Fecal Bacterial Diversity Research Articles

Bacillus-Based Probiotic Treatment Modified Bacteriobiome Diversity in Duck Feces

The intestinal health of poultry is of great importance for birds’ growth and development; probiotics-driven shifts in gut microbiome can exert considerable indirect effect on birds’ welfare and production performance. The information about gut microbiota of ducks is scarce; by using high throughput metagenomic sequencing with Illumina Miseq we examined fecal bacterial diversity of Peking ducks grown on conventional and Bacillus-probiotic-enriched feed. The probiotic supplementation drastically decreased the presence of the opportunistic pathogen Escherichia/Shigella, which was the major and sole common dominant in all samples. Seventy other bacterial species in the ducks’ fecal assemblages were found to have probiotic-related differences, which were interpreted as beneficial for ducks’ health as was confirmed by the increased production performance of the probiotic-fed ducks. Bacterial α-biodiversity indices increased in the probiotic-fed group. The presented inventory of the duck fecal bacteriobiome can be very useful for the global meta-analysis of similar data in order to gain a better insight into bacterial functioning and interactions with other gut microbiota to improve poultry health, welfare and production performance.

Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador.

Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with ADD, supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.

Experimental crossover study on the effects of withholding feed for 24\u2009h on the equine faecal bacterial microbiota in healthy mares

BackgroundAn association between equine gastrointestinal disease causing colic signs and changes in faecal bacterial microbiota has been identified. The reasons for these changes and their clinical relevance has not been investigated. Withholding feed, which is an integral part of managing horses with colic, may contribute to the observed changes in the microbiota and impact interpretation of findings in horses with colic. Study objectives were, therefore, to determine the effect of withholding feed for 24 h on equine faecal bacterial microbiota in healthy mares to differentiate the effects of withholding feed from the changes potentially associated with the disease.ResultsSpecies richness and Shannon diversity (alpha diversity) were significantly lower at the late withheld (10–24 h post withholding feed) and early refed (2–12 h post re-feeding) time points compared to samples from fed horses (P < 0.01). Restoration of species richness and diversity began to occur at the late refed (18–24 h post re-feeding) time points. Horses having feed withheld had a distinct bacterial population compared to fed horses (beta diversity). Bacteroidetes BS11 and Firmicutes Christensenellaceae, Christensenella, and Dehalobacteriaceae were significantly increased in horses withheld from feed primarily during the late withheld and early refed time points. Bacteroidetes Marinilabiaceae and Prevotellaceae, Firmicutes Veillonellaceae, Anaerovibrio, and Bulleidia, and Proteobacteria GMD14H09 were significantly decreased in horses with feed withheld at late withheld, early refed, and late refed time periods (P < 0.01). Changes in commensal gut microbiota were not significant between groups.ConclusionsWithholding feed has a significant effect on faecal bacterial microbiota diversity and composition particularly following at least 10 h of withholding feed and should be taken into consideration when interpreting data on the equine faecal bacterial microbiota in horses.

88 Effects of Saccharomyces cerevisiae fermentation product on microbiota populations of dogs subjected to travel stress

Abstract Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and function of circulating immune cells in adult dogs. The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of dogs subjected to travel stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (mean age: 7.1 y; mean BCS: 4.9) were used. Dogs were randomly assigned to control or SCFP-supplemented (250 mg/day) diets and fed for a few months prior to a travel stress challenge. Fresh fecal samples were collected for the measurement of fecal characteristics, microbiota, and metabolites before and after travel stress. Fecal microbiota data were evaluated using QIIME2. All other data were analyzed using the Mixed Models procedure of SAS, with P &amp;lt; 0.05 considered statistically significant. There were no differences between treatments on fecal characteristics, metabolites, and bacterial alpha and beta diversity measures. However, fecal Turicibacter increased in dogs fed SCFP (0.8% to 1.2%, P = 0.03), but decreased in dogs fed control (1.2% to 0.7%, P = 0.03). Fecal Prevotella (5% to 7%, P = 0.004), Oscillospira (0.07% to 0.1%, P = 0.004) and Sutterella (3% to 4%, P = 0.01) increased after travel stress in dogs fed control. In contrast, fecal Clostridium (11% to 15%, P = 0.01), Faecalibacterium (6% to 8%, P = 0.003), and Allobaculum (1% to 2%, P = 0.02) increased and fecal Phascolarctobacterium (1.4% to 1.1%, P = 0.001) decreased after travel stress in dogs fed SCFP. Our data demonstrate that both travel stress and SCFP alter fecal microbiota in dogs.

The pathophysiology of bile acid diarrhoea: differences in the colonic microbiome, metabolome and bile acids

Bile acid diarrhoea (BAD) is a common disorder resulting from increased loss of bile acids (BAs), overlapping irritable bowel syndrome with diarrhoea (IBS-D). The gut microbiota metabolises primary BAs to secondary BAs, with differing impacts on metabolism and homeostasis. The aim of this study was to profile the microbiome, metabolic products and bile acids in BAD. Patients with BAD diagnosed by SeHCAT testing, were compared with other IBS-D patients, and healthy controls. Faecal 16S ribosomal RNA gene analysis was undertaken. Faecal short chain fatty acid (SCFA) and urinary volatile organic compounds (VOCs) were measured. BAs were quantified in serum and faeces. Faecal bacterial diversity was significantly reduced in patients with BAD. Several taxa were enriched compared to IBS-D. SCFA amounts differed in BAD, controls and IBS-D, with significantly more propionate in BAD. Separation of VOC profiles was evident, but the greatest discrimination was between IBS-D and controls. Unconjugated and primary BA in serum and faeces were significantly higher in BAD. The faecal percentage primary BA was inversely related to SeHCAT. BAD produces dysbiosis, with metabolite differences, including VOC, SCFA and primary BAs when compared to IBS-D. These findings provide new mechanistic insights into the pathophysiology of BAD.

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations.

Simple SummaryHigh-producing dairy cows receive high-energy diets for maintenance and production. This study showed that 60% concentrate in the diet, containing 27.7% starch, changed the fecal-microbial community and lowered its diversity, suggesting hindgut dysbiosis. Both ruminal and fecal pH decreased with high-starch feeding, which suggests further investigations in fecal pH as rumen- and hindgut-acidosis diagnostic tool. Cows in the third lactation spent more time below the threshold for subacute-ruminal acidosis (pH 6.0) than second or fourth-or-below lactation cows. Their higher susceptibility was caused by their high dry matter intake but missing counter-regulation by increased rumination activity. Further, we suggest that body weight and rumen size might play a role in the absorptive capacity of short-chain fatty acids. The study also identified indicator-bacterial phylotypes that changed with starch-rich diet and lactation number. In conclusion, we suggest including lactation number as a factor in practical feeding management for identification of high risk-cows for acidosis, and in dairy cow research.Starch-rich diets can cause subacute ruminal acidosis (SARA) in dairy cows with potentially different susceptibility according to lactation number. We wanted to evaluate the bacterial community and the fermentation end products in feces to study susceptibility to hindgut acidosis and dysbiosis. Sixteen dairy cows received a medium-concentrate diet (MC, 40% concentrate, 18.8% starch) for one week and a high-concentrate diet (HC, 60% concentrate, 27.7% starch, DM) for four weeks. Milk yield, dry-matter intake, chewing activity, ruminal pH, milk constituents, and fecal samples for short-chain fatty acids (SCFA), pH, and 16S rRNA-gene sequencing were investigated. The HC feeding caused a reduction in fecal pH, bacterial diversity and richness, an increase in total SCFA, and a separate phylogenetic clustering of MC and HC samples. Ruminal and fecal pH had fair correlation (r = 0.5). Cows in the second lactation (2ndL) had lower dry matter intake (DMI) than cows of third or fourth or more lactations (3rdL; ≥4 L), whereas DMI/kg body weight was lower for ≥4 L than for 2ndL and 3rdL cows. The mean ruminal pH was highest in ≥4 L, whereas the time spent below the SARA threshold was highest for 3rdL cows. The latter also had higher total SCFA in the feces. Our results suggest that hindgut dysbiosis is caused by increased substrate flow to the hindgut, but further investigations are needed to define hindgut acidosis. The 3rdL cows were most susceptible to rumen acidosis and hindgut dysbiosis due to high DMI level, but missing counter regulations, as suggested happening in 2ndL and ≥4 L cows.

Relationship between Rainfall, Fecal Pollution, Antimicrobial Resistance, and Microbial Diversity in an Urbanized Subtropical Bay.

