Alpha Diversity Of Gut Microbiota Research Articles

Understanding the effects of intramuscular injection and feed withdrawal on Salmonella Typhimurium shedding and gut microbiota in pullets

BackgroundGut microbiota plays a key role in health, immunity, digestion, and production in layers. Factors such as environment, diet, diseases, stress, and flock management significantly affect gut microbiota; however, it is not known how potential stressors such as intramuscular injections or feed withdrawal alter the composition of gut microbiota that result in increased the shedding level of foodborne pathogens. In the current study, the effects of intramuscular corticosterone injection and feed withdrawal were evaluated to understand their role in Salmonella Typhimurium shedding and changes in the composition of gut microbiota in layers.ResultsSalmonella shedding was observed for 8 weeks post-infection. There was a significant increase in Salmonella Typhimurium count after intramuscular injection and feed withdrawal. The Salmonella infected and the negative control groups showed significant differences in the abundance of different genera in gut microbiota at week 1 and up to week 7 post infection. The infected group showed a significant reduction in alpha diversity of gut microbiota. Firmicutes reduced significantly (P < 0.05) after intramuscular injection, while the feed withdrawal groups did not cause any significant changes in Proteobacteria-Firmicutes ratio. Furthermore, intramuscular injection resulted in a significant change in alpha diversity of gut microbiota.ConclusionsExposure of chicks to relatively low dose of Salmonella Typhimurium can lead to persistent shedding in pullets. The Salmonella Typhimurium infection disrupted the gut microbiota composition immediately after infection. The potential stress of intramuscular injection and feed withdrawal significantly increased the Salmonella Typhimurium count in faeces. The intramuscular injection also resulted in a significant alteration of the Proteobacteria-Firmicutes ratio, which could increase the risk of dysbiosis.

Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age

BackgroundColonization of intestinal microbiota in ruminant during the early life is important to host health, metabolism and immunity. Accumulating evidence revealed the ameliorative effect of milk replacer administration in the gut microbial development of early-weaned ruminants. Yimeng black goats (YBGs) inhabiting Shandong, China show a complex intestinal microbial ecosystem, but studies of their gut microbiota are still insufficient to report. Here, this study was performed to investigate how the gut microbiota develops in weaned YBGs with the effect of age and milk replacer.ResultsResults indicated that both age and milk replacer were important factors to change the gut microbiota of YBGs. Although the alpha diversity of gut microbiota did not change with the age of YBGs, the taxonomic compositions significantly changed. The relative abundance of some beneficial bacteria such as Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Eubacterium and Barnesiella significantly decreased and subsequently increase with age, which contributes to maintain the stability of intestinal environment and realize the diversity of intestinal functions. The relative abundance of Porphyromonas, Brevundimonas, Flavobacterium, Stenotrophomonas, Propionibacterium, Acinetobacter, Enterococcus and Clostridium belong to pathogenic bacteria in milk replacer-treated YBGs was significantly decreased. Additionally, some beneficial bacteria such as Ruminococcus, Ruminococcaceae, Christensenellaceae and Ruminiclostridium also display a trend of decreasing first followed by gradually increasing.ConclusionsThis study first revealed the gut bacterial community alterations in YBGs with the effect of age and milk replacer. This study also characterized the gut microbial distribution in YBGs with different ages and provided better insight into microbial population structure and diversity of YBGs. Moreover, milk replacer may serve as a good applicant for improving gut microbial development in early-weaned YBGs.

