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NPJ Parkinson's Disease Dec 2022Gut microbiota and fecal bile acids were analyzed in 278 patients with α-synucleinopathies, which were comprised of 28 patients with dementia with Lewy bodies (DLB),...
Gut microbiota and fecal bile acids were analyzed in 278 patients with α-synucleinopathies, which were comprised of 28 patients with dementia with Lewy bodies (DLB), 224 patients with Parkinson's disease (PD), and 26 patients with idiopathic rapid eye movement sleep behavior disorder (iRBD). Similarly to PD, short-chain fatty acids-producing genera were decreased in DLB. Additionally, Ruminococcus torques and Collinsella were increased in DLB, which were not changed in PD. Random forest models to differentiate DLB and PD showed that high Ruminococcus torques and high Collinsella, which presumably increase intestinal permeability, as well as low Bifidobacterium, which are also observed in Alzheimer's disease, were predictive of DLB. As Ruminococcus torques and Collinsella are also major secondary bile acids-producing bacteria, we quantified fecal bile acids and found that the production of ursodeoxycholic acid (UDCA) was high in DLB. Increased UDCA in DLB may mitigate neuroinflammation at the substantia nigra, whereas neuroinflammation may not be critical at the neocortex. Theraeutic intervention to increase Bifidobacteirum and its metabolites may retard the development and progression of DLB.
PubMed: 36494405
DOI: 10.1038/s41531-022-00428-2 -
Digestion 2023Alteration of the gut microbial structure and function (dysbiosis) is associated with the pathogenesis of various disorders including inflammatory bowel disease (IBD). (Review)
Review
BACKGROUND
Alteration of the gut microbial structure and function (dysbiosis) is associated with the pathogenesis of various disorders including inflammatory bowel disease (IBD).
SUMMARY
Under normal conditions, β-oxidation of butyrate consumes oxygen in colonocytes and maintains the anaerobic environment in the lumen. Depletion of butyrate-producing bacteria results in anaerobic glycolysis in colonocytes and increases oxygen diffusion into the lumen, leading to a luminal facultative anaerobe expansion. Dysbiosis in IBD is characterized by the reduced abundance of the phylum Firmicutes (e.g., Faecalibacterium, Roseburia, and Ruminococcus) and an increase of the phylum Proteobacteria (e.g., Enterobacteriaceae). The overall structure of the gut mycobiome differs markedly in IBD patients, particularly Crohn's disease (CD), compared with healthy individuals. An increase in the genus Candida is a major contributory factor in the alteration of the mycobiome in Japanese CD patients, but an increase in the genus Saccharomyces is characteristic in Western patients. The gut virome, which is mainly composed of bacteriophages (phages), influences gut homeostasis and pathogenic conditions via an interaction with the gut bacterial community. Alterations in the gut virome have been suggested in patients with IBD. This may alter either the immunogenicity of bacteria, thus affecting the bacteria-host interactions, or the bacterial functions such as antibiotic resistance and toxin synthesis.
KEY MESSAGE
Advances in DNA sequencing technology and bioinformatics have revolutionized our understanding of the microbiome in the gut.
Topics: Humans; Gastrointestinal Microbiome; Dysbiosis; Feces; Inflammatory Bowel Diseases; Crohn Disease; Butyrates
PubMed: 35901721
DOI: 10.1159/000525925 -
Microbiology Spectrum Aug 2022Little is known about the bacteria that reside in the human gallbladder and the mechanisms that allow them to survive within this harsh environment. Here we describe...