Urbanized bays are vulnerable to fecal bacterial pollution, and the extent of this pollution, in marine recreational waters, is commonly assessed by quantifying enterococcus concentrations. Recent reports have questioned the utility of enterococci as an indicator of fecal bacterial pollution in subtropical bays impaired by non-point source pollution, and enterococcus data alone cannot identify fecal bacterial sources (i.e., hosts). The purpose of this study was to assess relationships between rainfall, fecal bacterial pollution, antimicrobial resistance, and microbial diversity in an urbanized subtropical bay. Thus, a comprehensive bacterial source tracking (BST) study was conducted using a combination of traditional and modern BST methods. Findings show that rainfall was directly correlated with elevated enterococcus concentrations, including the increased prevalence of Enterococcus faecium, although it was not correlated with an increase in the prevalence of antimicrobial-resistant strains. Rainfall was also correlated with decreased microbial diversity. In contrast, neither rainfall nor enterococcus concentrations were directly correlated with the concentrations of three omnipresent host-associated fecal markers (i.e., human, canine, and gull). Notably, the human fecal marker (HF183) was inversely correlated with enterococcus concentrations, signifying that traditional enterococcus data alone are not an accurate proxy for human fecal waste in urbanized subtropical bays.IMPORTANCE The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Human Milk Feeding Patterns at 6 Months of Age are a Major Determinant of Fecal Bacterial Diversity in Infants.

Maternal pre-pregnancy obesity and human milk feeding have been associated with altered infant gut microbiota. Determine the relationships between maternal pre-pregnancy BMI, human milk exposure, and their influence on the infant microbiota simultaneously. This was a cross-sectional study of infants at 6 months of age (N = 36), a time when many infants are fed a mixed diet of human milk and other foods. Fecal samples and participant information were collected from a subset of dyads enrolled in two related prospective cohorts (ARCHGUT and BABYGUT) in Michigan. Sequencing the V4 region of the 16S gene was used to analyze fecal bacterial samples collected from 6-month-old infants. Participants were grouped into four categories designated by their extent of human milk exposure (100%, 80%, 50%-80%, ≤ 20% human milk in the infant diet) and by maternal pre-pregnancy BMI category (normal, overweight, obese). Fewer participants with pre-pregnancy obesity were breastfeeding at 6 months postpartum compared to non-obese participants (35.7% and 81.8%, respectively). In univariate analyses, maternal pre-pregnancy BMI and human milk exposure were both significantly associated with alpha and beta diversity of the infant microbiota. However, in multivariate analyses, human milk exposure accounted for 20% of the variation in alpha diversity, but pre-pregnancy BMI was not significantly associated with any form of microbiota diversity. The proportion of the infant diet that was human milk at 6 months was the major determinant of alpha and beta diversity of the infant. Maternal obesity contributes to the gut microbiota by its association with the extent of human milk feeding.

Effects of trace mineral supply from rumen boluses on performance, carcass characteristics, and fecal bacterial profile in beef cattle

The experiment was conducted to evaluate trace mineral supplies of copper (Cu), cobalt (Co), selenium (Se), and iodine (I) using rumen boluses (a slow-release leaching technology) on performance, carcass characteristics, and fecal bacterial profile in beef cattle. Total 36 beef Angus steers were used in a completely randomized block design and received a diet without supplementation of Cu, Co, Se, and I (NCON), a diet supplemented with Cu, Co, Se, and I (PCON), or the NCON diet with rumen boluses providing Cu, Co, Se, and I (Bolus). The experiment consisted of 8 weeks of a backgrounding, 4 weeks of a transitioning, and 12 weeks of a finishing phase. Data collected from the experiment were dry matter intake (DMI), average daily gain (ADG), feed efficiency (gain to DMI, kg/kg), and carcass data from individual animals. In the last week of the backgrounding and finishing phase, fecal samples were collected from individual animals and fecal bacterial diversity was determined. All data were analyzed using the MIXED procedure of SAS. No difference in DMI and growth performance among treatments was observed during the backgrounding phase. Interactions of treatments by week for DMI (P < 0.01) and ADG (P = 0.09) were observed during the finishing phase where DMI and ADG were greater for PCON and Bolus compared with NCON during the first 6 weeks of the finishing phase. Carcass characteristics did not differ among treatments except that Bolus had higher quality grade (P = 0.036) compared with NCON and PCON. During the backgrounding phase, the relative abundance of Bifidobacterium was greater (P = 0.026) for Bolus vs. NCON and PCON and that of Treponema was greater (P = 0.01) for PCON vs. NCON and Bolus. During the finishing phase, the ratio of Firmicutes to Bacteroidetes was lower (P = 0.032) for PCON compared with NCON and Bolus without a difference between NCON and Bolus. However, those changes in bacterial diversity during the backgrounding and finishing phases did not influence performance and carcass characteristics of beef steers. In conclusion, trace minerals of Cu, Co, Se, and I need to be provided to meet or exceed the requirements for optimal performance especially during a finishing phase and the trace mineral supply via rumen boluses may have potential to improve a carcass quality grade. In addition, fecal bacterial diversity was altered by trace mineral supply and the method of the supply.

