Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 7000B Triple Quadrupole GC/MS
ORGANISM(S): Dietary Carbohydrates Alter Immune-modulatory Functionalities And Dna Inversions In Bacteroides Thetaiotaomicron
SUBMITTER: 
Naama Geva-Zatorsky
PROVIDER: MSV000097823 | MassIVE | Wed May 07 13:04:00 BST 2025
REPOSITORIES: MassIVE
Similar Datasets
Project description:The environment of gut bacteria is extremely dynamic. Environmental conditions were shown to affect microbial composition, however, their effects on bacterial functionality (e.g., immune-modulation activity) are mostly overlooked. Distinct strains of the same species, and even the same bacterial strain, may have different effects on the immune system depending on their growth environment. Therefore, studying the functionality of strains, under different conditions, is crucial. We analyzed functional alterations in the gut symbiont Bacteroides thetaiotaomicron (B. theta) under different diets in humans, under sugar consumption in mice, and in response to 190 different carbon sources in vitro. Dietary alterations affected the orientation of phase variable promoters in B. theta in humans, in vivo and in vitro and altered B. theta’s proteome and immune-modulatory functionality. Studying the effects of dietary components on the immune-modulatory functionalities of key members of the gut microbiota will allow tailored dietary recommendations to patients.
2025-05-04 | PXD060215 | Pride
Project description:Environmental influences such as infections and dietary changes strongly affect a host’s microbiota. In the steady state, however, host genetics may influence the microbiota composition, as suggested by the greater similarity between the microbiomes of identical twin pairs compared to non-identical twins. Understanding the role of polymorphic mechanisms in regulating the commensal communities is complicated by the variability of human genomes and microbiomes, and by microbial sensitivity to the environment. Animal studies allow genetic modifications, but are also sensitive to influences known as ‘cage’ or ‘legacy’ effects. Here, we analyzed ex-germ-free mice of various genetic backgrounds, including immunodeficient and Major Histocompatibility Complex (MHC)-congenic strains repopulated with identical input microbiota. We found that the host’s genetic polymorphic mechanisms did indeed affect the gut microbiome and that both innate (e.g. anti-microbial peptides, complement, pentraxins and enzymes affecting microbial survival), as well as adaptive (both MHC-dependent and MHC-independent) pathways influenced the microbiota. These polymorphic mechanisms regulated only a limited number of microbial lineages (independently of their abundance). In addition, our comparative analyses suggested that some microbes might benefit from the specific immune responses that they elicit.
2019-08-29 | GSE136572 | GEO
Project description:The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs.
2012-09-30 | GSE32207 | GEO
Project description:The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. Here, we focus on the comparison of gut microbial communities in miniature pigs developed for xenotransplantation in specific pathogen-free (SPF) and conventional (non-SPF) facilities. To identify the disparities in gut microbial composition and functionality between these two environments, 16S RNA metagenome sequencing was conducted using fecal samples. The results revealed that the non-SPF pigs had higher gut microbiota diversity than the SPF pigs. The genera Streptococcus and Ruminococcus were more abundant in SPF pigs than in non-SPF pigs. Blautia, Bacteroides, and Roseburia were exclusively observed in SPF pigs, whereas Prevotella was exclusively found in non-SPF pigs. Carbohydrate and nucleotide metabolism, as well as environmental information processing, were predicted to be enriched in SPF pigs. In addition, energy and lipid metabolism, along with processes related to genetic information, cellular communication, and diseases, were predicted to be enriched in non-SPF pigs. This study makes an important contribution to elucidating the impact of environments harboring a variety of microorganisms, including pathogens, on the gut microbiota of miniature pigs. Furthermore, we sought to provide foundational data on the characteristics of the gut microbiota in genetically modified pigs, which serve as source animals for xenotransplantation.
