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ABSTRACT: Comparative transcriptomics of cobalamin-dependent propionate production of Xylanibacter ruminicola cultures

PROVIDER: PRJNA1116615 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29185420_1.fastq.gz	Fastqsanger.gz
	SRR29185420_2.fastq.gz	Fastqsanger.gz
	SRR29185421_1.fastq.gz	Fastqsanger.gz
	SRR29185421_2.fastq.gz	Fastqsanger.gz
	SRR29185422_1.fastq.gz	Fastqsanger.gz

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Comparative proteomics of cobalamin-dependent propionate production by the rumen bacterium Xylanibacter ruminicola

Project description:Xylanibacter ruminicola is an abundant rumen bacterium that produces propionate in a cobalamin-dependent manner. However, the effect of cobalamin supplementation on the expression of propionate pathway enzymes has yet to be investigated. To assess this, comparative transcriptomics and proteomics was carried out on X. ruminicola KHP1 cultures grown in defined media in the presence and absence of cobalamin. Cobalamin supplementation did not affect expression of most propionate pathway proteins, with the only differentially abundant pathway enzyme being the cobalamin-dependent methylmalonyl-CoA mutase, which showed a minor upregulation in the presence of cobalamin. Our results demonstrate expression of the propionate pathway regardless of cobalamin availability, suggesting that cobalamin-dependent induction of propionate production by X. ruminicola is controlled post-translationally.

2024-10-14 | PXD053273 | Pride

Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in two ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1

Project description:Bacteria of the genera Xylanibacter and Segatella are one of the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. The knowledge of PUL presence in rumen Xylanibacter and Segatella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Xylanibacter ruminicola KHP1 and Segatella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, β-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems.

2024-05-08 | GSE262719 | GEO

Xylanibacter ruminicola

Project description:Xylanibacter ruminicola Raw sequence reads

| PRJNA358384 | ENA

Xylanibacter ruminicola strain:KHP1

Project description:Xylanibacter ruminicola strain:KHP1 Genome sequencing

| PRJNA715253 | ENA

Xylanibacter ruminicola Ga6B6

Project description:Xylanibacter ruminicola Ga6B6 Genome sequencing and assembly

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Xylanibacter ruminicola strain:ATCC 19189

Project description:Xylanibacter ruminicola strain:ATCC 19189 Genome sequencing

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Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids

Project description:Acetate, propionate and butyrate are the main short-chain fatty acids (SCFAs) that arise from the fermentation of fibers by the colonic microbiota. While many studies focus on the regulatory role of SCFAs, their quantitative role as a catabolic or anabolic substrate for the host has received relatively little attention. To investigate this aspect, we infused conscious mice with physiological quantities of stable isotopes [1-13C]acetate, [2-13C]propionate or [2,4-13C2]butyrate directly into the cecum, which is the natural production site in mice, and analyzed their interconversion by the microbiota as well as their metabolism by the host. Cecal interconversion - pointing to microbial cross-feeding - was high between acetate and butyrate, low between butyrate and propionate and almost absent between acetate and propionate. As much as 62% of infused propionate was used in whole-body glucose production, in line with its role as gluconeogenic substrate. Conversely, glucose synthesis from propionate accounted for 69% of total glucose production. The synthesis of palmitate and cholesterol in the liver was high from cecal acetate (2.8% and 0.7%, respectively) and butyrate (2.7% and 0.9%, respectively) as substrates, but low or absent from propionate (0.6% and 0.0%, respectively). Label incorporation due to chain elongation of stearate was approximately 8-fold higher than de novo synthesis of stearate. Microarray data suggested that SCFAs exert only a mild regulatory effect on the expression of genes involved in hepatic metabolic pathways during the 6h infusion period. Altogether, gut-derived acetate, propionate and butyrate play important roles as substrates for glucose, cholesterol and lipid metabolism. Mice were infused in cecum with stably-labelled isotopes of the three main short chain fatty acids or control solution. After 6 hrs, livers were removed and pooled RNA samples were subjected to gene expression profiling.

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Project description:Transcriptomics of propionate stress

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