Evaluation of fecal fermentation profile and bacterial community in organically fed dairy cows consuming forage-rich diets with different particle sizes

Organic cattle farming encourages the use of forage-rich diets, and the reduction of particle size has been suggested as an approach to improve forage utilization and enhance nutrient intake of cows. However, reducing forage particle size increases passage rate, as well as the flow of potentially fermentable nutrients out of the rumen, and the consequences for hindgut fermentation have not been evaluated yet. This study evaluated the effects of decreasing dietary forage particle size on the fecal short-chain fatty acid (SCFA) profile and the bacterial community structure of dairy cows fed forage-based rations. Twenty-one organically fed lactating Holstein cows (4 primiparous and 17 multiparous; mean and standard deviation 703 ± 65 kg body weight, 135 ± 104 days in milk) were divided into 2 groups and fed 1 of 2 diets for 34 d. Diets contained 20% concentrate and 80% forage (dry matter basis), and were fed either as a control with a forage geometric mean particle size of 52 mm (CON; 11 cows) or as a diet with the forage particle size reduced to a geometric mean size of 7 mm (RED; 10 cows). Fecal samples were collected at the end of the experiment, and samples were immediately frozen at -20°C. Samples were analyzed for SCFA, and the fecal bacterial community was evaluated using 16S rRNA sequencing. Data showed that the concentration of total SCFA was not affected by treatment, but the proportion of propionate, a key glucogenic precursor in cattle, tended to be greater for RED (13.3 and 13.8 ± 0.1%, respectively). The predominant bacterial phyla, including Firmicutes (58.0 ± 0.7%), Bacteroidetes (26.9 ± 0.4%), and Verrucomicrobia (4.0 ± 0.4%), were not affected by forage particle size. Family Lachnospiraceae increased in relative abundance when the RED diet was fed (12.1 and 13.9 ± 0.5% for CON and RED, respectively), and genera Acetitomaculum (1.1 and 1.8 ± 0.2%), Turicibacter (0.7 and 0.9 ± 0.1%), and Ruminobacter (0.1 and 0.4 ± 0.1%) increased in relative abundance when RED was fed. In addition, relative abundance of some fecal bacterial taxa was correlated with major fecal SCFA and pH. Reducing the particle size of forages, from 52 to 7 mm geometric mean particle size, maintained fecal concentration of total SCFA and tended to enhance propionate concentration, without risk of dysbiosis. Thus, results suggest that reduction of forage particle size represents an effective approach to optimizing forage utilization while maintaining hindgut fermentation and fecal bacterial diversity in dairy cows fed forage-rich diets.

Review article: bugs, inflammation and mood-a microbiota-based approach to psychiatric symptoms in inflammatory bowel diseases.

Psychiatric co-morbidities including depression and anxiety are common in inflammatory bowel diseases (IBD). Emerging evidence suggests that interactions between the gut microbiota and brain may play a role in the pathogenesis of psychiatric symptoms in IBD. To review the literature on microbiota-brain-gut interactions in gut inflammation, psychosocial stress and mental disorders and to discuss the putative mediating role of gut microbiota in the development of psychiatric symptoms or co-morbidities in IBD. A literature search was conducted on Ovid and Pubmed to select relevant animal and human studies reporting an association between IBD, mental disorders and gut microbiota. Gut microbial alterations are frequently reported in subjects with IBD and with mental disorders. Both have been associated with reduced faecal bacterial diversity, decreased taxa within the phylum Firmicutes and increased Gammaproteobacteria. In animal studies, microbial perturbations induce behavioural changes and modulate inflammation in mice. Anxiety- and depression-like behaviours in animals can be transferred via faecal microbiota. In humans, modulation of the gut microbiota with probiotics is associated with behavioural and mood changes. Recent data show correlations in changes of faecal and mucosal microbiota and psychological distress in patients with IBD independent of disease activity. Both IBD and mental disorders are associated with gut microbial alterations. Preclinical and preliminary human studies have shown a mediating role of the gut microbiota in intestinal inflammation and anxiety, depression and stress. Targeting the gut microbiota may represent a useful therapeutic approach for the treatment of psychiatric co-morbidities in IBD.