Little is known about the bacteria that reside in the human gallbladder and the mechanisms that allow them to survive within this harsh environment. Here we describe interactions between two strains from a human bile sample, one Ruminococcus gauvreauii (IPLA60001), belonging to the family, and the other, designated as Ruminococcoides bili (IPLA60002; DSM 110008) most closely related to Ruminococcus bromii within the family Ruminococcaceae. We provide evidence for bile salt resistance and sporulation for these new strains. Both differed markedly in their carbohydrate metabolism. The R. bili strain mainly metabolized resistant starches to form formate, lactate and acetate. R. gauvreauii mainly metabolized sugar alcohols, including inositol and also utilized formate to generate acetate employing the Wood Ljungdahl pathway. Amino acid and vitamin biosynthesis genomic profiles also differed markedly between the two isolates, likely contributing to their synergistic interactions, as revealed by transcriptomic analysis of cocultures. Transcriptome analysis also revealed that R. gauvreauii IPLA60001 is able to grow using the end-products of starch metabolism formed by the R. bili strain such as formate, and potentially other compounds (such as ethanolamine and inositol) possibly provided by the autolytic behavior of R. bili. Unique insights into metabolic interaction between two isolates; Ruminococcus gauvreauii IPLA60001 and Ruminococcoides bili IPLA60002, from the human gallbladder, are presented here. The R. bili strain metabolized resistant starches while R. gauvreauii failed to do so but grew well on sugar alcohols. Transcriptomic analysis of cocultures of these strains, provides new data on the physiology and ecology of two bacteria from human bile, with a particular focus on cross-feeding mechanisms. Both biliary strains displayed marked resistance to bile and possess many efflux transporters, potentially involved in bile export. However, they differ markedly in their amino acid catabolism and vitamin synthesis capabilities, a feature that is therefore likely to contribute to the strong synergistic interactions between these strains. This is therefore the first study that provides evidence for syntrophic metabolic cooperation between bacterial strains isolated from human bile.
Topics: Acetates; Amino Acids; Bacteria; Bile; Clostridiales; Formates; Humans; Inositol; Ruminococcus; Sugar Alcohols; Vitamins
PubMed: 35863028
DOI: 10.1128/spectrum.02776-21 -
Frontiers in Immunology 2023Gut microbial imbalance (dysbiosis) has been reported in patients with acute Kawasaki disease (KD). However, no studies have analyzed the gut microbiota while focusing...
INTRODUCTION
Gut microbial imbalance (dysbiosis) has been reported in patients with acute Kawasaki disease (KD). However, no studies have analyzed the gut microbiota while focusing on susceptibility to KD. This study aimed to evaluate whether dysbiosis elevates susceptibility to KD by assessing children with a history of KD.
METHODS
Fecal DNA was extracted from 26 children with a history of KD approximately 1 year prior (KD group, 12 boys; median age, 32.5 months; median time from onset, 11.5 months) and 57 age-matched healthy controls (HC group, 35 boys; median age, 36.0 months). 16S rRNA gene analysis was conducted with the Illumina Miseq instrument. Sequence reads were analyzed using QIIME2.
RESULTS
For alpha diversity, Faith's phylogenetic diversity was significantly higher in the KD group. Regarding beta diversity, the two groups formed significantly different clusters based on Bray-Curtis dissimilarity. Comparing microbial composition at the genus level, the KD and HC groups were significantly different in the abundance of two genera with abundance over 1% after Benjamini-Hochberg false discovery rate correction for multiple comparisons. Compared with the HC group, the KD group had higher relative abundance of group and lower relative abundance of .
DISCUSSION AND CONCLUSION
group reportedly includes pro-inflammatory bacteria. In contrast, suppresses inflammation via butyrate production. In the predictive functional analysis, the proportion of gut microbiota involved in several pathways was lower in the KD group. Therefore, dysbiosis characterized by distinct microbial diversity and decreased abundance of in parallel with increased abundance of group might be a susceptibility factor for KD.
Topics: Male; Child; Humans; Child, Preschool; Gastrointestinal Microbiome; Dysbiosis; RNA, Ribosomal, 16S; Mucocutaneous Lymph Node Syndrome; Phylogeny; Acute Disease; Ruminococcus
PubMed: 38022552
DOI: 10.3389/fimmu.2023.1268453 -
Frontiers in Microbiology 2024This study aimed to clarify the relationship between the gut microbiota and osteoporosis combining Mendelian randomization (MR) analysis with animal experiments.
BACKGROUND
This study aimed to clarify the relationship between the gut microbiota and osteoporosis combining Mendelian randomization (MR) analysis with animal experiments.
