Complete Genome Sequence of Escherichia coli Strain M8, Isolated from ob/ob Mice

ABSTRACT

Escherichia coli is one of the common inhabitants of the mammalian gastrointestinal track. We isolated a strain from an ob/ob mouse and performed whole-genome sequencing, which yielded a chromosome of ~5.1 Mb and three plasmids of ~160 kb, ~6 kb, and ~4 kb.

GENOME ANNOUNCEMENT

Escherichia coli has been frequently isolated from stool samples (1, 2) and is used as an indicator of fecal contamination in water supplies (3). In recent years, it has also been found to be associated with chronic and acute infections manifesting in various disease conditions (4, 5). There have been uses of E. coli as a probiotic (6), but a majority of the studies have been focused on pathogenic strains. Moreover, genomic information about E. coli variants have been specifically studied in the context of inflammatory conditions of the gut (7, 8). Strain M8 was isolated from conventionally raised ob/ob C57BL/6J mice using Drigalski medium.

Isolate M8 tested positive for beta-galactosidase, lysine decarboxylase, and ornithine decarboxylase activity using the API 20E system. Additionally, it tested positive for indole production and production of acids by metabolizing several sugar sources (glucose, mannitol, sorbitol, rhamnose, saccharose, melibiose, and arabinose). Isolate M8 showed strong positive activity for alkaline phosphatase, leucine arylamidase, acid phosphatase, and beta-galactosidase and weak activity for valine arylamidase, trypsin, phosphohydrolase, and beta-glucosidase using the API ZYM system.

Biochemically, isolate M8 tested positive for utilization of glycerol, d-arabinose, l-arabinose, ribose, d-xylose, galactose, glucose, fructose, mannose, rhamnose, dulcitol, mannitol, sorbitol, N-acetyl glucosidase, maltose, lactose, melibiose, sucrose, trehalose, raffinose, gentiobiose, l-fucose, and gluconate using the API 50 CHE system (aerobic and anaerobic). Analysis using the GEN III OmniLog system matched isolate M8 to the E. coli species. FAME lipid analysis of the M8 lipids matched those of Shigella sonnei GC, subgroup B, with a SIM index of 0.698, indicating that M8 shares high DNA homology with E. coli. This is consistent with FAME-based identification for E. coli isolates. The total proteomics showed a high homology with E. coli with a category match of level A. The closest species identified in the database was E. coli DSM 1576, which is a fecal isolate.

Total DNA was extracted using Qiagen genomic DNA tips, and the DNA was first used to perform an optical mapping of the genome. The DNA was subsequently used to prepare long distance (LJD) libraries and a shotgun library, which were sequenced with MiSeq V2 chemistry. The resulting paired-end reads were assembled de novo using Newbler version 2.9, and the gaps were closed after manual inspection with GapClosure version 1.12-r2 (part of SOAPde novo) using reads derived from Sanger sequencing. The overall assembly was guided using the optical mapping data; the assembly resulted in a singular chromosome of approximately 5.1 Mb and three plasmids of approximately 160 kb, 6 kb, and 4 kb each. These sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).

Accession number(s).

The completed whole-genome data are available at NCBI GenBank under BioSample number SAMN06445833, with accession numbers CP019953, CP019954, CP019955, and CP019956 for the chromosome and three plasmids.