Gut fungal dysbiosis and altered bacterial-fungal interaction in patients with diarrhea-predominant irritable bowel syndrome: An explorative study.

Little is known about intestinal fungi in IBS patients whose gut bacteria have been investigated a lot. In order to explore causal relationship between IBS and gut mycobiome, and use gut fungi to diagnose or even treat IBS, further characterization of it in IBS is required. Fifty-five diarrhea-predominant IBS (D-IBS) patients fulfilling Rome III criteria, and 16 healthy controls (HC) were recruited. Fresh fecal samples were collected and used for 16s rRNA and ITS2 high-throughput sequencing. Diversity and composition of gut bacteria and fungi, as well as bacterial-fungal interactions in D-IBS patients, were characterized. Specific fungal taxa differentiating D-IBS from HC were recognized by LEfSe and RandomForest methods, and their association with clinical symptoms was assessed by Spearman's correlation. Diarrhea-predominant irritable bowel syndrome patients showed abnormal (IBS-dysbiosis) or normal (HC-like IBS) fecal bacterial structure and diversity compared with healthy controls. However, fecal fungal signatures differed absolutely between D-IBS and HC, which indicated a more susceptible alteration of gut fungi than bacteria in D-IBS. Fecal fungi showed significant correlations with IBS symptoms, especially Mycosphaerella, Aspergillus, Sporidiobolus, and Pandora which were identified to potentially differentiate D-IBS from HC. Moreover, compared with HC there were markedly declined bacterial-fungal interactions in D-IBS, in which Candida changed from negative to positive correlations with bacteria, and Eurotium changed from positive correlations to irrelevance, while Debaryomyces gained negative correlations with bacteria. Gut fungal dysbiosis and altered bacterial-fungal interactions were present in patients with D-IBS, and gut fungi could be used to diagnose D-IBS.

A New Rat Model of Pouchitis After Proctocolectomy and Ileal Pouch-Anal Anastomosis Using 2,4,6-Trinitrobenzene Sulfonic Acid

BackgroundPouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) in patients with ulcerative colitis. However, an ideal model remains lacking. Therefore, we aimed to establish an appropriate model resembling human pouchitis. MethodsSprague-Dawley rats were randomly assigned to five groups: TNBS group, DSS group, NS group (following IPAA procedure, administrated with TNBS enema, DSS orally, normal saline enema, respectively), NI group (underwent IPAA), and sham group (underwent switch abdominal surgery). General status, weight change, hematochezia, and fecal scores were recorded. Fecal microbiota were counted under a microscope and analyzed by 16S rRNA gene high-throughput sequencing. Specimens of ileal pouch and small intestine (proximal, mid, distal) were collected to evaluate myeloperoxidase and occludin expression by immunohistochemistry and mRNA expression of pro-inflammatory markers by PCR. ResultsGeneral status, hematochezia, fecal score, and increased mRNA expression of interleukin-6 and TNF-α in the TNBS group were similar to those in the DSS group, whereas the TNBS-induced model displayed a more stable weight change and more serious dysbacteriosis, not only was fecal bacterial diversity reduced, the dominant microbiota was altered. Histopathology scores of the distal small intestine in the TNBS group were lower compared with those in the DSS group (P < 0.05). A significant difference in myeloperoxidase and occludin expression in the small intestine was also detected between the TNBS and DSS groups. ConclusionsOur model mimicked the characteristics of human pouchitis and avoided potential side effects in the small intestine, and thus could be employed for further research.

