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opencc-zeroNov 2020View details →

The phylogeny and function of gut microbiota associated with host geographic/genetic distance and biological characteristics (data S1)

Symbiotic microbiomes play important roles in hosts' adaptation and evolution. Here, the gut bacterial communities in Cephalcia chuxiongica, a key pest of pines in China, were studied for the first time by using 16S rRNA amplicon sequencing. The composition of gut bacterial communities differed in different C. chuxiongica geographic populations, while the various microbes performed similar functions, suggesting some kinds of functional complementation. The predicted functional profiles of microbes indicated that most of identified KEGG Pathways were shared by different populations, in which metabolism was the most dominant functional pathway. Moreover, the function of major microbes associated with host dietary specialization (pine needles), such as cellulose degradation. All samples contained abundant Wolbachia, which may play important roles on the parthenogenesis of C. chuxiongica. The high abundances of Serratia and Sphingomonas in samples suggest that gut microbiota may crucial for the long-term larval diapause in C. chuxiongica. Interestingly, this study found that the phylogeny and diversity of gut microbiota correlated to host geographic/genetic distance, i.e., the microbiota was more similar as the geographic/genetic distance decreased, and vice versa. Therefore, the synergy of environmental and host factors appears to be the main force shaping the structure and variability of gut microbiota and likewise, gut microbiota may exert a significant effect on its host by shaping host biological characters, suggesting some kinds of extraordinary symbiosis and coevolution. These results demonstrate the important contribution of gut microbiota and provide a sound foundation for developing control strategies for this pest.

opencc-zeroDec 2018View details →

Data from: Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: comparison between subgroups according to clinical criteria and toxin gene load

Data concerning the human microbiota composition during Clostridioides (Clostridium) difficile infection (CDI) using next-generation sequencing are still limited. We aimed to confirm key features indicating tcdB positive patients and compare the microbiota composition between subgroups based on toxin gene load (tcdB gene) and presence of significant diarrhea. Ninety-nine fecal samples from 79 tcdB positive patients and 20 controls were analyzed using 16S rRNA gene sequencing. Chao1 index for alpha diversity were calculated and principal coordinate analysis was performed for beta diversity using Quantitative Insights into Microbial Ecology (QIIME) pipeline. The mean relative abundance in each group was compared at phylum, family, and genus levels. There were significant alterations in alpha and beta diversity in tcdB positive patients (both colonizer and CDI) compared with those in the control. The mean Chao1 index of tcdB positive patients was significantly lower than the control group (P<0.001), whereas there was no significant difference between tcdB groups and between colonizer and CDI. There were significant differences in microbiota compositions between tcdB positive patients and the control at phylum, family, and genus levels. Several genera such as Phascolarctobacterium, Lachnospira, Butyricimonas, Catenibacterium, Paraprevotella, Odoribacter, and Anaerostipes were not detected in most CDI cases. We identified several changes in the microbiota of CDI that could be further evaluated as predictive markers. Microbiota differences between clinical subgroups of CDI need to be further studied in larger controlled studies.

opencc-zeroDec 2017View details →

Data from: The effect of gut microbiota elimination in Drosophila melanogaster: a how-to guide for host-microbiota studies

In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behaviour, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster. We test the efficacy of a low-dose streptomycin diet, egg dechorionation, and an axenic or sterile diet, in the removal of gut bacteria within this species in a fully factorial design. We further determine potential side effects of these methods on host physiology by performing a series of standard physiological assays. Our results showed that individuals from all treatments took significantly longer to develop, and weighed less, compared to normal flies. Males and females that had undergone egg dechorionation weighed significantly less than streptomycin reared individuals. Similarly, axenic female flies, but not males, were much less active when analysed in a locomotion assay. All methods decreased the egg to adult survival, with egg dechorionation inducing significantly higher mortality. We conclude that low-dose streptomycin added to the dietary media is more effective at removing the gut bacteria than egg dechorionation and has somewhat less detrimental effects to host physiology. More importantly, this method is the most practical and reliable for use in behavioural research. Our study raises the important issue that the efficacy of and impacts on the host of these methods, requires investigation in a case by case manner, rather than assuming homogeneity across species and laboratories.

