundances of different genera in all samples, we also examined potential associations among intestinal microbes. Strong positive correlations were found between abundances of Veillonella and both Haemophilus and Streptococcus , between Anaerovorax and Verrucomicrobium , and between Tannerella and Anaerophaga . CONCLUSIONS: Although at the higher taxonomical level gut microbiota was similar between healthy and IBS-D children, specific differences in the abundances of several bacterial genera were revealed. Core microbiome in children was dominated by Clostridia. Putative relationships identified among microbial genera provide testable hypotheses of cross-species associations among members of human gut microbiota