2024-04-22 | GSE264183 | GEO
Project description:Dietary fiber can suppress excess adipose tissue and weight gain in rodents and humans when fed high fat diets. The gut microbiome is thought to have a key role, although exactly how remains unclear. In a tightly controlled murine study, we explored how different types of dietary fiber and doses affect the gut microbiota and gut epithelial gene expression. We show that 10% pectin and 10% FOS suppress high fat diet (HFD)-induced weight gain, effects not seen at 2% doses. Furthermore, 2 and 10% mixtures of dietary fiber were also without effect. Distinct gut microbiota profiles were stimulated at the family and operational taxonomic unit (OTU) level by the different fiber treatments. Plasma levels of the gut hormone PYY were elevated by 10% pectin and FOS, but not 10% mixed fibers, and similarly RNA seq revealed some distinct effects of the 10% single fibers on gut epithelial gene expression. These data show how the ability of dietary fiber to suppress HFD-induced weight gain is dependent upon both fiber type and dose. It also shows that the microbial response to dietary fiber is distinct and that there is not a single microbial response associated with the inhibition of adiposity and weight gain. PYY seems key to the latter response, although the role of other factors such as Reg3g and CCK needs to be explored.
2025-02-05 | GSE288466 | GEO
Project description:The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs. In vitro transcriptional profiles of Bacteroides fragilis obtained from biological duplicate cultures taken at middle log phase in minimal media glucose (MM-Glu) and in minimal media with human milk oligosaccharides (MM-HMO).
2012-09-30 | E-GEOD-32207 | biostudies-arrayexpress
Project description:Recent advances in (meta)genomic methods have provided new opportunities to examine host-microbe-environment interactions in the human gut. While opportunities exist to extract DNA from freshly sourced colonic tissue there are potentially valuable sources of DNA from historical studies that might also be examined. We examined how four different tissue DNA extraction methods employed in past clinical trials might impact the recovery of microbial DNA from a colonic tissue sample as assessed using a custom designed phylogenetic microarray for human gut bacteria and archaebacteria. While all methods of DNA extraction produced similar phylogenetic profiles some extraction specific biases were also observed. Real time PCR analysis targeting several bacterial groups substantiated this observation. These data suggest that while the efficacy of different DNA extraction methods differs somewhat all the methods tested produce an accurate representation of microbial diversity. This suggests that DNA samples archived in biobanks should be suitable for retrospective analyses. Three technical replicates per sample (extraction method) were analysed
2010-05-16 | E-GEOD-18420 | biostudies-arrayexpress
Project description:Dietary lipids can affect metabolic health through gut microbiota-mediated mechanisms, but the influence of lipid-microbiota interaction on liver steatosis is unknown. We investigated the effect of dietary lipid composition on human microbiota in an observational study and combined diet experiments with microbiota transplants to study lipid-microbiota interactions and liver status in mice. In humans, low intake of saturated fatty acids (SFA) was associated with increased microbial diversity independent of fiber intake. In mice, cecum levels of SFA correlated negatively with microbial diversity and were associated with a shift in butyrate and propionate producers. Mice fed poorly absorbed SFA had improved metabolism and liver status. These features were transmitted by microbial transfer. Diets enriched in n-6- and/or n-3-polyunsaturated fatty acids were protective against steatosis but had minor influence on the microbiota. In summary, we find that unabsorbed SFA correlate with microbiota features that may be targeted to decrease liver steatosis.
2023-08-03 | GSE222060 | GEO
Project description:The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption actually hinge on gut microbial metabolism. However, flavonoids are consumed in a largely glycosylated form, rendering them poorly available for small intestinal absorption and subjecting them to microbial metabolism in the colon. We show that a single gut microbial flavonoid catabolite is sufficient to reduce diet-induced cardiometabolic disease burden in mice. Dietary supplementation with elderberry extract attenuated obesity and continuous delivery of the catabolite 4-hydroxphenylacetic acid was sufficient to reverse hepatic steatosis. Analysis of human gut metagenomes revealed that under one percent contains a flavonol catabolic pathway, underscoring the rarity of this process. Our study will impact the design of dietary and probiotic interventions to complement traditional cardiometabolic treatment strategies.
2022-11-30 | GSE188967 | GEO
Project description:High consumption of dietary red or processed meat and fat are linked to increased risk of colorectal cancer (CRC). A number of potential mechanisms have been reported, such as the presence of dietary carcinogenic compounds, and elevated gut microbial degradation of proteins and glycoproteins. Tyramine is a commonly found biogenic amine in processed food and can also be produced by the gut microbiota from the dietary amino acid tyrosine. The role of tyramine in intestinal mucosal health and CRC tumorigenesis has not been well studied. Therefore, we used the human colorectal HCT116 cell line and the ApcMin/+ mouse model to investigate the role of tyramine in CRC.
2025-03-05 | GSE235264 | GEO