The equine gastrointestinal microbiome: impacts of weight-loss

BackgroundObesity is an important equine welfare issue. Whilst dietary restriction is the most effective weight-loss tool, individual animals range in their weight-loss propensity. Gastrointestinal-derived bacteria play a fundamental role in host-health and have been associated with obesity and weight-loss in other species. This study evaluated the faecal microbiome (next-generation sequencing of 16S rRNA genes) of 15 obese Welsh Mountain pony mares, in the same 11-week period across 2 years (n = 8 Year 1; n = 7 Year 2). Following a 4-week acclimation period (pre-diet phase) during which time individuals were fed the same hay to maintenance (2% body mass (BM) as daily dry matter (DM) intake), animals underwent a 7-week period of dietary restriction (1% BM hay as daily DM intake). Faeces were sampled on the final 3 days of the pre-diet phase and the final 3 days of the dietary restriction phase. Bacterial communities were determined using Next Generation Sequencing of amplified V1-V2 hypervariable regions of bacterial 16S rRNA.ResultsLosses in body mass ranged from 7.11 to 11.59%. Changes in the faecal microbiome composition following weight-loss included a reduction in the relative abundance of Firmicutes and Tenericutes and a reduction in indices of bacterial diversity. Pre-diet diversity was negatively associated with weight-loss. Pre-diet faecal acetate concentration was a strong predictor of subsequent weight-loss and negatively associated with Sphaerochaeta (Spirochaetes phylum) abundance. When animals were divided into 3 groups (high, mid, low) based overall weight loss, pre-diet bacterial community structure was found to have the greatest divergence between the high and low weight-loss groups (R = 0.67, p < 0.01), following PERMANOVA and ANOSIM analysis.ConclusionsWeight-loss in this group of ponies was associated with lower pre-diet faecal bacterial diversity and greater pre-diet acetate concentration. Overall, these data support a role for the faecal microbiome in weight-loss propensity in ponies and provide a baseline for research evaluating elements of the faecal microbiome in predicting weight-loss success in larger cohorts.

Influence of Exercise on the Human Gut Microbiota of Healthy Adults: A Systematic Review

OBJECTIVES:To summarize the literature on the influence of exercise on the gut microbiota of healthy adults.METHODS:A systematic and comprehensive search in electronic database, including SciELO, Scopus, PubMed, and Web of Science up to July 5, 2019. Eligibility criterion was original studies conducted on healthy humans including exercise interventions or interventions involving any type of physical activity.RESULTS:The initial search retrieved 619 articles of which 18 met the inclusion criteria, 9 were observational, 4 reported very short-term exercise interventions, and 5 reported medium/long-term exercise interventions. Higher levels of physical activity or cardiorespiratory fitness were positively associated with fecal bacterial alpha diversity. Contrasting associations were detected between both the level of physical activity and cardiorespiratory fitness and fecal counts for the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Higher levels of physical activity and cardiorespiratory fitness were positively associated with the fecal concentration of short-chain fatty acids. Reports on the effects of very short-term and medium/long-term exercise interventions on the composition of the gut microbiota were inconsistent.DISCUSSION:Higher levels of physical activity and cardiorespiratory fitness are associated with higher fecal bacterial alpha diversity and with the increased representation of some phyla and certain short-chain fatty acids in the feces of healthy adults. Very short-term and medium/long-term exercise interventions seem to influence the fecal counts of some phyla. However, the heterogeneity between studies hampers any strong conclusions from being drawn. Better-designed studies are needed to unravel the possible mechanisms through which exercise might influence the composition and activity of the human gut microbiota.

The Pathophysiology of Bile Acid Diarrhoea: Differences in the Colonic Microbiome, Metabolome and Bile Acids

