The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

Galens, Kevin; Orvis, Joshua; Daugherty, S. J.; Creasy, Heather Huot; Angiuoli, Samuel V.; White, Owen; Wortman, Jennifer; Mahurkar, Anup; Giglio, Michelle

doi:10.4056/sigs.1223234

Cited by 118 publications

(123 citation statements)

References 18 publications

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“…The BSR was determined by dividing the score of a gene compared to a genome by the score of the gene compared to its own sequence. The predicted protein function of each gene cluster was determined with an ergatisbased (38) in-house annotation pipeline (39).…”

Section: Methodsmentioning

confidence: 99%

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics

et al. 2016

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Enteroinvasive Escherichia coli (EIEC) is a unique pathovar that has a pathogenic mechanism nearly indistinguishable from that of Shigella species. In contrast to isolates of the four Shigella species, which are widespread and can be frequent causes of human illness, EIEC causes far fewer reported illnesses each year. In this study, we analyzed the genome sequences of 20 EIEC isolates, including 14 first described in this study. Phylogenomic analysis of the EIEC genomes demonstrated that 17 of the isolates are present in three distinct lineages that contained only EIEC genomes, compared to reference genomes from each of the E. coli pathovars and Shigella species. Comparative genomic analysis identified genes that were unique to each of the three identified EIEC lineages. While many of the EIEC lineage-specific genes have unknown functions, those with predicted functions included a colicin and putative proteins involved in transcriptional regulation or carbohydrate metabolism. In silico detection of the Shigella virulence plasmid (pINV), which is essential for the invasion of host cells, demonstrated that a form of pINV was present in nearly all EIEC genomes, but the Mxi-Spa-Ipa region of the plasmid that encodes the invasion-associated proteins was absent from several of the EIEC isolates. The comparative genomic findings in this study support the hypothesis that multiple EIEC lineages have evolved independently from multiple distinct lineages of E. coli via the acquisition of the Shigella virulence plasmid and, in some cases, the Shigella pathogenicity islands. Enteroinvasive Escherichia coli is a unique group of diseasecausing E. coli bacteria that have a virulence mechanism most similar to that of Shigella bacteria, involving the invasion of intestinal epithelial cells (1-4). In contrast, the other pathovars of E. coli do not invade host cells and, instead, typically associate with the surface of the host cell and secrete or translocate virulence factors onto or into the cell (1, 2, 4). While Shigella bacteria are among the leading agents of diarrheal illness, causing an estimated 165 million annual cases worldwide (5), EIEC bacteria are seldom identified but can occasionally be linked to small food-or waterborne outbreaks (2, 6). Although EIEC bacteria cause disease very similar to the disease caused by Shigella bacteria, they share biochemical and cultural traits that are intermediate between those of commensal E. coli and Shigella bacteria (7). Thus, it is not clear if the reported low incidence is due to the lack of acceptable and defined biochemical/molecular markers for this group or whether EIEC disease truly has a low incidence rate.The virulence of Shigella and EIEC bacteria has been attributed to genes associated with mobile genetic elements including pathogenicity islands and a virulence plasmid, pINV (1-3, 8-11). The pINV plasmid is required for invasion of intestinal epithelial cells and encodes a type III secretion system (T3SS) and many associated effectors (8-10). Meanwhile, on the chromosome,...

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Section: Methodsmentioning

confidence: 99%

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics

et al. 2016

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“…Long-insert libraries were made, and each genomic library DNA was run on two SMART cells. The IGS Annotation Engine Manatee was used for structural and functional annotation of the sequences (41).…”

Section: Methodsmentioning

confidence: 99%

The Microbiota of Freshwater Fish and Freshwater Niches Contain Omega-3 Fatty Acid-Producing Shewanella Species

Dailey

McGraw

Jensen

et al. 2016

Appl Environ Microbiol

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Approximately 30 years ago, it was discovered that free-living bacteria isolated from cold ocean depths could produce polyunsaturated fatty acids (PUFA) such as eicosapentaenoic acid (EPA) (20:5n-3) or docosahexaenoic acid (DHA) (22:6n-3), two PUFA essential for human health. Numerous laboratories have also discovered that EPA-and/or DHA-producing bacteria, many of them members of the Shewanella genus, could be isolated from the intestinal tracts of omega-3 fatty acid-rich marine fish. If bacteria contribute omega-3 fatty acids to the host fish in general or if they assist some bacterial species in adaptation to cold, then cold freshwater fish or habitats should also harbor these producers. Thus, we undertook a study to see if these niches also contained omega-3 fatty acid producers. We were successful in isolating and characterizing unique EPA-producing strains of Shewanella from three strictly freshwater native fish species, i.e., lake whitefish (Coregonus clupeaformis), lean lake trout (Salvelinus namaycush), and walleye (Sander vitreus), and from two other freshwater nonnative fish, i.e., coho salmon (Oncorhynchus kisutch) and seeforellen brown trout (Salmo trutta). We were also able to isolate four unique free-living strains of EPA-producing Shewanella from freshwater habitats. Phylogenetic and phenotypic analyses suggest that one producer is clearly a member of the Shewanella morhuae species and another is sister to members of the marine PUFA-producing Shewanella baltica species. However, the remaining isolates have more ambiguous relationships, sharing a common ancestor with non-PUFA-producing Shewanella putrefaciens isolates rather than marine S. baltica isolates despite having a phenotype more consistent with S. baltica strains.

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“…If necessary, subsequent gap closure was done by conventional Sanger sequencing. Genome annotation was performed using the IGS prokaryotic annotation pipeline (3).…”

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confidence: 99%