Composition Of Human Gut Microbiota Research Articles

Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder.

Major depressive disorder (MDD) is among the most prevalent mental disorders worldwide. Factors causing the pathogenesis of MDD include gut microbiota (GM), which interacts with the host through the gut–brain axis. In previous studies of GM in MDD patients, 16S rRNA sequencing was used, which provided information about composition but not about function. In our study, we analyzed whole metagenome sequencing data to assess changes in both the composition and functional profile of GM. We looked at the GM of 36 MDD patients, compared with that of 38 healthy volunteers. Comparative taxonomic analysis showed decreased abundances of Faecalibacterium prausnitzii, Roseburia hominis, and Roseburia intestinalis, and elevated abundances of Escherichia coli and Ruthenibacterium lactatiformans in the GM of MDD patients. We observed decreased levels of bacterial genes encoding key enzymes involved in the production of arginine, asparagine, glutamate, glutamine, melatonin, acetic, butyric and conjugated linoleic acids, and spermidine in MDD patients. These genes produced signature pairs with Faecalibacterium prausntizii and correlated with decreased levels of this species in the GM of MDD patients. These results show the potential impact of the identified biomarker bacteria and their metabolites on the pathogenesis of MDD, and should be confirmed in future metabolomic studies.

Epidemiological Studies of Children's Gut Microbiota: Validation of Sample Collection and Storage Methods and Microbiota Analysis of Toddlers' Feces Collected from Diapers.

The composition of human gut microbiota influences human health and disease over the long term. Since the flora in specimens can easily change at ambient temperature outside the body, epidemiological studies need feasible methods of stool specimen collection and storage to be established. We aimed to validate two methods: feces frozen-stored in tubes containing guanidine thiocyanate solution for two months after collection (Method B), and feces excreted in diapers and frozen-stored (Method C). Validation was by comparison with a gold standard Method A. Bacterial flora of five adults were sampled and stored by all three methods. Bacterial composition was examined by amplicon sequencing analysis. Bland–Altman analyses showed that Methods B and C might change relative abundances of certain bacterial flora. Thereafter, we analyzed the bacterial flora of 76 toddlers (two age groups) in stools sampled and processed by Method C. The diversity indices of toddlers’ flora were less than those of adults. The relative abundance of some bacteria differed significantly between children aged 1.5 and 3 years. The specimen collection and storage methods validated in this study are worth adopting in large-scale epidemiological studies, especially for small children, provided the limited accuracy for some specific bacteria is understood.

Effect of Fructooligosaccharides Supplementation on the Gut Microbiota in Human: A Systematic Review and Meta-Analysis.

Background: Numerous studies have investigated the effects of the supplementation of fructooligosaccharides (FOS) on the number of bacteria in the gut that are good for health, but the results have been inconsistent. Additionally, due to its high fermentability, supplementation of FOS may be associated with adverse gastrointestinal symptoms such as bloating and flatulence. Therefore, we assessed the effects of FOS interventions on the composition of gut microbiota and gastrointestinal symptoms in a systematic review and meta-analysis. Design: All randomized controlled trials published before 10 July 2022 that investigated the effects of FOS supplementation on the human gut microbiota composition and gastrointestinal symptoms and met the selection criteria were included in this study. Using fixed or random-effects models, the means and standard deviations of the differences between the two groups before and after the intervention were combined into weighted mean differences using 95% confidence intervals (CIs). Results: Eight studies containing 213 FOS supplements and 175 controls remained in this meta-analysis. Bifidobacterium spp. counts significantly increased during FOS ingestion (0.579, 95% CI: 0.444–0.714) in comparison with that of the control group. Subgroup analysis showed greater variation in Bifidobacterium spp. in adults (0.861, 95% CI: 0.614–1.108) than in infants (0.458, 95% CI: 0.297–0.619). The increase in Bifidobacterium spp. counts were greater in the group with an intervention duration greater than 4 weeks (0.841, 95% CI: 0.436–1.247) than an intervention time less than or equal to four weeks (0.532, 95% CI: 0.370–0.694), and in the group with intervention doses > 5 g (1.116, 95% CI: 0.685–1.546) the counts were higher than those with doses ≤ 5 g (0.521, 95% CI: 0.379–0.663). No differences in effect were found between FOS intervention and comparators in regard to the abundance of other prespecified bacteria or adverse gastrointestinal symptoms. Conclusions: This is the first meta-analysis to explore the effect of FOS on gut microbiota and to evaluate the adverse effects of FOS intake on the gastrointestinal tract. FOS supplementation could increase the number of colonic Bifidobacterium spp. while higher dose (7.5–15 g/d) and longer duration (>4 weeks) showed more distinct effects and was well tolerated.