Cecal microbiota contribute to the development of woody breast myopathy

The objective of this study was to characterize the bacterial diversity of cecal microbiota in broilers related to breast phenotype, diet, and genetic strain. Broilers from 2 genetic strains (120 birds/strain) were fed a control diet (15 birds/pen) and an amino acid reduced diet (15 birds/pen, digestible lysine, total sulfur amino acids, and threonine reduced by 20% compared to the control diet). At 8 wk of age, 4 male broilers with normal breast (NB, 1 chick per pen) and 4 male broilers with woody breast (WB, 1 chick per pen) were selected for each treatment (strain × diet). The DNA of cecal samples was extracted and the 16S rRNA genes were sequenced and analyzed. There were no differences (P > 0.05) in the alpha diversity of gut microbiota between 2 phenotypes (NB vs. WB), 2 strains, or 2 diets (control vs. reduced). However, principal coordinate analysis plots (beta diversity) revealed that there were composition differences in samples between the 2 phenotypes (P = 0.001) and the 2 diets (P = 0.024). The most abundant phyla in all samples were Firmicutes, followed by Bacteroidetes and Proteobacteria. There were differences (false discovery rate, FDR < 0.05) in bacterial relative abundance between phenotypes and between diet treatments, but not (FDR > 0.05) between the 2 genetic strains. Selenomonas bovis (12.6%) and Bacteroides plebeius (12.3%) were the top 2 predominant bacteria in the ceca of WB birds; however, the relative abundances of these 2 bacteria were only 5.1% and 1.2% in NB birds, respectively. Function analysis predicted that the metabolic activities differed (q < 0.05) only between phenotypes. The microbiota of WB birds was characterized as reduced glycolysis and urea cycle but increased tricarboxylic acid (TCA) cycles, sugar degradation, and purine and pyrimidine nucleotides biosynthesis. Further studies are needed to investigate if WB incidence could be reduced by regulating gut microbiota and the potential mechanism that leads to decreased WB incidence.

Diet, Immunity, and Microbiota Interactions: An Integrative Analysis of the Intestine Transcriptional Response and Microbiota Modulation in Gilthead Seabream (Sparus aurata) Fed an Essential Oils-Based Functional Diet.

Essential oils (EOs) are promising alternatives to chemotherapeutics in animal production due to their immunostimulant, antimicrobial, and antioxidant properties, without associated environmental or hazardous side effects. In the present study, the modulation of the transcriptional immune response (microarray analysis) and microbiota [16S Ribosomal RNA (rRNA) sequencing] in the intestine of the euryhaline fish gilthead seabream (Sparus aurata) fed a dietary supplementation of garlic, carvacrol, and thymol EOs was evaluated. The transcriptomic functional analysis showed the regulation of genes related to processes of proteolysis and inflammatory modulation, immunity, transport and secretion, response to cyclic compounds, symbiosis, and RNA metabolism in fish fed the EOs-supplemented diet. Particularly, the activation of leukocytes, such as acidophilic granulocytes, was suggested to be the primary actors of the innate immune response promoted by the tested functional feed additive in the gut. Fish growth performance and gut microbiota alpha diversity indices were not affected, while dietary EOs promoted alterations in bacterial abundances in terms of phylum, class, and genus. Subtle, but significant alterations in microbiota composition, such as the decrease in Bacteroidia and Clostridia classes, were suggested to participate in the modulation of the intestine transcriptional immune profile observed in fish fed the EOs diet. Moreover, regarding microbiota functionality, increased bacterial sequences associated with glutathione and lipid metabolisms, among others, detected in fish fed the EOs supported the metabolic alterations suggested to potentially affect the observed immune-related transcriptional response. The overall results indicated that the tested dietary EOs may promote intestinal local immunity through the impact of the EOs on the host-microbial co-metabolism and consequent regulation of significant biological processes, evidencing the crosstalk between gut and microbiota in the inflammatory regulation upon administration of immunostimulant feed additives.

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors

BackgroundGastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls.ResultsWe found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients.ConclusionsOur analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.

Effect of Antibiotics on The Gut Microbiota in Children with Chronic Pancreatitis

