Dataset Information

The gut microbiota heterogeneity and assembly changes associated with the IBD.

ABSTRACT: Inflammatory bowel disease (IBD) is an immunologically mediated disease and may be caused by abnormal immunological response to gut microbes. Although several studies on the ecological changes associated with IBD, such as community diversities, were reported, no previous studies have investigated the changes in the spatial heterogeneity and the mechanism of community assembly of the gut microbiota associated with IBD. In the present study, we first applied the Taylor's power law extensions to compare the community spatial heterogeneity between the gut microbial communities of the IBD patients and those of the healthy individuals. We found that the community spatial heterogeneity of gut microbiota in IBD patients is slightly lower than in the healthy individuals. This finding suggests that IBD may lower the spatial heterogeneity of gut microbiota, possibly via lowering the abundance of dominant species. We further applied the neutral theory of biodiversity to comparatively investigate the community assembly and diversity maintenance of the gut microbiota with and without IBD, and our application suggested that deterministic factors such as host immunity should be dominant forces shaping gut microbiota assembly, and diseases such as IBD may not be strong enough to change the trend set by the deterministic host factors.

SUBMITTER: Sun Y

PROVIDER: S-EPMC6345861 | biostudies-other | 2019 Jan

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

The gut microbiota heterogeneity and assembly changes associated with the IBD.

Sun Yang Y Li Lianwei L Xia Yao Y Li Wendy W Wang Kunhua K Wang Lan L Miao Yinglei Y Ma Sam S

Scientific reports 20190124 1

Inflammatory bowel disease (IBD) is an immunologically mediated disease and may be caused by abnormal immunological response to gut microbes. Although several studies on the ecological changes associated with IBD, such as community diversities, were reported, no previous studies have investigated the changes in the spatial heterogeneity and the mechanism of community assembly of the gut microbiota associated with IBD. In the present study, we first applied the Taylor's power law extensions to co ...[more]

PMID: 30679676

Similar Datasets

Project description:BackgroundPost-cholecystectomy diarrhea (PCD) frequently occurs in patients following gallbladder removal. PCD is part of the post-cholecystectomy (PC) syndrome, and is difficult to treat. After cholecystectomy, bile enters the duodenum directly, independent of the timing of meals. The interaction between the bile acids and the intestinal microbes is changed. Therefore, the occurrence of PCD may be related to the change in microbiota. However, little is known about the relationship between the gut microbiota and PCD.AimTo better understand the role of the gut microbiota in PCD patients.MethodsFecal DNA was isolated. The diversity and profiles of the gut microbiota were analyzed by performing high-throughput 16S rRNA gene sequencing. The gut microbiota were characterized in a healthy control (HC) group and a PC group. Subsequently, the PC group was further divided into a PCD group and a post-cholecystectomy non-diarrhea group (PCND) according to the patients' clinical symptoms. The composition, diversity and richness of microbial communities were determined and compared.ResultsIn the PC and HC groups, 720 operational taxonomic units (OTUs) were identified. The PC group had fewer OTUs than the HC group. β-diversity was decreased in the PC group. This indicated decreased microbial diversity in the PC group. Fifteen taxa with differential abundance between the HC and PC groups were identified. In the PCD group compared to the PCND group, significant decreases in microbial diversity, Firmicutes/Bacteroidetes ratio, and richness of probiotic microbiota (Bifidobacterium and Lactococcus), and an increase in detrimental microbiota (Prevotella and Sutterella) were observed. Moreover, a negative correlation was found between Prevotella and Bifidobacterium. Using a Kyoto Encyclopedia of Genes and Genomes functional analysis, it was found that the abundances of gut microbiota involved in lipid metabolism pathways were markedly lower in the PCD group compared to the PCND group.ConclusionThis study demonstrated that gut dysbiosis may play a critical role in PCD, which provides new insights into therapeutic options for PCD patients.

Project description:Antibiotic therapy is a causative agent of severe disturbances in microbial communities. In healthy individuals, the gut microbiota prevents infection by harmful microorganisms through direct inhibition (releasing antimicrobial compounds), competition, or stimulation of the host's immune defenses. However, widespread antibiotic use has resulted in short- and long-term shifts in the gut microbiota structure, leading to a loss in colonization resistance in some cases. Consequently, some patients develop Clostridium difficile infection (CDI) after taking an antibiotic (AB) and, at present, this opportunistic pathogen is one of the main causes of antibiotic-associated diarrhea in hospitalized patients. Here, we analyze the composition and functional differences in the gut microbiota of C. difficile infected (CDI) vs. non-infected patients, both patient groups having been treated with AB therapy. To do so we used 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. Samples were taken before, during and after AB treatment and were checked for the presence of the pathogen. We performed different analyses and comparisons between infected (CD+) vs. non-infected (CD-) samples, allowing proposing putative candidate taxa and functions that might protect against C. difficile colonization. Most of these potentially protective taxa belonged to the Firmicutes phylum, mainly to the order Clostridiales, while some candidate protective functions were related to aromatic amino acid biosynthesis and stress response mechanisms. We also found that CDI patients showed, in general, lower diversity and richness than non-infected, as well as an overrepresentation of members of the families Bacteroidaceae, Enterococcaceae, Lactobacillaceae and Clostridium clusters XI and XIVa. Regarding metabolic functions, we detected higher abundance of genes involved in the transport and binding of carbohydrates, ions, and others compounds as a response to an antibiotic environment.

Dataset Information

The gut microbiota heterogeneity and assembly changes associated with the IBD.

Publications

The gut microbiota heterogeneity and assembly changes associated with the IBD.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets