DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

Goris, Johan; Konstantinidis, Konstantinos T.; Klappenbach, Joel A.; Coenye, Tom; Vandamme, Peter; Tiedje, James M.

doi:10.1099/ijs.0.64483-0

Cited by 3,833 publications

(3,163 citation statements)

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“…The genome was more closely related to commensal strains, such as W, IAI1, and SE11, than pathogenic ones among all of the B1 strains, which was also supported by the ANI analysis (5). The resulting phylogenetic trees using both approaches placed the W26 genome into a basal position of the commensal cluster, suggesting that the strain might have diverged earlier from an ancestral strain of group B1.…”

supporting

confidence: 57%

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

Kim

Cho³

et al. 2012

J. Bacteriol.

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An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.E scherichia coli generally occurs in the intestines of humans and most warm-blooded animals and is also known to be able to survive in natural habitats, such as freshwater and soil (7). The members of the species E. coli have been divided into five major phylogroups (A, B1, B2, D, and E) based on the phylogenetic relationships of 1,878 genes that are common in all strains (10). A recent genome-based study suggests that highly diverse forms of E. coli strains can be found in natural environments, as well as the gut and contaminated feces in which their commensal E. coli counterparts reside (7). We carried out genome sequencing of an E. coli strain, designated W26, isolated from feces from a healthy cow to expand our knowledge about genetic diversity among commensal E. coli strains.The whole-genome sequencing was performed using a combination of a 100-bp single-end Illumina Genome Analyzer IIx (48,548,147 reads; 400-fold coverage) and 454 GS FLX Titanium system (208,533 reads) with an 8-kb paired-end library. The resultant sequences were assembled using the CLC Genomics Workbench 4.7.2 (CLCbio) and GS assembler 2.6 (Roche). Gene prediction was performed using Glimmer 3 (3), followed by annotation through searching against the Clusters of Orthologous Groups (COG) (9) and SEED databases (4). The total length of the assembled high-quality contigs (165 contigs; N 50 ϭ 79,401) was 5,118,532 bp, with a GϩC content of 50.65%. The draft genome of E. coli W26 contained 4,852 predicted coding sequences with 1,072 hypothetical proteins (22.1%) of unknown functions, 7 copies of rRNA operons, and 66 tRNA genes. The test strain was taxonomically identified on the basis of 16S rRNA gene sequence comparison using the EzTaxon-e database (http://eztaxon-e .ezbiocloud.net) (6) and average nucleotide identity (ANI) values (5). Both methods confirmed that the strain belongs to E. coli.Phylogenetic inference (2) of 1,910 homologous genes consisting of the E. coli core genome revealed that E. coli W26 belongs to phylogroup B1, which contains both commensal (1) and pathogenic (8) strains. The genome was more closely related to commensal strains, such as W, IAI1, and SE11, than pathogenic ones among all of the B1 strains, which was also supported by the ANI analysis (5). The resulting phylogenetic trees using both approaches placed the W26 genome into a basal position of the commensal cluster, suggesting that the strain might have diverged earlier from an ancestral strain of group B1.The W26 genome was compared to the genomes of nine B1 strains to understand the function, genome structure, and evolutionary relationship within the B1 lineage. Phage-related genes, IncI1 plasmid conjugative transfer proteins, and putative plasmid maintenance proteins are shared between W26 and other co...

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supporting

confidence: 57%

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

Kim

Cho³

et al. 2012

J. Bacteriol.

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“…The details of draft genomes for the five strains, PAMC 27389 T and the four reference strains, are summarized in Table S1 (available in the online Supplementary Material). The ANI values calculated for estimation of the degree of pairwise genome-based relatedness between strain PAMC 27389 T and P. wandonensis KCTC 23672 T , P. antarcticus KCTC 23700 T , P. ferrugineus LMG 22047 T and P. aquimaris KCTC 23043 T were 70.8, 70.9, 71.0 and 70.5 %, respectively (Table S2) and this level is well below the ANI cut-off values (95-96 %) that have been proposed for delineating bacterial species (Goris et al, 2007;Richter & Rosselló -Mó ra, 2009). Mean DNA-DNA hybridization values between strain PAMC 27389 T and the other type strains estimated by genome-to-genome distance calculation were 18.4-19.1 % ( Table S2), indicating that strain PAMC 27389 T is distinguishable from other Pseudorhodobacter species (Rosselló -Mora and Amann, 2001).…”

mentioning

confidence: 78%

“…Celera Assembler (version 7.0) was used for assembly (Myers et al, 2000). The degree of pairwise genome-based relatedness was estimated by both the average nucleotide identity (ANI) value following the BLAST-based ANI calculation method described by Goris et al (2007) and the genome-to-genome distance calculation method described by Auch et al (2010). The genomic DNA G+C content was calculated directly from the genome sequence.…”

mentioning

confidence: 99%

Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter

Lee

Yang

Baek

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Comparative genomics showed that the dominant Methanohalophilus and Halanaerobium near-complete genomes (Supplementary Table 2) in the Utica enrichment were closely related strains 32 to the Marcellus genomes (∼99% ANI) (Supplementary Table 5 and Supplementary Data File 2). In contrast, ANI values between the Marcellus and Utica Methanohalophilus and other sequenced species (M. mahii and M. halophilus, both isolated from surface waters), were ∼91 and 92%, respectively.…”

Section: Strain Metabolic Diversity Across Shalesmentioning

confidence: 99%

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

et al. 2016

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Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface. S hale gas accounts for one-third of natural gas energy resources worldwide. It has been estimated that shale gas will provide half of the natural gas in the USA, annually, by 2040, with the Marcellus shale in the Appalachian Basin projected to produce three times more than any other formation 1 . Recovery of these hydrocarbons is dependent on hydraulic fracturing technologies, where the high-pressure injection of water and chemical additives generates extensive fractures in the shale matrix. Hydrocarbons trapped in tiny pore spaces are subsequently released and collected at the wellpad surface, together with a portion of the injected fluids that have reacted with the shale formation. The mixture of injected fluids and hydrocarbons collected is referred to as 'produced fluids'.Microbial metabolism and growth in hydrocarbon reservoirs has both positive and negative impacts on energy recovery. Whereas stimulation of methanogens in coal beds enhances energy recovery 2 , bacterial hydrogen sulfide production ('reservoir souring') decreases profits and contributes to corrosion and the risk of environmental contamination 3 . Additionally, biomass accumulation within newly generated fractures may reduce their permeability, decreasing natural gas recovery. Despite these potential microbial impacts, little is known about the function and activity of microorganisms in hydraulically fractured shale.Initial work by our group and others 4-9 used single marker gene analyses to identify microorganisms from several geographically distinct shale formations. These analyses showed similar halotolerant taxa in produced fluids several months after hydraulic fracturing. To assign functional roles to these organisms, we conducted metagenomic and metabolite analyses on input and produced fluids up to a year after hydraulic fracturing (HF) from two Appala...

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DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

Cited by 3,833 publications

References 39 publications

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

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