METHODS
We conducted an analysis on the relationship between differential bacteria and osteoporosis using open-access genome-wide association study (GWAS) data on gut microbe and osteoporosis obtained from public databases. The analysis was performed using two-sample MR analysis, and the causal relationship was examined through inverse variance weighting (IVW), MR Egger, weighted median, and weighted mode methods. Bilateral oophorectomy was employed to replicate the mouse osteoporosis model, which was assessed by micro computed tomography (CT), pathological tests, and bone transformation indexes. Additionally, 16S rDNA sequencing was conducted on fecal samples, while SIgA and indexes of IL-6, IL-1β, and TNF-α inflammatory factors were examined in colon samples. Through immunofluorescence and histopathology, expression levels of tight junction proteins, such as claudin-1, ZO-1, and occludin, were assessed, and conduct correlation analysis on differential bacteria and related environmental factors were performed.
RESULTS
A positive correlation was observed between and the risk of osteoporosis, while showed a negative correlation with the risk of osteoporosis. Furthermore, there was no evidence of heterogeneity or pleiotropy. The successful replication of the mouse osteoporosis model was assessed, and it was found that the abundance of the was significantly reduced, while the abundance of was significantly increased in the ovariectomized (OVX)-mice. The intestinal SIgA level of OVX mice decreased, the expression level of inflammatory factors increased, barrier damage occurred, and the content of LPS in the colon and serum significantly increased. The abundance level of is strongly positively correlated with bone formation factors, gut barrier indicators, bone density, bone volume fraction, and trabecular bone quantity, whereas it was strongly negatively correlated with bone resorption factors and intestinal inflammatory factors, The abundance level of shows a strong negative correlation with bone formation factors, gut barrier indicators, and bone volume fraction, and a strong positive correlation with bone resorption factors and intestinal inflammatory factors.
CONCLUSION
and may regulate the development of osteoporosis through the microbiota-gut-bone axis.
PubMed: 38835486
DOI: 10.3389/fmicb.2024.1373013 -
Microbial Genomics Jul 2023is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being....
is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being. We postulate the ambiguities of its function in different cases may be attributed to strain-level variability of genomic features of . We performed comparative genomic and pathogenicity prediction analysis on 152 filtered high-quality genomes, including 4 genomes of strains isolated from healthy adults in this study. The mean G+C content of genomes of was 42.73±0.33 mol%, and the mean genome size was 3.46±0.34 Mbp. Genome-wide evolutionary analysis revealed genomes were divided into three major phylogenetic clusters. Pan-core genome analysis revealed that there was a total of 28 072 predicted genes, and the core genes, soft-core genes, shell genes and cloud genes accounted for 3.74 % (1051/28 072), 1.75 % (491/28 072), 9.88 % (2774/28 072) and 84.63 % (23 756/28 072) of the total genes, respectively. The small proportion of core genes reflected the wide divergence among strains. We found certain coding sequences with determined health benefits (such as vitamin production and arsenic detoxification), whilst some had an implication of health adversity (such as sulfide dehydrogenase subunits). The functions of the majority of core genes were unknown. The most widespread genes functioning in antibiotic resistance and virulence are (tetracycline-resistance gene, present in 75 strains) and (capsular polysaccharide biosynthesis protein Cps4J encoding gene, detected in 3 genomes), respectively. Our results revealed genomic divergence and the existence of certain safety-relevant factors of . This study provides new insights for understanding the genomic features and health relevance of , and raises concerns regarding predicted prevalent pathogenicity and antibiotic resistance among most of the strains.
Topics: Adult; Animals; Humans; Ruminococcus; Phylogeny; Clostridiales; Genomics
PubMed: 37486746
DOI: 10.1099/mgen.0.001071 -
Gut Microbes 2022The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of... (Review)
Review
The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of interest since the nineteenth century. Cellulolytic bacteria are key participants in this breakdown process of cellulose, which is otherwise indigestible by the host. They critically contribute to host nutrition and health through the production of short-chain fatty acids, in addition to maintaining the balance of intestinal microbiota. Despite this key role, cellulolytic bacteria have not been well studied. In this review, we first retrace the history of the discovery of cellulolytic bacteria in the large intestine. We then focus on the current knowledge of cellulolytic bacteria isolated from the large intestine of various animal species and humans and discuss the methods used for isolating these bacteria. Moreover, we summarize the enzymes and the mechanisms involved in cellulose degradation. Finally, we present the contribution of these bacteria to the host.
