Microbial Genomic Taxonomy.

Thompson, Cristiane C.; Vidal, Leonardo; Salazar, Vinícius; Swings, Jean; Thompson, Fabiano L.

doi:10.1079/9781789244984.0168

“…Genome-to-genome distance was calculated using the Genome-to-genome distance calculator (GGDC) (Meier-Kolthoff et al 2013). The parameters used for the delimitation of a new species are less than 95% (AAI/ANI) and less than 70% GGDH with their closest neighbors, in conformity with the method previously described (Thompson et al 2013;De Vos et al 2017). Useful in silico phenotypes analyses were performed as previously described (Amaral et al 2014).…”

Section: Methodsmentioning

confidence: 99%

Vibrio Gaelis sp. nov. Isolated From the Skin of Southern Atlantic Sharpnose-puffer (Canthigaster Figueiredoi)

Azevedo¹,

Mattsson²,

Tonon³

et al. 2021

Preprint

Self Cite

0

View full text Add to dashboard Cite

Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A621T obtained from the skin of the pufferfish Canthigaster figuereidoi (Tetraodontidae Family), collected in Arraial do Cabo, Brazil. Optimum growth occurs at 20 - 28 °C in the presence of 3% NaCl. The Genome sequence of the novel isolate consisted of 4.224 Mb, 4,431 coding genes and G+C content of 44.5%. Genomic taxonomy analysis based on Average Amino Acid (AAI), Genome-to-Genome-Distance (GGDH) and phylogenetic reconstruction placed A621T (= CBAS 741T) into a new species of the genus Vibrio (Vibrio gaelis sp. nov.). The genome of the novel species contains 4 gene clusters (~56.17 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the pufferfish host.

show abstract

“…The AAI value between D. swuensis DY59 T and D. radiopugnans ATCC 19172 T was 97% (Fig. 3b), which was higher than the 95% cut-off for distinct species [24,36]; whereas, the rest of the species had AAI values outside the species circumscription limit (Table S3). In order to further validate the wholegenome relatedness between these species, dDDH value was estimated using genome-to-genome distance calculator version 2.1 (GDGC; http:// ggdc.…”

mentioning

confidence: 87%

“…Deinococcus species have been mostly characterized employing polyphasic approach of taxonomy. Recently, it has been demonstrated that wholegenome based analyses present a reliable and reproducible tool for prokaryotic taxonomy and provide successful insights into the evolutionary relationships [19][20][21][22][23][24]. Furthermore, Deinococcus species have been reclassified as synonyms based on whole-genome analyses.…”

mentioning

confidence: 99%

“…To further evaluate the genomic relatedness, we performed several recommended Overall Genome Related Indices (OGRI) analyses among D. radiopugnans ATCC 19172 T and D. swuensis DY59 T along with other Deinococcus species. These OGRI analyses included average nucleotide identity (ANI) [35,36], average amino acid identity (AAI) [24,36], digital DNA-DNA hybridization (dDDH) [23], and Percentage Of Conserved Proteins (POCP).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

Lakra

¹

,

Verma

²

,

Talwar

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

show abstract

“…de/)[29]. Values of ANI, AAI and dDDH between strains HY60 T and HY54 were 99.1, 98.6 and 92.3 %, respectively, all higher than the respective threshold of 95-96[30], 95[31] and 70 %[32] for species delineation, indicating that strains HY60 T and HY54 belong to the same species (Table1). A similar conclusion was reached for strains HY82 T and HY89 as well based on the same set of scores (98.8, 98.6, 90.2%) (Table…”

mentioning

confidence: 90%

Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species

Zhou

¹

,

Huang

²

,

Yang

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.

show abstract

Microbial Genomic Taxonomy.

Cited by 32 publications

References 50 publications

Vibrio Gaelis sp. nov. Isolated From the Skin of Southern Atlantic Sharpnose-puffer (Canthigaster Figueiredoi)

Vibrio Gaelis sp. nov. Isolated From the Skin of Southern Atlantic Sharpnose-puffer (Canthigaster Figueiredoi)

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species

Contact Info

Product

Resources

About