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Functional microbiome in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking

ABSTRACT: Functional microbiome in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking

PROVIDER: PRJEB34540 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3556096_1.fastq.gz	Fastqsanger.gz
	ERR3556096_2.fastq.gz	Fastqsanger.gz
	ERR3556097_1.fastq.gz	Fastqsanger.gz
	ERR3556097_2.fastq.gz	Fastqsanger.gz
	ERR3556098_1.fastq.gz	Fastqsanger.gz

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Project description:The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be M-bM-^@M-^\hot spotsM-bM-^@M-^] for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers. Twelve isolates of E. coli ( 3 from bear, 3 from cattle, 3 from deer and 3 from humans) were isolated from feces and/or raw sewage. Genome content for each strain was assessed in duplicate using comparative genome hybridization with E. coli K12 MG1655 as the reference for a total of 24 arrays.

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Functional microbiome in methanogenic sludge digesters revealed by E. coli-fed digestion and microbial source tracking

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