Objectives: Little is known about the effect of antibiotic treatment on the gut microbiota in children with chronic pancreatitis (CCP). Our objective was to identify the effect of antibiotic treatment on the gut microbiota in children with chronic pancreatitis (CCP), the main gut microbiota genera and characterize the patients’ functional mutations after using antibiotics. Methods: The 16S rRNA sequencing method was used to compare the gut microbiota of healthy controls (HCs) with CCP using and not using antibiotics. Results: All CCP demonstrated a significantly reduced alpha diversity of the gut microbiota (P＜0.01). The gut microbiota's alpha diversity and the abundance of genera’s beta diversity did not show statistical differences between the non-antibiotics and antibiotics groups. There were 15 altered genera with common abundance in the non-antibiotics and antibiotics groups compared to the HC group. The area under the curve (AUC) of the top three probiotics, i.e., Faecalibacterium, Eubacterium, and Subdoligranulum, was 0.91. Among the 13 genera altered in the non-antibiotics group, the top three genera were not appropriate as biomarkers for cases receiving antibiotics. Compared to these 13 genera, the differences between the genera and the proportion of gram-positive bacteria in the 17 genera altered only in the antibiotics group were not statistically significant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the antibiotics caused alterations in the abundance of certain genera. The enriched functions and the altered gut microbiota in the two groups had their enriched functions. Conclusion: The use of antibiotics affects the gut microbiota of CCP, but the effect of disease on gut microbiota is still obvious, which may help diagnosis and further investigation into the pathogenic mechanisms of CP. Chronic pancreatitis (CP) is a persistent fibro-inflammatory process of the pancreas associated with genetic, environmental, and other pathogenic factors. This disease eventually led to the pancreas' irreversible injury and increased risk of pancreatic cancer and impaired mental health [1-3].

Inbreeding Alters the Gut Microbiota of the Banna Minipig.

Simple SummaryThe mammalian gut microbiota is an indispensable part of host health. The gut microbiota plays a crucial role in nutrient digestibility, preventing colonization of pathogens and maintaining the host immune system. Host genetics has been conclusively shown to closely related to gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity, however, remarkably little is understood about the gut microbiota of pigs during inbreeding. The Banna minipig inbred is the world’s first successful large mammalian experimental animal inbred line since 1980 from full and half-siblings of the Diannan small-ear pig. Now, Banna minipig inbred has been inbred for over 37 generations, and the inbreeding coefficient is more than 99%. This study is the first to characterize and compare the composition and function of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to better understand the influence of inbreeding on the gut microbiota.The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner.

T cell immunoglobulin and mucin domain-containing protein-3 (Tim-3) is an immune checkpoint molecule and a target for anti-cancer therapy. In this study, we examined whether gut microbiota manipulation altered the anti-tumour efficacy of Tim-3 blockade. The gut microbiota of mice was manipulated through the administration of antibiotics and oral gavage of bacteria. Alterations in the gut microbiome were analysed by 16S rRNA gene sequencing. Gut dysbiosis triggered by antibiotics attenuated the anti-tumour efficacy of Tim-3 blockade in both C57BL/6 and BALB/c mice. Anti-tumour efficacy was restored following oral gavage of faecal bacteria even as antibiotic administration continued. In the case of oral gavage of Enterococcus hirae or Lactobacillus johnsonii, transferred bacterial species and host mouse strain were critical determinants of the anti-tumour efficacy of Tim-3 blockade. Bacterial gavage did not increase the alpha diversity of gut microbiota in antibiotic-treated mice but did alter the microbiome composition, which was associated with the restoration of the anti-tumour efficacy of Tim-3 blockade. Conclusively, our results indicate that gut microbiota modulation may improve the therapeutic efficacy of Tim-3 blockade during concomitant antibiotic treatment. The administered bacterial species and host factors should be considered in order to achieve therapeutically beneficial modulation of the microbiota.

Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi

BackgroundGut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of vertebrate, remains less explored. In this study, we characterized the gut microbial communities of urochordate ascidian (Halocynthia roretzi) across the changes of season and starvation stress using a comprehensive set of omic approaches including 16S rRNA gene amplicon sequencing, shotgun metagenomics, metabolomic profiling, and transcriptome sequencing.ResultsThe 16S rRNA gene amplicon profiling revealed that ascidians harbor indigenous gut microbiota distinctly different to the marine microbial community and significant variations in composition and abundance of gut bacteria, with predominant bacterial orders representing each season. Depressed alpha-diversities of gut microbiota were observed across starvation stress when compared to the communities in aquafarm condition. Synechococcales involving photosynthesis and its related biosynthesis was reduced in abundance while the enrichments of Xanthomonadales and Legionellales may facilitate bile acid biosynthesis during starvation. Metabolomics analysis found that long chain fatty acids, linolenic acid, cyanoamino acid, and pigments derived from gut bacteria were upregulated, suggesting a beneficial contribution of the gut microbiome to the ascidian under starvation stress.ConclusionsOur findings revealed seasonal variation of ascidian gut microbiota. Defense and energy-associated metabolites derived from gut microbiome may provide an adaptive interplay between gut microbiome and ascidian host that maintains a beneficial metabolic system across season and starvation stress. The diversity-generating metabolisms from both microbiota and host might lead to the co-evolution and environmental adaptation.Graphical

Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger.