Mild intermittent hypoxia exposure alters gut microbiota composition in men with overweight and obesity.

Results from high altitude studies in humans and controlled animal experiments suggest that hypoxia exposure induces alterations in gut microbiota composition, which may in turn affect host metabolism. However, well-controlled studies investigating the effects of normobaric hypoxia exposure on gut microbiota composition in humans are lacking. The aim of this study was to explore the impact of mild intermittent hypoxia (MIH) exposure on gut microbiota composition in men with overweight and/or obesity. We performed a randomised, single-blind crossover study, in which participants were exposed to MIH (FiO2: 15%, 3×2 h per day) and normoxia (FiO2: 21%) for seven consecutive days. Following the MIH and normoxia exposure regimens, faecal samples were collected for determination of faecal microbiota composition using 16S rRNA gene-amplicon sequencing in the morning of day 8. Paired faecal samples were available for five individuals. Furthermore, tissue-specific insulin sensitivity was determined using the gold-standard two-step hyperinsulinemic-euglycemic clamp. MIH did not affect microbial alpha and beta-diversity but reduced the relative abundance of Christensenellaceae and Clostridiaceae bacterial families. MIH significantly increased the abundances of obligate anaerobic bacterial genera including Fusicatenibacter, Butyricicoccus and Holdemania, whilst reducing Christensenellaceae R-7 group and Clostridium sensu stricto 1, although these findings were not statistically significant after correction for multiple testing. Furthermore, MIH-induced alterations in abundances of several genera were associated with changes in metabolic parameters such as adipose and peripheral insulin sensitivity, plasma levels of insulin, fatty acids, triacylglycerol and lactate, and substrate oxidation. In conclusion, we demonstrate for the first time that MIH exposure induces modest effects on faecal microbiota composition in humans, shifting several bacterial families and genera towards higher abundances of anaerobic butyrate-producing bacteria. Moreover, MIH-induced effects on faecal microbial composition were associated with parameters related to glucose and lipid homeostasis, supporting a link between MIH-induced alterations in faecal microbiota composition and host metabolism. The study was registered at the Netherlands Trial Register: NL7120/NTR7325.

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing

BackgroundGut pathological microbial imbalance or dysbiosis is closely associated with colorectal cancer. Although there are observable differences in molecular and clinical characteristics between patients with right- and left-sided colon cancer, differences in their gut microbiomes have not been thoroughly investigated. Furthermore, subsequent changes in microbiota status after partial colectomy remain unknown. We examined the human gut microbiota composition to determine its relationship with colon cancer and partial colon resection according to location.MethodsStool samples from forty-one subjects (10 in the control group, 10 in the right-sided colon cancer [RCC] group, 6 in the sigmoid colon cancer [SCC] group, 9 in the right colon resection [RCR] group and 6 in the sigmoid colon resection [SCR] group) were collected, and DNA was extracted. After terminal restriction fragment length polymorphism (T-RFLP) analysis, the samples were subjected to 16S rRNA gene amplicon sequencing, and the metabolic function of the microbiota was predicted using PICRUSt2.ResultsT-RFLP analysis showed a reduced ratio of clostridial cluster XIVa in the SCC patients and clostridial cluster IX in the RCC patients, although these changes were not evident in the RCR or SCR patients. 16S rRNA gene amplicon sequencing demonstrated that the diversity of the gut microbiota in the RCC group was higher than that in the control group, and the diversity in the SCR group was significantly higher than that in the RCR group. Principal coordinate analysis (PCoA) revealed significant differences according to the group. Analyses of the microbiota revealed that Firmicutes was significantly dominant in the RCC group and that the SCC group had a higher abundance of Verrucomicrobia. At the genus level, linear discriminant analysis effect size (LEfSe) revealed several bacteria, such as Ruminococcaceae, Streptococcaceae, Clostridiaceae, Gemellaceae, and Desulfovibrio, in the RCC group and several oral microbiomes in the SCC group. Metabolic function prediction revealed that cholesterol transport- and metabolism-related enzymes were specifically upregulated in the RCC group and that cobalamin metabolism-related enzymes were downregulated in the SCC group.ConclusionGut microbial properties differ between RCC and SCC patients and between right hemicolectomy and sigmoidectomy patients and may contribute to clinical manifestations.

