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.
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.
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.
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).
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>
Project description:To study the gene expression profile of patient derived glioblastoma tissues and perform cross platform analysis with metabolite data derived from matching tissues
Project description:The transcriptional response of H. virescens larvae was analyzed after feeding on gossypol supplemented diet, a toxic secondary metabolite produced in cotton plants, to detect potential detoxification enzymes possibly involved in detoxification of gossypol by H. virescens.