It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.

Micro-encapsulated essential oils and organic acids combination improves intestinal barrier function, inflammatory responses and microbiota of weaned piglets challenged with enterotoxigenic Escherichia coli F4 (K88+).

This study evaluated the effects of micro-encapsulated (protected) organic acids (OA) and essential oils (EO) combination, P(OA + EO), and effects of a regular blend of free acids (FA) on the growth, immune responses, intestinal barrier and microbiota of weaned piglets challenged with enterotoxigenic Escherichia coli (ETEC) F4 (K88+). A total of 30 crossbred (Duroc × Landrace × Large White) weaned barrows (7.41 ± 0.06 kg, 28 d old) were assigned randomly to 5 treatments: 1) non-challenged positive control (PC), 2) ETEC F4 (K88+)-challenged negative control (NC), 3) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + free acidifier (FA) at 5 g/kg, 4) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + P(OA + EO) at 1 g/kg (P1), 5) NC + kitasamycin at 50 mg/kg + olaquindox at 100 mg/kg + P(OA + EO) at 2 g/kg (P2). Each dietary treatment had 6 replicates of one piglet each and the study lasted for 3 wk. On d 7, pigs in NC, FA, P1 and P2 were orally dosed with 10 mL of ETEC F4 (K88+) culture (1 × 109 CFU/mL). From d 7 to 14 after the ETEC F4 (K88+) challenge, P1 increased gain-to-feed ratio (G:F) significantly (P < 0.05) compared with NC and FA groups. From d 14 to 21, P2 increased the average daily gain of pigs (P < 0.05) compared with NC and FA groups. Compared with NC, P2 reduced tumor necrosis factor-α (TNF-α), interleukin (IL)-6 and IL-10 concentrations (P < 0.05) in sera collected at 4 h later after ETEC F4 (K88+) challenge. On d 21, P1 increased occludin and zonula occludens-1 protein expression in ileum compared with NC (P < 0.05). After this 3-wk experiment, alpha diversity of gut microbiota was decreased by P2 compared with PC, and P1 increased the relative abundance of Lactobacillus in ileum, cecum and colon (P < 0.05). In conclusion, dietary P(OA + EO) additive at 2 g/kg combined with antibiotics could improve piglet performance and attenuate inflammation, and P(OA + EO) additive at 1 g/kg combined with antibiotics improved intestinal barrier and increased beneficial microbiota composition after an F4 (K88+) challenge.

Lactobacillus plantarum DR7 Modulated Bowel Movement and Gut Microbiota Associated with Dopamine and Serotonin Pathways in Stressed Adults.