Coevolution of the Human Host and Gut Microbiome: Metagenomics of Microbiota.

It is estimated that humans have trillions of microbial cells living in their gut as part of their microbiota. Each human being has an entirely unique microbiome and human gut microbiota composition has been shown to alter with age due to several factors including physical stress, diet, use of antibiotics, prolonged treatments, chronic disease processes, physiological changes, and geographical location. The gut microbiome contributes to overall well-being in a multitude of ways, including digestion, metabolism, immunity, and the creation of vital compounds that the body cannot synthesize on its own. Disequilibrium in the microbiota has been correlated to obesity, heart disease, irritable bowel disease, and certain cancers. The evolution of the human host allowed for the diversity of the microbial community present in the gut. Although previous studies portray the correlation between diet and disequilibrium in host microbiota, the evolutionary dynamics of bacterial commensal flora and the extent to which it is beneficial are still unclear and need additional investigation.

Human gut microbiota composition and its predicted functional properties in people with western and healthy dietary patterns

PurposeSome dietary habits cluster together, and for this reason it is advised to study the impact of entire dietary patterns on human health, rather than that of individual dietary habits. The main objective of this study was to evaluate differences in gut microbiota composition and their predicted functional properties between people with a healthy (HDP) and western (WDP) dietary pattern.MethodsA cross-sectional, observational study was carried out on 200 participants enrolled 2017–2018 in Poznań, Poland, equally distributed into HDP and WDP groups. Diet was estimated using 3-day food records and information on stool transit times was collected. Fecal microbiota composition was assessed by 16S rRNA gene sequencing and its functional properties were predicted by the PICRUSt2 workflow.ResultsThe α-diversity did not differ between people with WDP and HDP, but β-diversity was associated with dietary pattern. People with HDP had higher relative abundances (RA) of Firmicutes and Faecalibacterium and lower RA of Bacteroidota and Escherichia–Shigella than participants with WDP. Only a small proportion of the variance in microbiota composition (1.8%) and its functional properties (2.9%) could be explained by dietary intake (legumes, simple sugars and their sources, like fruit, soft drinks) and stool transit characteristics.ConclusionGut microbiota composition and predicted metabolic potential is shaped by overall diet quality as well as the frequency of defecation; however, the cumulative effect of these explain only a relatively low proportion of variance.

Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs

Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4–5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs’ microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.

Impact of Compost Amendments on the Human Gut Microbiota During Gardening

ObjectivesTo measure associations between gardening with three different types of compost amendments and the human gut microbiota composition.MethodsGardeners (n = 25) were provided with one of three types of compost: chicken manure (CM), compost with dairy manure and plant material (DMP), or plant-based compost (P). Stool samples were collected before gardening (T1), after amending soil with compost (T2), and at the peak of garden harvest (T3). Compost and soil samples were also collected. DNA was extracted from the samples, 16S rRNA libraries were made, and libraries were sequenced by Illumina MiSeq. Sequences were processed using mothur, and data were analyzed in R. Kruskal-Wallis with post hoc Dunn test was performed to compare Shannon Alpha diversity. Individual taxa were compared between time points using a negative binomial test. Fast expectation-maximization microbial source tracking (FEAST) analysis was used to determine stool bacteria sources. Proportions were compared by Chi-Square.ResultsAt T2 and T3, gut bacterial communities of participants who used P compost had lower Shannon alpha diversity compared to the gut bacterial communities of participants using the other two compost types, and this was also the trend at T1. In T2 stool, Ruminococcus 1 and Ruminococcus 2 were less abundant in the microbiotas of those using P compost as compared to those using CM or DMP. However, at T1, Ruminococcus 2 was less abundant in the microbiotas of individuals that later used P as well as those that later used CM compared to those who later used DMP. During T2, Prevotella 9 had the highest abundance in the microbiotas of those using P compost. In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from CM compared to soil.ConclusionsSoil exposure through gardening was associated with a small but detectable change in the gardeners’ gut microbiota composition. These results suggest that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota.Funding SourcesUSDA NIFA AFRI.