opencc-zeroDec 2016View details →

Data from: Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota

Subclinical chronic inflammation (SCI) is associated with impaired animal growth. Previous work has demonstrated that olive-derived plant bioactives exhibit anti-inflammatory properties that could possibly counteract the growth-depressing effects of SCI. To test this hypothesis and define the underlying mechanism, we conducted a 30-day study in which piglets fed an olive-oil bioactive extract (OBE) and their control counterparts (C+) were injected repeatedly during the last 10 days of the study with increasing doses of Escherichia coli lipopolysaccharides (LPS) to induce SCI. A third group of piglets remained untreated throughout the study and served as a negative control (C-). In C+ pigs, SCI increased the circulating concentration of interleukin 1 beta (p < 0.001) and decreased feed ingestion (p < 0.05) and weight gain (p < 0.05). These responses were not observed in OBE animals. Although intestinal inflammation and colonic microbial ecology was not altered by treatments, OBE enhanced ileal mRNA abundance of tight and adherens junctional proteins (p < 0.05) and plasma recovery of mannitol (p < 0.05) compared with C+ and C-. In line with these findings, OBE improved transepithelial electrical resistance (p < 0.01) in TNF-α-challenged Caco-2/TC-7 cells, and repressed the production of inflammatory cytokines (p < 0.05) in LPS-stimulated macrophages. In summary, this work demonstrates that OBE attenuates the suppressing effect of SCI on animal growth through a mechanism that appears to involve improvements in intestinal integrity unrelated to alterations in gut microbial ecology and function.

opencc-zeroDec 2012View details →

Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the community that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any known Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising 26,750 isogenic transposon mutants into gnotobiotic mice along with other model community members confirmed that these loci represent critical diet-specific fitness determinants. The specific carbohydrates that trigger overexpression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota.

The Role of the Microbiota-gut-brain Axis in Brain Development and Mental Health

ClinicalTrials.gov study NCT03835468. IPD Sharing: NO. Countries: 1. Publications: 0.

Gut Microbiota is Associated With Autoimmune Thyroid Disease

ClinicalTrials.gov study NCT03390582. IPD Sharing: NO. Countries: 1. Publications: 0.

Gut Microbiota and Alzheimer's Diseases

ClinicalTrials.gov study NCT03827733. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.

The Interaction Between Protein Intake, Gut Microbiota and Type 2 Diabetes in Subjects With Different Ethnic Backgrounds

ClinicalTrials.gov study NCT03732690. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Microbiota and Bone Fragility:Study of the Relation Between Gut Microbiota and Bone Microarchitecture

ClinicalTrials.gov study NCT04265742. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Study of the Interactions Between Dientamoba Fragilis and the Gut Microbiota

ClinicalTrials.gov study NCT02534272. IPD Sharing: Not stated. Countries: 1. Publications: 0.

controlledIPD-YESFeb 2026View details →

Can the Reduction of Iron Availability Caused by Tea Consumption Change the Gut Microbiota Composition and Disrupt Host Body-iron Status

ClinicalTrials.gov study NCT05019573. IPD Sharing: YES. Countries: 1. Publications: 0.

Lactobacillus Reuteri DSM 17938 in Gut Microbiota Development in Infant Born by Caesarean Section

ClinicalTrials.gov study NCT03675048. IPD Sharing: Not stated. Countries: 1. Publications: 0.

controlledIPD-YESFeb 2026View details →

Exploring Gut-Brain and Brain-Gut Interactions in Alcohol Use Disorder Via Microbiota Investigations: A Pilot Study

ClinicalTrials.gov study NCT03152760. IPD Sharing: YES. Countries: 1. Publications: 0.

Characteristics of Gut Microbiota in Patients With Colon Cancer of Different Traditional Chinese Medicine Syndromes

ClinicalTrials.gov study NCT03892252. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Composition and Function of Gut Microbiota in Porto-sinusoidal Vascular Disease Associated With Variable Common Immunodeficiency

ClinicalTrials.gov study NCT05481554. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Response of Gut Microbiota in Type 2 Diabetes to Hypoglycemic Agents

ClinicalTrials.gov study NCT04287387. IPD Sharing: NO. Countries: 1. Publications: 0.

Study of Gut Microbiota in Crohn's Disease Patients Suffering From Spondylarthritis

ClinicalTrials.gov study NCT03072836. IPD Sharing: NO. Countries: 1. Publications: 0.