We have previously reported that the administration of Lactobacillus plantarum DR7 for 12 weeks reduced stress and anxiety in stressed adults as compared to the placebo group, in association with changes along the brain neurotransmitters pathways of serotonin and dopamine-norepinephrine. We now aim to evaluate the effects of DR7 on gut functions, gut microbiota compositional changes, and determine the correlations between microbiota changes and the pathways of brain neurotransmitters. The administration of DR7 prevented an increase of defecation frequency over 12 weeks as compared to the placebo (p = 0.044), modulating the increase of stress-induced bowel movement. Over 12 weeks, alpha diversity of gut microbiota was higher in DR7 than the placebo group across class (p = 0.005) and order (p = 0.018) levels, while beta diversity differed between groups at class and order levels (p < 0.001). Differences in specific bacterial groups were identified, showing consistency at different taxonomic levels that survived multiplicity correction, along the phyla of Bacteroides and Firmicutes and along the classes of Deltaproteobacteria and Actinobacteria. Bacteroidetes, Bacteroidia, and Bacteroidales which were reduced in abundance in the placebo group showed opposing correlation with gene expression of dopamine beta hydrolase (DBH, dopamine pathway; p < 0.001), while Bacteroidia and Bacteroidales showed correlation with tryptophan hydroxylase-II (TPH2, serotonin pathway; p = 0.001). A correlation was observed between DBH and Firmicutes (p = 0.002), Clostridia (p < 0.001), Clostridiales (p = 0.001), Blautia (p < 0.001), and Romboutsia (p < 0.001), which were increased in abundance in the placebo group. Blautia was also associated with TDO (p = 0.001), whereas Romboutsia had an opposing correlation with TPH2 (p < 0.001). Deltaproteobacteria and Desulfovibrionales which were decreased in abundance in the placebo group showed opposing correlation with DBH (p = 0.001), whereas Bilophila was associated with TPH2 (p = 0.001). Our present data showed that physiological changes induced by L. plantarum DR7 could be associated with changes in specific taxa of the gut microbiota along the serotonin and dopamine pathways.

Differences in Gut Microbiota Following a High-Fiber Diet During Pregnancy

Abstract Objectives To assess the effect of a high fiber diet on changes in gut microbiota and gestational weight gain. Methods Women were block randomized to a 12-week high-fiber (HF; ≥30g/day) intervention (n = 12) or usual care (n = 8). The HF group met weekly for phone counseling with a Registered Dietitian to learn ways in increase fiber intake and given HF snacks (10-12g/day) for the first six weeks. Three 24-hour dietary recalls were performed (baseline, 6 weeks, and 12 weeks). Body weight and stool were collected at baseline and 12 weeks. Gestational weight gain was calculated by subtracting the end study body weight from baseline. Microbial composition was determined by sequencing the 16S rRNA gene targeting the V3-V4 region using MiSeq. Taxa assignment was based on 97% similarity to the Greengenes database and rarefaction were performed with QIIME2. Three measures of alpha diversity were evaluated. T-tests evaluated differences in microbial changes between groups. Pearson's correlations related relative abundance of bacteria to gestational weight gain. Results During the study, the HF group had greater fiber intake (26.1 vs 16.7g; P = 0.02), and gained less weight (5.2 vs 6.6kg; P = 0.11). For alpha diversity, the change in number of observed species and whole tree phylogenetic diversity were different between groups (P = 0.002 and P = 0.004, respectively). No between group differences for change in Shannon Index was found. Taxa from the family Veillonellaceae and genus Dialister were different between groups (P &amp;lt; 0.05). Differences for families Tannerellaceae and Acidaminococcaceae and genera Parabacteroides and Phascolarctobacterium approached significance (P = 0.08-0.09). In the fiber group only, correlations between gestational weight gain and change in Bacteroides (r = -0.586, P = 0.06) and Parabacteroides (r = -0.580, P = 0.10) approached significance. Conclusions After a high-fiber intervention, pregnant women increased fiber intake and gut microbiota alpha diversity, leading to less gestational weight gain. Changes in several taxa at the family and genus level were different between the groups. A larger study is needed to further explore these relationships. Funding Sources This study was supported by a NIH Clinical and Translational Science Award.

Exercise Reverses the Alterations in Gut Microbiota Upon Cold Exposure and Promotes Cold-Induced Weight Loss.