Tiliae flos metabolites and their beneficial influence on human gut microbiota biodiversity ex vivo

Ethnopharmacological relevanceThe linden flower (Tiliae flos) has been used for centuries to treat and relieve symptoms of the common cold, throat irritation, and upper respiratory tract disturbances. Traditionally, this herb is administered orally, and thus it undergoes intestinal metabolism. Although it is pharmacopeial plant material, there are no reports about its interaction with human gut microbiota. Aim of the studyThe study aimed to determine the interaction between human gut microbiota and the linden flower extracts, resulting in the biotransformation of the extract's constituents and changes in the microbiota composition. Material and methodsThe linden flower metabolites were obtained by incubation of extract with human faecal slurries from 5 healthy donors. The UHPLC-DAD-MSn analysis determined the composition of raw extract and analysis of microbial metabolites. The intestinal microbiota isolation and sequencing were used to determine changes in microbiota composition. The anti-inflammatory activity was tested using the LPS-stimulated human neutrophils model and ELISA test. ResultsAfter incubation of linden flower extract with human gut microbiota, twenty metabolites were detected and characterized, and three among them were identified. The extract changed human gut microbiota composition but did not cause dysbiosis (change in the abundance of forty-three genera). Raw extract and their metabolites exhibit different levels of inhibition of cytokines production by LPS-stimulated neutrophils, but the reduction of TNF-α production was observed. ConclusionsThe linden flower extract has a beneficial influence on human gut microbiota because it promotes increasing the abundance of bacteria responsible for SCFAs production. The anti-inflammatory effect might be linked to both microbiota composition changes and direct activity of bioavailable metabolites. Increased abundance of SCFAs producers may inhibit the production of pro-inflammatory cytokines. A low concentration of phenolic compounds in metabolized linden flower extract and responsible for anti-inflammatory properties, and the multitude of biological and chemical particles and their interactions may weaken these properties.

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome.

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.

Effect of Moderate Consumption of Different Phenolic-Content Beers on the Human Gut Microbiota Composition: A Randomized Crossover Trial.

The moderate consumption of beer has been associated with positive effects on health, and these benefits are driven, in part, by the antioxidant properties of phenolic compounds found in this beverage. However, the potential impact of beer polyphenols on the human gut microbiome and their consequences are yet to be elucidated. In this study, our aim was to evaluate the effect of three different phenolic-content beers on the gut microbiome and the potential role of the induced shifts in the antioxidant capacity of beer polyphenols. In total, 20 subjects (10 healthy volunteers and 10 individuals with metabolic syndrome) were randomly assigned in a crossover design to consume each of the different beers (alcohol-free, lager or dark beer) during a 2-week intervention. Significant changes in the relative abundance of Streptococcaceae and Streptococcus were found after beer consumption. An increased abundance of Streptococcaceae and Streptococcus was observed after the consumption of dark beer, with no detected differences between baseline and alcohol-free/lager beer intervention. Moreover, some of the detected differences appeared to be related to the metabolic status. Finally, a decrease in porphyrin metabolism and heme biosynthesis was found after the intervention, especially after the consumption of dark beer. These results show that the antioxidant capacity of beer polyphenols may induce positive shifts in gut microbiota composition, and some of the observed changes may also boost the antioxidant capacity of these compounds.

In vitro fecal fermentation characteristics of bamboo insoluble dietary fiber and its impacts on human gut microbiota

Bamboo contains abundant hemicellulose, cellulose, and lignin, which are a high-quality insoluble dietary fiber (IDF) raw material. To investigate IDF- induced changes in the production of short-chain fatty acids (SCFAs) and the composition of human gut microbiota, IDF was extracted by alkaline hydrogen peroxide (named BIDF), complex enzymatic hydrolysis method (named OIDF) from bamboo, and commercial bamboo fiber BF90. The in vitro fecal fermentation characteristics of BIDF, OIDF, BF90 and its impacts on human gut microbiota were studied for the first time. Results showed that BIDF, OIDF, and BF90 could promote the production of total SCFAs after 24 h fermentation. Additionally, BIDF could alter the composition and microbial diversity of gut microbiota, especially increase the relative abundance of Bacteroides and decrease the ratio of Firmicutes to Bacteroidetes (F/B) value. These results revealed that the IDF from bamboo could be partially utilized by specific bacteria in human intestines and provide a reference for the study of the effects of IDF fermentation on SCFAs production and microbial composition.

Differences in the gut microbiome composition of Korean children and adult samples based on different DNA isolation kits.

Recent studies have revealed that the composition of human gut microbiota varies according to region, race, age, diet, living environment, and sampling and DNA extraction method. The purpose of this study was to broaden our understanding of the intestinal microbial composition of Koreans by conducting a 16S rRNA amplicon sequencing on 78 Korean samples composed of adults, children, normal and obese groups. We compared the microbiome composition and diversity of these groups at different levels including the phylum and genus level using two different stool DNA extraction kits of QIAamp® PowerFecal® DNA Kit (Qiagen, Hilden, Germany) and CT Max Fecal DNA Kit (Ct bio, Korea). We found that Ct bio (Ct) kit recovered higher DNA yields and OTUs than QIAamp® PowerFecal® DNA Kit (Qia). The Ct kit, which adopted more rigorous bead beating method, detected the most Gram-positive (G+) bacteria, Firmicutes, at the Phylum level, whereas the Qia kit, which used a less rigorous cell lysis method, found the most Gram-negative (G-) bacteria, Bacteroidetes. The Firmicutes-to-Bacteroidetes (F/B) ratio showed no significant difference between the obese and the normal groups of same kit; however, they were significantly different with two different kits. There was a difference in the intestinal flora between healthy Korean adults and children. The taxa that differed significantly between the adults and children were Bacteroides, Bifidobacterium, Prevotella, and Subdoligranulum. There was no significant difference in the intestinal flora between the normal weight group and the obese group in adults and children, respectively. This is probably because the difference in body mass index (BMI) between the sample groups collected in this study is statistically significant, but it is not large enough to show a clear difference in the flora. Therefore, these results should be interpreted with caution while considering the BMI values and Korean obesity criterion together.

Supporting Maternal and Child Mental Health Through Dietary Changes Focused on the Gut Microbiota

Growing evidence from preclinical studies, epidemiology, and randomized controlled trials supports a causal role for diet quality in mental disorder risk, and clinical psychiatric guidelines now place diet, along with other lifestyle behaviors, as foundational treatment targets for mood disorders. Diet quality in the perinatal period is related to both mothers' mental health and children's emotional and neurodevelopment outcomes. The human gut microbiota composition is influenced by diet, and emerging evidence suggests that disturbances in gut microbiota, at least in part, mediate these relationships. Thus, optimizing maternal diet should be prioritized as part of a multidisciplinary approach for promoting physical and mental health in mothers and their off spring. This paper addresses the current evidence base and discusses its application in perinatal health care. [ Psychiatr Ann . 2022;52(2):51–55.]

From Alpha Diversity to Zzz: Interactions among sleep, the brain, and gut microbiota in the first year of life.

Sleep disorders have been linked to alterations of gut microbiota composition in adult humans and animal models, but it is unclear how this link develops. With longitudinal assessments in 162 healthy infants, we present a so far unrecognized sleep-brain-gut interrelationship. First, we report a link between sleep habits and gut microbiota: daytime sleep is associated with bacterial diversity, and nighttime sleep fragmentation and variability are linked with bacterial maturity and enterotype. Second, we demonstrate a sleep-brain-gut link: bacterial diversity and enterotype are associated with sleep neurophysiology. Third, we show that the sleep-brain-gut link is relevant in development: sleep habits and bacterial markers predict behavioral-developmental outcomes. Our results demonstrate the dynamic interplay between sleep, gut microbiota, and the maturation of brain and behavior during infancy, which aligns with the newly emerging concept of a sleep-brain-gut axis. Importantly, sleep and gut microbiota represent promising health targets since both can be modified non-invasively. As many adult diseases root in early childhood, leveraging protective factors of adequate sleep and age-appropriate gut microbiota in infancy could constitute a health promoting factor across the entire human lifespan.