Background: Bile acid diarrhoea (BAD) is common, often unrecognised, or thought to be irritable bowel syndrome with diarrhoea (IBS-D). It results from increased loss of bile acids (BAs) into the colon but mechanisms are unclear. The gut microbiota plays key roles in the metabolism of primary BAs to form secondary BAs, which have differing impacts on intestinal metabolism and homeostasis. The aim of this study was to profile the gut microbiome in BAD and to investigate the differences in bacterial metabolic products and specific bile acids. Methods: Patients with BAD diagnosed by SeHCAT testing, were compared with other IBS-D patients, and healthy controls. Faecal 16S ribosomal RNA gene analysis was undertaken. Faecal short chain fatty acid (SCFA) and urinary fermentation metabolite profiles (volatile organic compounds; VOCs) were measured. BAs were quantified in serum and faeces. Findings: Faecal bacterial diversity was significantly reduced in patients with BAD, but several taxa were enriched compared to IBS-D. SCFA amounts differed in BAD, controls and IBS-D, with significantly more propionate in BAD. Separation of VOC profiles was evident between all groups with the greatest discrimination between IBS-D and controls. Unconjugated and primary BA in serum and faeces were significantly higher in BAD. The proportion of faecal primary BA was inversely related to SeHCAT values. Interpretation: BAD results in dysbiosis, with differences in metabolites including VOC, SCFA and higher concentrations of primary BAs when compared to IBS-D. These findings provide new mechanistic insights into the pathophysiology of BAD. Funding Statement: Funding was from UHCW Trust’s charity as well as the Midlands Gastroenterology Society and Bardhan Research and Education Trust (BRET). Declaration of Interests: JW has been a consultant for, and reports institutional grant funding from GE Healthcare, and Prometheus diagnostics. RA has delivered educational talks for GE Healthcare. No disclosures are made by all authors Ethics Approval Statement: Scientific and ethical approval was acquired from the local Research and Development Office as well as Warwickshire Ethical committee ref: 09/H1211/38. Written informed consent was obtained from all participants in the study.

Composition and functional diversity of fecal bacterial community of wild boar, commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing.

The bacterial community in mammalian gastrointestinal tract is abundant and complex. To date, little is known about the gut microbiota of wild boar. This study aimed to investigate the fecal bacterial diversity of wild boar and compare with commercial pig and domestic native pig. The diet composition showed that the diets of wild boar, commercial pig and domestic native pig were different from each other. More than 1,760,000 quality-filtered sequences were obtained, and the results revealed distinct compositions and diversity of fecal microbiota in three groups. PCoA and NMDS analyses showed that fecal bacterial communities of wild boar, commercial pig and domestic native pig formed distinctly different clusters. Although the three groups shared a large size of OTUs comprising a core microbiota community, a strong distinction existed at family and genus levels. Ruminococcaceae, Prevotellaceae and Christensenellaceae were more abundant in the feces of wild boar than in domestic native pig and commercial pig. At the genus level, the proportion of unidentified Christensenellaceae was remarkably higher in wild boar group, while commercial pig and domestic native pig group had a higher abundance of Streptococcus and Lactobacillus. Tax4Fun predictions of metagenome function showed statistically significant differences in the functions of fecal microbiota in three groups. There were more bacteria genes with amino acid metabolism, cell growth and death, cell motility, energy metabolism, immune system and environmental adaptation observed in wild boar feces, while commercial pig feces contained more bacteria genes with carbohydrate metabolism, drug resistance, aging, infectious diseases, lipid metabolism, endocrine and metabolic diseases. These results indicated that the fecal microbial ecosystem of the wild boar is significantly different from that of domestic native pig and commercial pig, suggesting that diet is an important factor leading to differences in bacterial abundance and diversity in feces.

PSXII-24 Effects of supplementing ruminally protected and non-protected active dried yeast on fecal bacterial community of finishing beef steers

Abstract The objective of this study was to evaluate the effects of supplementing ruminally protected and non-protected active dried yeast (ADY; AB Vista, UK) on fecal bacterial diversity of finishing beef steers. Seventy-five Angus steers (initial BW 448 kg) were randomly assigned to one of five treatments: control, antibiotics (ANT, 330 mg monensin + 110 mg tylosin/d), ADY (1.5 g/d), encapsulated ADY (EDY; 3 g/d), and mixture of ADY and EDY (MDY). The ADY (1.7×1010 cfu/g) was encapsulated with equal amount of ADY and capsule material. Steers were fed a diet containing 10% barley silage and 90% barley concentrate (DM basis), ANT, ADY, EDY and MDY were top-dressed at feeding. Fecal samples were rectally collected from 10 steers of each treatment on d 56 to determine fecal bacterial diversity using high throughput MiSeq sequencing. Alpha diversity indices were not different among treatments. Principal coordinate analysis revealed that samples were not clustered by treatments. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P &amp;lt; 0.10) of ANT, EDY and MDY to have greater relative abundance of Bacteroidetes (averaged 51.3 vs 46.8%) but lesser Firmicutes (averaged 39.5 vs 47.9%) than control steers. About 50 to 61% of sequences remained unclassified and identified 32 genus, with Prevotella ranging from 15.8 to 25.5% as the dominant genus in all treatments. Notably, steers with ANT, EDY, MDY vs. control had greater (P &amp;lt; 0.05) relative abundance of Prevotella (averaged 23.5 vs 16.8%) but lesser (P &amp;lt; 0.03) Oscillospira (averaged 1.7 vs 2.8%). No differences between ADY and control were observed for aforementioned variables. The results indicate that supplementing ruminally protected or non-protected ADY have limited effect on diversity of fecal bacteria, whereas feeding protected ADY and ANT to finishing beef steers altered dominant fecal bacteria at phylum and genus level.

Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity

BackgroundGut microbiota has been increasingly acknowledged to shape significantly human health, contributing to various autoimmune diseases, both intestinal and non-intestinal, including multiple sclerosis (MS). Gut microbiota studies in patients with relapsing remitting MS strongly suggested its possible role in immunoregulation; however, the profile and potential of gut microbiota involvement in patients with primary progressive MS (PPMS) patients has received much less attention due to the rarity of this disease form. We compared the composition and structure of faecal bacterial assemblage using Illumina MiSeq sequencing of V3-V4 hypervariable region of 16S rRNA genes amplicons in patients with primary progressive MS and in the healthy controls.ResultsOver all samples 12 bacterial phyla were identified, containing 21 classes, 25 orders, 54 families, 174 genera and 1256 operational taxonomic units (OTUs). The Firmicutes phylum was found to be ultimately dominating both in OTUs richness (68% of the total bacterial OTU number) and in abundance (71% of the total number of sequence reads), followed by Bacteroidetes (12 and 16%, resp.) and Actinobacteria (7 and 6%, resp.). Summarily in all samples the number of dominant OTUs, i.e. OTUs with ≥1% relative abundance, was 13, representing much less taxonomic richness (three phyla, three classes, four orders, six families and twelve genera) as compared to the total list of identified OTUs and accounting for 30% of the sequence reads number in the healthy cohort and for 23% in the PPMS cohort. Human faecal bacterial diversity profiles were found to differ between PPMS and healthy cohorts at different taxonomic levels in minor or rare taxa. Marked PPMS-associated increase was found in the relative abundance of two dominant OTUs (Gemmiger sp. and an unclassified Ruminococcaceae). The MS-related differences were also found at the level of minor and rare OTUs (101 OTUs). These changes in OTUs’ abundance translated into increased bacterial assemblage diversity in patients.ConclusionThe findings are important for constructing a more detailed global picture of the primary progressive MS-associated gut microbiota, contributing to better understanding of the disease pathogenesis.

Helicobacter pylori Infection Aggravates Dysbiosis of Gut Microbiome in Children With Gastritis.

Introduction: Helicobacter pylori infection consistently leads to chronic and low degree of inflammatory response in gastric mucosa and is closely related with gastrointestinal and extra-gastric diseases. Effects of local microbiome in the stomach have been studied in adults and children with H. pylori infection. It is, however, not known whether the intestinal microbial community differs in children with varying H. pylori infection. The aim of this study is to characterize the altered composition of microbiome induced by H. pylori infection and in gastritis.Materials and Methods: This study involved 154 individuals, including 50 children affected by H. pylori-induced gastritis, 42 children with H. pylori-negative gastritis, and 62 healthy controls. Gut microbiome composition was analyzed using 16S rRNA gene-based pyrosequencing. Fecal bacterial diversity and composition were then compared.Results: On the basis of an analysis of similarities and differences, we found that children with H. pylori-induced gastritis exhibited gut bacteria dysbiosis. The ratio of Firmicutes/Bacteroidetes (F:B) at the phylum level had dramatically decreased in H. pylori-positive gastritis group (HPG) and H. pylori-negative gastritis group (HNG), compared with the healthy control group (HCG). At the family and genus levels, relative abundance of Bacteroidaceae and Enterobacteriaceae was prevalent in HPG and HNG, whereas relative abundance of Lachnospiraceae, Bifidobacteriaceae, and Lactobacillaceae was seen in HCG. Prevalence of different taxa of gut microbiome at the class, order, family, and genus levels was also observed among the three groups.Conclusions: Gastritis can cause changes in composition of fecal microbiome, which is exacerbated by H. pylori infection. These changes in gut microbiome may be related to drug resistance and development of chronic gastrointestinal diseases.