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ABSTRACT: WGS of Escherichia coli LF82 isolated from gnotbiotic mice harboring the altered Schaedler flora

PROVIDER: PRJNA912691 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22752060_1.fastq.gz	Fastqsanger.gz
	SRR22752060_2.fastq.gz	Fastqsanger.gz
	SRR22752061_1.fastq.gz	Fastqsanger.gz
	SRR22752061_2.fastq.gz	Fastqsanger.gz
	SRR22752062_1.fastq.gz	Fastqsanger.gz

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Project description:Metagenomic sequencing of colon contents from gnotobiotic mice harboring the altered Schaedler flora

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Transcriptional profile of AIC Escherichia coli LF82 wild-type vs their delta-nrdR mutant.

Project description:We aim to compare global transcriptomic analysis of wt and delta-nrdRmutant in Escherichia coli LF82 strain.

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Transcriptional profile of AIC Escherichia coli LF82 wild-type vs their delta nrdR mutant.

Project description:We aim to compare global transcriptomic analysis of wt and delta nrdRmutant in Escherichia coli LF82 strain.

2016-06-27 | E-MTAB-2295 | biostudies-arrayexpress

E. coli Pathobionts and Crohn’s Disease: Varied genetic paths leading to similar phenotypes

Project description:Crohn’s disease (CD), an inflammatory bowel disease that arises from an immune attack of the GI tract, affects roughly 1.6 million Americans. The etiology of CD and the other major irritable bowel disease, ulcerative colitis, is not known, but host genetics and immunology, the gut microbiome, and environmental factors are all thought to be involved. In addition, Adherent Invasive Escherichia coli (AIEC) strains are frequently found to be associated with CD. Key features distinguish AIEC from commensal E. coli, including adherence/invasion of the intestinal epithelium, increased biofilm formation, increased antibiotic resistance, and survival/replication within macrophages. However, these pathobionts lack genetic features typical of frank pathogens. Thus, the potential role AIEC play in CD pathogenesis is not clear. The E. coli pathobiont LF82, isolated from ileum of a patient with CD, has been a well-studied, prototypic AIEC. Dozens of single nucleotide polymorphisms (SNPs) distinguish LF82 and other AIEC from commensal E. coli, suggesting that some of these genetic features might account for particular LF82 phenotypes. In this review, we summarize changes in the CD gut, the association of AIEC with CD, genes and SNPs associated with AIEC, and recent work connecting a specific SNP within a bacterial RNA polymerase gene to the expression of genes associated with the LF82 lifestyle.

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Project description:AOM/DSS model of colitis associated cancer in immunocompetent gnotobiotic mice harboring the altered Schaedler flora

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Lactobacillus from the Altered Schaedler Flora maintain IFNγ homeostasis to promote behavioral stress resilience.

Project description:The gut microbiome consists of trillions of bacteria, fungi, and viruses that inhabit the digestive tract. These communities are sensitive to disruption from environmental exposures ranging from diet changes to illness. Disruption of the community of lactic acid producing bacteria, Lactobaccillacea, has been well documented in mood disorders and stress exposure. In fact, oral supplement with many Lactobacillus species can ameliorate these effects, preventing depression- and anxiety-like behavior. Here, we utilize a gnotobiotic mouse colonized with the Altered Schaedler Flora to remove the two native species of Lactobaccillacea. Using this novel microbial community, we found that the Lactobacillus species themselves, and not the disrupted microbial communities are protective from environmental stressors. Further, we determine that Lactobaccillacea are maintaining homeostatic IFNγ levels which are mediating these behavioral and circuit level responses. By utilizing the Altered Schaedler Flora, we have gained new insight into how probiotics influence behavior and provide novel methods to study potential therapies to treat mood disorders.

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A single rare sigma 70 variant establishes a different gene expression pattern in the E.coli pathobiont LF82

Project description:LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. We demonstrate that sigma70 D445V results in transcriptome and phenotypic changes consistent with LF82 phenotypes, including increased biofilm formation and antibiotic resistance. The position of D445V within RNAP is predicted to affect spacer interaction; in vitro transcriptions reveal that the variant increases transcription from several promoters with a 16 bp spacer and a -14G:C. Our work demonstrates that a single SNP within the bacterial primary sigma can lead to myriad gene expression changes/ new phenotypes and suggests an underrecognized mechanism by which pathobionts and other strain variants can emerge.

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2020-02-12 | E-MTAB-6560 | biostudies-arrayexpress

Project description:EMG produced TPA metagenomics assembly of PRJNA838940 data set (Metagenomic sequencing of colon contents from gnotobiotic mice harboring the altered Schaedler flora).

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