Topics: Animals; Bacteria; Cellulose; Gastrointestinal Microbiome; Humans; Intestine, Large; Mammals
PubMed: 35184689
DOI: 10.1080/19490976.2022.2031694 -
Frontiers in Veterinary Science 2021Ducks with the same genetic background vary greatly in their adiposity phenotypes. The gut microbiota plays an essential role in host physiological development and...
Ducks with the same genetic background vary greatly in their adiposity phenotypes. The gut microbiota plays an essential role in host physiological development and metabolism including fat deposition. However, the association of the gut microbiota with the lipogenic phenotype of ducks remains unknown. In this study, we investigated the cecal microbiota of adult Muscovy ducks and the correlation of the cecal microbiota with fat phenotypes. A total of 200 Muscovy ducks were selected from a population of 5,000 Muscovy ducks to record their abdominal fat weight and collect their cecal contents after being slaughtered and defeathered. The cecal contents were subjective to DNA isolation and 16S rRNA gene sequencing. The results were sorted according to the percentage of abdominal fat and the top 20% ( = 40) and the bottom 20% ( = 40) were set as the high and low groups, respectively. Our results indicated that in the cecum of Muscovy ducks, Bacteroidetes, Firmicutes, and Fusobacteria were the predominant phyla while , and were the top 4 dominant genera. Abdominal fat weight (18.57~138.10 g) and percentage of abdominal fat (1.02~27.12%) were significantly correlated ( = 0.92, < 0.001). Although the lipogenic phenotypes of ducks had a significant difference ( < 0.05), the α-diversities of the high and low groups were not significantly different ( > 0.05). Nevertheless, after random forest analysis, we identified two genera, and , that were significantly associated with fat deposition in Muscovy ducks. In addition, the abundances of and gave a significantly negative and positive association with abdominal fat weight, respectively ( < 0.05). Ducks with a low level of exhibited a tendency toward a high percentage of abdominal fat ( < 0.01), while the percentage of abdominal fat in ducks with high abundance tended to be higher than that in ducks with low abundance ( < 0.01). These findings could provide the basic data on the cecal microbiota in Muscovy ducks as well as a theoretical foundation to limit the fat deposition by modulating the gut microbiota in the duck industry.
PubMed: 33869315
DOI: 10.3389/fvets.2021.609348 -
Journal of Hazardous Materials May 2024Studies on the role of the gut microbiota in the associations between per- and polyfluoroalkyl substance (PFAS) exposure and adverse neurodevelopment are limited....
Studies on the role of the gut microbiota in the associations between per- and polyfluoroalkyl substance (PFAS) exposure and adverse neurodevelopment are limited. Umbilical cord serum and faeces samples were collected from children, and the Strengths and Difficulties Questionnaire (SDQ) was conducted. Generalized linear models, linear mixed-effects models, multivariate analysis by linear models and microbiome regression-based kernel association tests were used to evaluate the associations among PFAS exposure, the gut microbiota, and neurobehavioural development. Perfluorohexane sulfonic acid (PFHxS) exposure was associated with increased scores for conduct problems and externalizing problems, as well as altered gut microbiota alpha and beta diversity. PFHxS concentrations were associated with higher relative abundances of Enterococcus spp. but lower relative abundances of several short-chain fatty acid-producing genera (e.g., Ruminococcus gauvreauii group spp.). PFHxS exposure was also associated with increased oxidative phosphorylation. Alpha and beta diversity were found significantly associated with conduct problems and externalizing problems. Ruminococcus gauvreauii group spp. abundance was positively correlated with prosocial behavior scores. Increased alpha diversity played a mediating role in the associations of PFHxS exposure with conduct problems. Our results suggest that the gut microbiota might play an important role in PFAS neurotoxicity, which may have implications for PFAS control.
Topics: Child; Female; Pregnancy; Humans; Gastrointestinal Microbiome; Dysbiosis; Ruminococcus; Fluorocarbons; Environmental Pollutants; Alkanesulfonic Acids; Sulfonic Acids
PubMed: 38457972
DOI: 10.1016/j.jhazmat.2024.133920 -
BMC Microbiology Apr 2024Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional... (Meta-Analysis)
Meta-Analysis
Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.
Topics: Humans; Gastrointestinal Microbiome; Metagenome; Obesity; Bacteria; Feces; Clostridiales; Akkermansia
PubMed: 38580930
DOI: 10.1186/s12866-024-03278-5