Gut microbiota has been reported to contribute to reduced diet-induced obesity upon cold exposure. Furthermore, gut microbiome fermentation determines the efficacy of exercise for diabetes prevention and enhances exercise performance. However, there have been no systematic examinations of changes in gut microbiome composition in relation to exercise performed under low-temperature conditions. In this study, we investigated the effects of exercise performed under different conditions (room temperature, acute cold, intermittent cold, and sustained cold) in obese rats maintained on a high-fat diet at four time points during experimental trials (days 0, 1, 3, and 35), including observations on white fat browning, weight loss, cardiovascular effects, and changes in gut microbiota among treatment groups. We found that exercise under sustained cold conditions produced a remarkable shift in microbiota composition. Unexpectedly, exercise was found to reverse the alterations in gut microbiota alpha-diversity and the abundance of certain bacterial phyla observed in response to cold exposure (e.g., Proteobacteria decreased upon cold exposure but increased in response to exercise under cold conditions). Moreover, exercise under cold conditions (hereafter referred to “cold exercise”) promoted a considerably higher level of white fat browning and greater weight loss and protected against the negative cardiovascular effects of cold exposure. Correlation analysis revealed that cold exercise-related changes in gut microbial communities were significantly correlated with white fat browning and cardiovascular phenotypes. These results could reveal novel mechanisms whereby additional health benefits attributable to both cold and exercise are mediated via altered gut microbes differently compared with either of them alone.

Case-Control Study of the Effects of Gut Microbiota Composition on Neurotransmitter Metabolic Pathways in Children With Attention Deficit Hyperactivity Disorder.

BackgroundAttention-deficit/hyperactivity disorder (ADHD) is a neuropsychiatric condition that may be related to an imbalance of neural transmitters. The gut microbiota is the largest ecosystem in the human body, and the brain-gut axis theory proposes that the gut microbiome can affect brain function in multiple ways. The purpose of this study was to explore the gut microbiota in children with ADHD and assess the possible role of the gut microbiota in disease pathogenesis to open new avenues for ADHD treatment.MethodsA case-control design was used. We enrolled 17 children aged 6–12 years with ADHD who were treated in the Pediatric Outpatient Department of the First Medical Center of the Chinese PLA General Hospital from January to June, 2019. Seventeen children aged 6–12 years were selected as the healthy control (HC) group. Fecal samples of cases and controls were analyzed by shotgun metagenomics sequencing. Alpha diversity and the differences in the relative abundances of bacteria were compared between the two groups. Functional annotations were performed for the microbiota genes and metabolic pathways were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG).ResultsThere was no significant difference in the alpha diversity of gut microbiota between the ADHD and HC groups. Compared with HCs, Faecalibacterium and Veillonellaceae were significantly reduced in children with ADHD (P < 0.05), Odoribacter and Enterococcus were significantly increased [linear discriminant analysis (LDA) > 2]. At the species level, Faecalibacterium prausnitzii, Lachnospiraceae bacterium, and Ruminococcus gnavus were significantly reduced in the ADHD group (P < 0.05), while Bacteroides caccae, Odoribacter splanchnicus, Paraprevotella xylaniphila, and Veillonella parvula were increased (P < 0.05). Metabolic pathway analysis revealed significant between-group differences in the metabolic pathways of neurotransmitters (e.g., serotonin and dopamine) (P < 0.05).ConclusionComposition differences of gut microbiota in subjects with ADHD may contribute to brain-gut axis alterations and affect neurotransmitter levels, which could contribute to ADHD symptoms.

Differences in gut microbiota composition in metabolic syndrome and type 2 diabetes subjects in a multi-ethnic population: the HELIUS study

AbstractRecently, increased attention has been drawn to the composition of the intestinal microbiota and its possible role in metabolic syndrome and type 2 diabetes (T2DM). However, potential variation in gut microbiota composition across ethnic groups is rarely considered despite observed unequal prevalence for these diseases. Our objective was therefore to study the gut microbiota composition across health, metabolic syndrome and T2DM in a multi-ethnic population residing in the same geographical area. 16S rRNA gene sequencing was performed on fecal samples from 3926 participants to the HELIUS cohort (Amsterdam, The Netherlands), representing 6 ethnic groups (Dutch, Ghanaians, Moroccans, Turks, Surinamese of either African or South-Asian descent). Included participants completed a questionnaire and underwent a physical examination and overnight fasted blood sampling. Gut microbiota composition was compared across metabolic status (diabetes with and without metformin use, metabolic syndrome and its subsequent components, health) and ethnicities using Wilcoxon-Mann-Withney tests and logistic regressions. Overall, the gut microbiota alpha-diversity (richness, Shannon index and phylogenetic diversity) decreased with worsening of the metabolic state (comparing health to metabolic syndrome to T2DM) but this was only partially reproduced in ethnic-specific analyses. In line, a lower alpha-diversity was found in relation to all metabolic syndrome components as well as in T2DM subjects using metformin compared to non-users. Alterations, mainly decreased abundances, were also observed at the genus level (many Clostridiales) in metabolic syndrome subjects and more strongly in T2DM subjects with differences across ethnic groups. In particular, we observed decreased abundances of members of the Peptostreptococcaceae family and of Turicibacter and an increased abundance of a member of the Enterobacteriaceae family. Our data highlight several compositional differences in the gut microbiota of individuals with metabolic syndrome or T2DM. These features, confirming prior observations, give some insights into potential key intestinal bacteria related to a worsening of metabolic state. Our results also underscore possible ethnic-specific profiles associated with these microbiota alterations that should be further explored.

