Food chain microbiomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB72104 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The diets of industrialized countries reflect the increasing use of processed foods, often with the inclusion of novel food additives. Xanthan gum is a complex polysaccharide with unique rheological properties that have established its use as a widespread stabilizer and thickening agent. Xanthan gum’s chemical structure is distinct from the host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fiber polysaccharides. Here, we show that the ability to digest xanthan gum is surprisingly common in industrialized human gut microbiomes and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Surprisingly, some individuals harbor a Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that this additive can drive expansion of this primary degrader along with exogenously introduced Bacteroides intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework to understand how widespread consumption of a recently introduced food additive influences human microbiomes.
2022-02-28 | PXD031522 | Pride
Project description:RNA was extracted from the meninges of mice from either Specific pathogen free or Germ free facilities or from the offspring of mice reconstituted with different human microbiomes.
2020-11-13 | GSE135620 | GEO
Project description:Ecology of food waste chain-elongating microbiome
| PRJNA872917 | ENA
Project description:HuMiChip2 was applied to analyze perform both strain-level identification and the functional profiling of human gut microbiomes from alcoholic cirrhosis patients and healthy individuals with alcohol abuse.
2016-08-30 | GSE86162 | GEO
Project description:Direct Conversion of Food Waste Extract into Caproate: Metagenomics Assessment of Chain Elongation Process
| PRJNA872912 | ENA
Project description:The health and resilience of species in natural environments are increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors, we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizard (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays. Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms between transcript expression and toxicological phenotype. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia, and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses contrasted with adverse effects on lizard growth at high doses. Functional enrichment and inguinal fat body weights suggest inhibition of lipid mobilization and catabolism by TNT coupled with a decreased overall energy budget. Malaria infection elicited enrichment of the expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune response consistent with a decrease in WBC levels. Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bioenergetic constraints. Interestingly, each TNT and malaria individually tended to increase transcriptional expression of immune-related genes and increase overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated.
2018-11-15 | GSE116021 | GEO
Project description:The health and resilience of species in natural environments are increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors, we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizard (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays. Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms between transcript expression and toxicological phenotype. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia, and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses contrasted with adverse effects on lizard growth at high doses. Functional enrichment and inguinal fat body weights suggest inhibition of lipid mobilization and catabolism by TNT coupled with a decreased overall energy budget. Malaria infection elicited enrichment of the expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune response consistent with a decrease in WBC levels. Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bioenergetic constraints. Interestingly, each TNT and malaria individually tended to increase transcriptional expression of immune-related genes and increase overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated.
2018-11-15 | GSE116024 | GEO