Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589897 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vitamins mediate a web of cross-feeding interactions in the human gut. Many Gram-positive gut microbes, in particular, are predicted to be vitamin auxotrophs. Previous studies of these microbes, however, have tended to use rich media, precluding controlled perturbations of low abundance nutrients. We tested the ability of diverse Lachnospiraceae, the most common Gram-positives in the gut, to grow on a chemically defined medium. Even though this medium contained riboflavin, we found that predicted riboflavin auxotrophs grew poorly, including the bile metabolizer Clostridium scindens. Riboflavin supplementation increased C. scindens final density in a concentration-dependent manner up to at least 200μM. Surprisingly, despite being an auxotroph, C. scindens also catabolized riboflavin into lumichrome. The only previously described catabolic pathway for riboflavin requires oxygen and has no homologs in C. scindens. In 200µM riboflavin, a single gene neighborhood with an aldolase, oxidoreductases, and a riboflavin kinase/adenylyltransferase was upregulated, suggesting an alternative anaerobic degradation or overflow pathway. Similar neighborhoods were detected in several other Lachnospiraceae, including Faecalicatena fissicatena, the only other anaerobe reported to degrade riboflavin. Reanalysis of published metabolomic data showed that in vivo, both riboflavin and lumichrome were more abundant in colonized (vs. germ-free) mouse ceca, and that in vitro, Lachnospiraceae isolates depleted riboflavin while certain Gram-negative isolates overproduced it. These results demonstrate that a member of the Lachnospiraceae can anaerobically convert an essential B vitamin into lumichrome, a molecule recently shown to have anti-inflammatory properties. Vitamin catabolism may both structure cross-feeding interactions in the gut and affect host health.
2026-02-15 | GSE319166 | GEO
Project description:Little is known about the bacteria that reside in human gallbladder and the mechanisms that allow them to survive within this harsh environmental niche. Furthermore, certain bacterial species are considered to exhibit antagonistic activities whilst others may form mutualistic interactions through, for example, cross-feeding. We isolated two new strains from healthy human bile samples, one belonging to Ruminococcus gauvreauii, of Lachnospiraceae family, and other constituting a new specie in Ruminococcaceae family, named Ruminocoides biliarensis. The two strains differed markedly in their carbohydrate metabolism as R. gauvreauii mainly metabolised sugar alcohols, including inositol, to form acetate as unique fermentation product, and Rc. biliarensis mainly metabolised resistant starches to mainly form formate and acetate as fermentation end products. Both strains exhibited resistance to different bile salts, and the ability to sporulate. Amino acid and vitamin biosynthesis profiles also markedly differed between the two bile isolates. Finally,RNAseq was used to analyse the co-cultures of both isolates, to analyze the activities involved in the possible cross-feeding relationship.
2022-07-05 | GSE140753 | GEO
Project description:This is supplemental, raw mass spectrometry data for "Cross-feeding of internal metabolites by non-growing bacteria rescues cell death and stabilizes dynamic coexistence under acid stress.", Kapil Amarnath et al.
Vibrio sp. 1A01 is grown in monoculture or in coculture with Neptunomonas sp. 3B05 and metabolite secretions are measured over time.
2021-03-31 | MSV000087136 | MassIVE
Project description:Bifidobacterium species cross-feeding transcriptome
| PRJNA284883 | ENA
Project description:mRNA expression of hearts obtained from mice with Stimulated by retinoic acid gene 6 (Stra6) germline deletion, Vitamin A deficiency (VAD) induced by lecithin-retinol acyltransferase (Lrat) germline deletion and feeding with vitamin A-deficient diet, and the combination of both. Mice were subjected to myocardial infarction (MI) or Sham surgery.
2025-09-06 | GSE307187 | GEO
Project description:This agent-based model is based on an adaptive laboratory evolution (ALE) experiment scenario of two mutually cross feeding strains of bacteria and yeast. The bacterial strain secretes vitamins for which the yeast strain is auxotrophic and the yeast strain secrets amino acids for which the bacterial strain is auxotrophic. In particular, the model simulates a situation where a mutation arises in the bacterial strain that results in the emergence of individuals (mutant bacteria) with a higher secretion of vitamins as compared to the wild type (WT). This increase in secretion comes with a cost in terms of fitness (growth rate) of the mutant bacteria. The model can be used to assess if this mutant is able to persist and increase in frequency in the cross-feeding community.
2022-08-01 | MODEL2106100001 | BioModels
Project description:In women undergoing in vitro fertilization, higher vitamin D status has been associated with improved live birth rates. Among women with polycystic ovarian syndrome (PCOS), vitamin D has been associated with improvements in spontaneous ovulation. Vitamin D receptor (VDR) is a nuclear receptor activated by 1,25 dihydroxyvitamin D which is the most active metabolite of vitamin D. Mice that lack the vitamin D receptor exhibit arrested follicular development, uterine hypoplasia, prolonged estrous cycles, and subfertility. Also, one study of mice reported that the vitamin D receptor is expressed in gonadotropin-releasing hormone (GnRH) neurons, which might suggest a role for vitamin D in hypothalamic signaling. Since the vitamin D receptor knockout mouse is sub fertile with uterine hyperplasia, the most likely cause of vitamin D deficiency may be due to estrogen production by the ovary or estrogen responsiveness of the uterus. So, in this study, we want to identify the effect of vitamin D on human endometrial stromal cells associated with female reproduction.
2025-12-31 | GSE254251 | GEO
Project description:Interventions: Observation group:None
Primary outcome(s): Serum vitamin A levels;Serum vitamin B1 levels;Serum vitamin B2 levels;Serum vitamin B6 levels;Serum vitamin B9 levels;Serum vitamin B12 levels;Serum vitamin C levels;Serum vitamin D levels;Serum vitamin E levels
Study Design: Cross-sectional
| 85437 | ecrin-mdr-crc
Project description:In this study, we focused on the time-course of transcriptional changes in freshly isolated human PBMCs 4, 8, 24 and 48 h after onset of stimulation with the active vitamin D metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) compared to vehicle (0.1% EtOH).
2022-01-22 | GSE189984 | GEO
Project description:<p>Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness-costly metabolites through natural selection. In this strategy, metabolic cross-feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co-evolved wild-type lactic acid bacteria and engineered auxotrophic <em>Saccharomyces cerevisiae</em> in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B-group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.</p>
2021-07-02 | MTBLS2217 | MetaboLights