Metagenome of Gut Microbiota of Children With Nonalcoholic Fatty Liver Disease.

Aim: To investigate the intestinal flora of nonalcoholic fatty liver disease (NAFLD) in Chinese children and adolescents using metagenomic approach.Methods: All participants underwent magnetic resonance spectroscopy (MRS) to quantify liver fat content. Hepatic steatosis was defined as MRS proton density fat fraction (MRS-PDFF) >5%. A total of 58 children and adolescents were enrolled in this study, including 25 obese NAFLD patients, 18 obese non-NAFLD children, and 15 healthy children. Stool samples were collected and analyzed with metagenomics. We used Shannon index to reflect the alpha diversities of gut microbiota. Wilcoxon rank sum test and Kruskal-Wallis test were performed to evaluate alpha diversities between groups. At last, the differences of gut microbiota composition and functional annotations between obese with and without NAFLD and healthy children were assessed by Kruskal-Wallis test.Results: Significant differences in gut microbiota composition and functional annotations among three groups of children and adolescents have been observed. Deep sequencing of gut microbiota revealed high abundance of phylum Proteobacteria (Gammaproteobacteria) in obese NAFLD patients, comparing with the control group. Overall, obese children without NAFLD had less abundant Helicobacter and Helicobacter pylori. Compared to the control group, in obese children with NAFLD, the abundance of Bacteroidetes (Alistipes) were significantly reduced. Faecalibacterium prausnitzii was the only species representing a difference between obese children with and without NAFLD. There were not significant differences in terms of alpha diversity among three groups. Functional annotations demonstrated that several pathways were differentially enriched between groups, including metabolism of other amino acids, replication and repair, folding, sorting, degradation, and glycan biosynthesis and metabolism.Conclusion: Significantly differences are observed in gut microbiota composition and functional annotations between obese children with and without NAFLD in comparison to the healthy children group. The characteristic of gut microbiota in this study may contribute to a further understanding the gut-liver axis of pediatric NAFLD in China.

Comparative characterization of bacterial communities in geese consuming of different proportions of ryegrass.

Geese are extremely well-adapted to utilizing plant-derived roughage in their diet, so the grass must be added to commercial diets under intensive rearing systems. However, it is unclear whether the gut microbiota will change significantly when adding different proportions of ryegrass. In this study, 240 healthy male Yangzhou geese (28 days old) with similar body weights were randomly divided into four groups and fed different proportions grass (CK, whole commercial diets; EG1, ryegrass: commercial diets = 1.5:1; EG2, ryegrass: commercial diets = 2:1; EG3, ryegrass: commercial diets = 3:1) respectively. When the geese grew to 70 days old, their intestines were collected and high-throughput sequencing technology was performed to investigate the microbial diversity in the caecum of geese with different dietary supplements. There was no obvious change in the alpha diversity of gut microbiota of geese with ryegrass intake (P > 0.05) and the composition of dominant bacterium (including Bacteroidetes and Firmicutes) was also similar. However, the ratio between Firmicutes and Bacteroidetes was remarkably reduced with ryegrass intake (P < 0.05), and the relative abundance of 30 operational taxonomic units (OTUs) significantly differed. Additionally, the content of cellulose-degrading microbiota such as Ruminiclostridium and Ruminococcaceae UCG-010 were significantly increased in geese fed with increasing amounts of grass. Finally, the functional profiles of the goose gut microbiota were explored using the PICRUSt tool. Carbohydrate metabolism and amino acid metabolism were dominant metabolic pathways. Lipid metabolism was significantly increased in EG3 compared that in the CK group (P < 0.05). Interestingly, Turicibacter and Parasutterella may have affected abdominal fat deposition as grass intake increased. Taken together, although the diversity of bacterial communities was similar in geese fed with different proportions of ryegrass, cellulose-degrading microbiota (Ruminiclostridium and Ruminococcaceae UCG-010) were abundant and the lipid metabolic pathway was enriched, which may reduce abdominal fat accumulation in high-ryegrass fed geese.

