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Oxalobacter formigenes OXCC13

ABSTRACT: Reference genome for the Human Microbiome Project

PROVIDER: PRJNA32499 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR015631.fastq.gz	Fastqsanger.gz
	SRR015644.fastq.gz	Fastqsanger.gz
	SRR015650.fastq.gz	Fastqsanger.gz
	SRR015671.fastq.gz	Fastqsanger.gz

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Oxalobacter formigenes OXCC13

Project description:Genome sequence of Oxalobacter formigenes Human Strain OXCC13

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Genome Sequence of Oxalobacter formigenes Strain OXCC13.

Project description:The lack of Oxalobacter formigenes colonization in the human gut is generally acknowledged as a risk factor for kidney stone formation since this microorganism can play an important role in oxalate homeostasis. Here, we present the genome sequence of OXCC13, a human strain isolated from an individual residing in Germany.

| S-EPMC5511905 | biostudies-literature

Genome Sequence of Oxalobacter formigenes Strain SSYG-15.

Project description:Colonization of the intestine with Oxalobacter formigenes reduces urinary oxalate excretion and lowers the risk of forming calcium oxalate kidney stones. Here, we report the genome sequence of Oxalobacter formigenes SSYG-15, a strain isolated from a stool sample from a healthy Chinese boy.

| S-EPMC6797538 | biostudies-literature

Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes.

Project description:Oxalobacter formigenes is a unique intestinal organism that relies on oxalate degradation to meet most of its energy and carbon needs. A lack of colonization is a risk factor for calcium oxalate kidney stone disease. The release of the genome sequence of O. formigenes has provided an opportunity to increase our understanding of the biology of O. formigenes. This study used mass spectrometry based shotgun proteomics to examine changes in protein levels associated with the transition of growth from log to stationary phase. Of the 1867 unique protein coding genes in the genome of O. formigenes strain OxCC13, 1822 proteins were detected, which is at the lower end of the range of 1500-7500 proteins found in free-living bacteria. From the protein datasets presented here it is clear that O. formigenes contains a repertoire of metabolic pathways expected of an intestinal microbe that permit it to survive and adapt to new environments. Although further experimental testing is needed to confirm the physiological and regulatory processes that mediate adaptation with nutrient shifts, the O. formigenes protein datasets presented here can be used as a reference for studying proteome dynamics under different conditions and have significant potential for hypothesis development.

| S-EPMC4764995 | biostudies-literature

Probiotic properties of Oxalobacter formigenes: an in vitro examination.

Project description:Oxalobacter formigenes (O. formigenes) is a nonpathogenic, Gram-negative, obligate anaerobic bacterium that commonly inhabits the human gut and degrades oxalate as its major energy and carbon source. Results from a case-controlled study suggested that lack of O. formigenes colonization is a risk factor for recurrent calcium oxalate stone formation. Hence, O. formigenes colonization may prove to be an efficacious method for limiting calcium oxalate stone risk. However, challenges exist in the preparation of O. formigenes as a successful probiotic due to it being an anaerobe with fastidious growth requirements. Here we examine in vitro properties expected of a successful probiotic strain. The data show that the Group 1 O. formigenes strain OxCC13 is sensitive to pH < 5.0, persists in the absence of oxalate, is aerotolerant, and survives for long periods when freeze-dried or mixed with yogurt. These findings highlight the resilience of this O. formigenes strain to some processes and conditions associated with the manufacture, storage and distribution of probiotic strains.

| S-EPMC5083200 | biostudies-literature

Genome Sequence of <i>Oxalobacter formigenes</i> Strain HC-1.

Project description:The lack of Oxalobacter formigenes colonization of the human gut has been correlated with the formation of calcium oxalate kidney stones and also with the number of recurrent kidney stone episodes. Here, we present the genome sequence of HC-1, a human strain isolated from an individual residing in Iowa, USA.

| S-EPMC5502849 | biostudies-literature

Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist.

Project description:Oxalobacter formigenes, a unique anaerobic bacterium that relies solely on oxalate for growth, is a key oxalate-degrading bacterium in the mammalian intestinal tract. Degradation of oxalate in the gut by O. formigenes plays a critical role in preventing renal toxicity in animals that feed on oxalate-rich plants. The role of O. formigenes in reducing the risk of calcium oxalate kidney stone disease and oxalate nephropathy in humans is less clear, in part due to difficulties in culturing this organism and the lack of studies which have utilized diets in which the oxalate content is controlled. Herein, we review the literature on the 40th anniversary of the discovery of O. formigenes, with a focus on its biology, its role in gut oxalate metabolism and calcium oxalate kidney stone disease, and potential areas of future research. Results from ongoing clinical trials utilizing O. formigenes in healthy volunteers and in patients with primary hyperoxaluria type 1 (PH1), a rare but severe form of calcium oxalate kidney stone disease, are also discussed. Information has been consolidated on O. formigenes strains and best practices to culture this bacterium, which should serve as a good resource for researchers.

| S-EPMC8388816 | biostudies-literature

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