Update on RefSeq microbial genomes resources

Tatusova, Tatiana; Ciufo, Stacy; Federhen, Scott; Fedorov, Boris; McVeigh, Richard; O’Neill, Kathleen; Tolstoy, Igor; Zaslavsky, Leonid

doi:10.1093/nar/gku1062

Cited by 125 publications

(127 citation statements)

References 15 publications

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“…A substantial proportion of complete bacterial genomes in the public domain belong to human pathogens and very closely related genomes representing variations within the species (Tatusova et al, 2014). As first reported by Graur, 2014, it has been suggested that this fact might introduce a bias to the bimodal distribution seen in the previous analyses.…”

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confidence: 87%

Assessment of the bimodality in the distribution of bacterial genome sizes

2016

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Bacterial genome sizes have previously been shown to exhibit a bimodal distribution. This phenomenon has prompted discussion regarding the evolutionary forces driving genome size in bacteria and its ecological significance. We investigated the level of inherent redundancy in the public database and the effect it has on the shape of the apparent bimodal distribution. Our study reveals that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution. The true genome size distribution and its wider ecological implications will soon emerge as we are currently witnessing rapid growth in the number of sequenced genomes from diverse environmental niches across a range of habitats at an unprecedented rate.

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confidence: 87%

Assessment of the bimodality in the distribution of bacterial genome sizes

2016

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“…This has led to a rapid increase in the sequencing of whole genomes of microorganisms, including eukarya, bacteria, archaea, and viruses. These sequences have been deposited in the National Center for Biotechnology Information (NCBI) RefSeq genome collection database (http://www.ncbi.nlm.nih.gov/genome) (Tatusova et al, 2015). In 2014, over 10 000 microbial genomes were released (Tatusova et al, 2015).…”

Section: Whole Genome Sequencing Is a Feasible Way To Investigate Thementioning

confidence: 99%

“…These sequences have been deposited in the National Center for Biotechnology Information (NCBI) RefSeq genome collection database (http://www.ncbi.nlm.nih.gov/genome) (Tatusova et al, 2015). In 2014, over 10 000 microbial genomes were released (Tatusova et al, 2015). Along with the next generation platforms, wholegenome analysis of multi-drug resistance mechanisms has emerged.…”

Section: Whole Genome Sequencing Is a Feasible Way To Investigate Thementioning

confidence: 99%

Antibiotic resistance mechanisms of Myroides sp.

Yuan

et al. 2016

J. Zhejiang Univ. Sci. B

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Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp. infections have been reported mainly in China. Myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve this, it fails to give information on the status and mechanisms of antibiotic resistance, because the 16S rRNA sequence contains no information on resistance genes, resistance islands or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections. As Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial infections and pandemics. For better management of Myroides sp. infections, it is imperative to apply next generation sequencing technologies to clarify the antibiotic resistance mechanisms in these bacteria.

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“…All three strains were annotated using the Rapid Annotations using Subsystems Technology (RAST version 2.0) (34) with parameters allowing for frameshift error corrections. The genomes were also annotated using the NCBI Prokaryotic Genome Annotation Pipeline (35).…”

Section: Methodsmentioning

confidence: 99%

Characterization and Recognition of Brachyspira hampsonii sp. nov., a Novel Intestinal Spirochete That Is Pathogenic to Pigs

Mirajkar

Phillips

et al. 2016

J Clin Microbiol

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T he genus Brachyspira includes Gram-negative aerotolerant anaerobic spirochetes that colonize the intestine of and/or cause disease in a wide range of host species (1). Over several decades, multiple taxonomic changes were applied to members of this genus (originally Treponema, which was then transferred to Serpula, to Serpulina, and finally to Brachyspira) (2-5). Currently, the genus Brachyspira consists of eight valid species, B. hyodysenteriae, B. pilosicoli, B. intermedia, B. innocens, B. murdochii, B. aalborgi, B. alvinipulli, and most recently, B. suanatina (1, 6). This genus also consists of several provisional species (1), of which the most clinically significant is the recently discovered "Brachyspira hampsonii" (7). Within the Brachyspira genus, all currently identified strongly beta-hemolytic species (B. hyodysenteriae, B. suanatina, and the novel B. hampsonii) are known to cause severe mucohemorrhagic diarrhea in pigs, while weakly beta-hemolytic Brachyspira species are either commensals (B. innocens) or are capable of causing diarrhea and/or colitis (B. pilosicoli, B. murdochii, B. intermedia, B. aalborgi, and B. alvinipulli) in pigs, chickens and/or humans (1). B. hyodysenteriae, the most virulent and clinically significant Brachyspira species, has historically also been the most researched or investigated species. It causes swine dysentery (SD), a disease characterized by mucohemorrhagic diarrhea that is most commonly observed in grower-finisher pigs (1). In addition to the adverse impact on the health and welfare of pigs, its negative effect on productivity (such as decreased weight gain and poor feed conversion) leads to significant economic losses to livestock-raising communities and countries (1). The recently validated B. suanatina also causes SD in pigs; however, its isolation has been limited to a few northern European countries (8). The isolation of different bacterial species from clinically and pathologically indistinguishable dysentery cases of pigs highlights the evolving and expanding etiology of SD. Thus, the definition of SD should include all strongly beta-hemolytic Brachyspira species that cause mucohemorrhagic colitis and dysentery in pigs (9). The genetically diverse B. pilosicoli is the primary etiological agent of colonic spirochetosis, a disease characterized by diarrhea and/or colitis in a wide range of host species, including pigs (porcine intestinal spirochetosis [PIS]) (10), chickens (avian intestinal spirochetosis [AIS]) (11), and human beings (human intestinal spirochetosis [HIS]) (12). AIS also can be caused by other Brachyspira species, including B. intermedia (13) and B. alvinipulli (14), while HIS is also caused by B. aalborgi (15). Although long considered to be a commensal, the association of B. murdochii with mild diarrhea and/or colitis in pigs has been reported (16,17). These Brachyspira-associated disease conditions negatively impact the health and welfare of the affected host species and reduce the productivity of livestock (1).Clinical SD was rarely report...

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Update on RefSeq microbial genomes resources

Cited by 125 publications

References 15 publications

Assessment of the bimodality in the distribution of bacterial genome sizes

Assessment of the bimodality in the distribution of bacterial genome sizes

Antibiotic resistance mechanisms of Myroides sp.

Characterization and Recognition of Brachyspira hampsonii sp. nov., a Novel Intestinal Spirochete That Is Pathogenic to Pigs

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