Modulation of human gut microbiota composition and metabolites by arabinogalactan and Bifidobacterium longum subsp. longum BB536 in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

• Arabinogalactan (AG) gave higher amounts of SCFA, A. muciniphila and F. prausnitzii than starch . • The SCFA changes induced by the AG/ B. longum combination continued after B. longum supplementation. • The AG/ B. longum combination increased AG degradation, butyrate and F. prausnitzii . • The effect of the AG/ B. longum combination was dependent on the colon region. The Mucosal-Simulator of the Human Intestinal Microbial Ecosystem (SHIME) was used to differentiate the gut microbial fermentation of arabinogalactan (AG) and starch before (T1), during (T2), and after (T3) one-week Bifidobacterium longum subsp. longum BB536 supplementation. Adding 10 g/L of either AG or starch to the basal medium (T1) promoted short-chain fatty acid (SCFA) production in three successive SHIME colon vessels. AG fermentation (T1) resulted in higher total SCFAs ( P < 0.05) and luminal live Faecalibacterium prausnitzii ( P < 0.0001) in the transverse colon than starch fermentation (T1). Compared to AG fermentation alone (T1), B. longum supplementation (T2) significantly enhanced butyrate production ( P < 0.05) and the abundance of luminal live F. prausnitzii ( P < 0.0001) in the transverse colon. The results indicate that combining a potential prebiotic and a probiotic strain increases SCFA production and particular gut commensals which could have a beneficial effect on gut health.

Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model.

Gut microbiota, a major contributor to human health, is influenced by physical activity and diet, and displays a functional cross-talk with skeletal muscle. Conversely, few data are available on the impact of hypoactivity, although sedentary lifestyles are widespread and associated with negative health and socio-economic impacts. The study aim was to determine the effect of Dry Immersion (DI), a severe hypoactivity model, on the human gut microbiota composition. Stool samples were collected from 14 healthy men before and after 5 days of DI to determine the gut microbiota taxonomic profiles by 16S metagenomic sequencing in strictly controlled dietary conditions. The α and β diversities indices were unchanged. However, the operational taxonomic units associated with the Clostridiales order and the Lachnospiraceae family, belonging to the Firmicutes phylum, were significantly increased after DI. Propionate, a short-chain fatty acid metabolized by skeletal muscle, was significantly reduced in post-DI stool samples. The finding that intestine bacteria are sensitive to hypoactivity raises questions about their impact and role in chronic sedentary lifestyles.

Lysozyme-like Protein Produced by Bifidobacterium longum Regulates Human Gut Microbiota Using In Vitro Models.

The extracellular secreted protein of Bifidobacterium longum (B. longum) plays an important role in maintaining the homeostasis of the human intestinal microenvironment. However, the mechanism(s) of interaction remain unclear. Lysozyme is a kind of antibacterial peptide. In this study, the amino acid sequence of a lysozyme-like protein of B. longum based on whole-genome data of an isolate from human gut feces was found. We further predicted functional domains from the amino acid sequence, purified the protein, and verified its bioactivity. The growth of some bacteria were significantly delayed by the 020402_LYZ M1 protein. In addition, the gut microbiota was analyzed via high-throughput sequencing of 16S rRNA genes and an in vitro fermentation model, and the fluctuations in the gut microbiota under the treatment of 020402_LYZ M1 protein were characterized. The 020402_LYZ M1 protein affected the composition of human gut microbiota significantly, implying that the protein is able to communicate with intestinal microbes as a regulatory factor.

A Bayesian Negative Binomial Hierarchical Model for Identifying Diet-Gut Microbiome Associations.

The human gut microbiota composition plays an important role in human health. Long-term diet intervention may shape human gut microbiome. Therefore, many studies focus on discovering links between long-term diets and gut microbiota composition. This study aimed to incorporate the phylogenetic relationships between the operational taxonomic units (OTUs) into the diet-microbe association analysis, using a Bayesian hierarchical negative binomial (NB) model. We regularized the dispersion parameter of the negative binomial distribution by assuming a mean-dispersion association. A simulation study showed that, if over-dispersion is present in the microbiome data, our approach performed better in terms of mean squared error (MSE) of the slope-estimates compared to the standard NB regression model or a Bayesian hierarchical NB model without including the phylogenetic relationships. Data of the Healthy Life in an Urban Setting (HELIUS) study showed that for some phylogenetic families the (posterior) variances of the slope-estimates were decreasing when including the phylogenetic relationships into the analyses. In contrast, when OTUs of the same family were not similarly affected by the food item, some bias was introduced, leading to larger (posterior) variances of the slope-estimates. Overall, the Bayesian hierarchical NB model, with a dependency between the mean and dispersion parameters, proved to be a robust method for analyzing diet-microbe associations.