Oral selective serotonin reuptake inhibitors activate vagus nerve dependent gut-brain signalling

The vagus nerve can transmit signals to the brain resulting in a reduction in depressive behavior as evidenced by the long-term beneficial effects of electrical stimulation of the vagus in patients with intractable depression. The vagus is the major neural connection between gut and brain, and we have previously shown that ingestion of beneficial bacteria modulates behaviour and brain neurochemistry via this pathway. Given the high levels of serotonin in the gut, we considered if gut-brain signaling, and specifically the vagal pathway, might contribute to the therapeutic effect of oral selective serotonin reuptake inhibitors (SSRI). Mesenteric nerve recordings were conducted in mice after treatment with SSRI to ascertain if this class of drugs resulted in increased vagal excitability. Patch clamp recordings of enteric neurons were carried out to measure activity of primary afferent neurons in the gut in response to SSRI and to assess the importance of gut epithelium in transducing signal. The tail suspension test (TST) was used following 14d feeding of SSRI in vagotomised and surgical sham mice to measure depressive-like behaviour. Brain mRNA expression was examined via PCR and the intestinal microbiome was assessed. Mesenteric nerve recordings in BALB/c mice demonstrated that oral treatment with SSRI leads to a significant increase in vagal activity. This effect was not observed in mice treated with a representative noradrenaline-dopamine reuptake inhibitor. It is known that signals from the gut can be transmitted to the vagus via the enteric nervous system. Exposure of the gut to SSRI increased the excitability of intrinsic primary afferent neurons in the myenteric plexus, through an intestinal epithelium dependent mechanism, and alpha-diversity of gut microbiota was altered. Critically, blocking vagal signaling from gut to brain, via subdiaphragmatic vagotomy, abolished the antidepressive effects of oral SSRI treatment as determined by the tail suspension test. This work suggests that vagus nerve dependent gut-brain signaling contributes to the effects of oral SSRI and further, highlights the potential for pharmacological approaches to treatment of mood disorders that focus on vagal stimulation and may not even require therapeutic agents to enter the circulation.

A decreased abundance of clostridia characterizes the gut microbiota in eosinophilic esophagitis.

Abnormalities in the gut microbiome are associated with suppressed Th2 response (Belizario et al., 2018 Mediators Inflamm. 2018:2037838) and predisposition to atopic disease such as asthma and eczema. We investigated if this applies to eosinophilic esophagitis (EoE). Stool bacterial DNA was extracted and followed by 16S rRNA amplification from 12 patients with eosinophilic esophagitis and 12 controls. Alpha‐ and beta‐diversity were analyzed. Only two patients had asthma or atopy and one patient was on budesonide. No patients were on PPIs. Patients with EoE had lower gut microbiota alpha diversity (species richness, P = 0.09; Shannon index, P = 0.01). The microbial composition was distinct as evidenced by significantly different beta diversity (P = 0.03) when compared to healthy controls. There were also significant differences in relative abundance at multiple taxonomic levels when comparing the two communities; at the phylum level, we observed a marked decrease in Firmicutes and increase in Bacteroidetes and at the order and family level there were significant decreases in Clostridia and Clostridiales in patients with EoE (q ≤ 0.1). We conclude that there are significant differences in microbial community structure, microbial richness, and evenness and a significant decrease in taxa within the Clostridia in patients with EoE. Our data suggest that Clostridia based interventions could be tested as adjuncts to current therapeutic strategies in EoE.