Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

Nikolaos Strepis; Irene Sánchez-Andrea; Ton van Gelder; Henri van Kruistum; Nicole Shapiro; Nikos Kyrpides; Markus Göker; H.P. Klenk; Peter Schaap; Fons Stams; Diana Z. Sousa

doi:10.1099/ijsem.0.001294

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

Nikolaos Strepis, Irene Sánchez-Andrea, Ton van Gelder, Henri van Kruistum, Nicole Shapiro, Nikos Kyrpides, Markus Göker, H.P. Klenk, Peter Schaap, Fons Stams, Diana Z. Sousa^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

26 Citations (Scopus)

Abstract

Trichococcus species share high similarity of their 16S rRNA gene sequences (> 99%). Digital DNA-DNA hybridization values (dDDH) among all described Trichococcus species (T. flocculiformis DSM 2094T, T. pasteurii DSM 2381T, T. collinsii DSM 14526T, T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus. The dDDH values showed a low DNA relatedness between strain R210T and all other Trichococcus spp. (23-32 %). Cells of strain R210T were motile, slightly curved rods with sizes 0.63-1.40 x 0.48-0.90 μm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30°C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol. The genomic DNA G+C content of strain R210T was 47.9%. Based on morphological, physiological, biochemical characteristics of strain R210T and along with measured dDDH values for all Trichococcus spp. we propose to separate this isolate into a new taxon on species level within Trichococcus genus. The name Trichococcus ilyis is proposed. The type strain of Trichococcus ilyis is R210T (=DSM 22150T =JCM 31247T).

Original language	English
Pages (from-to)	3957-3963
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	66
Issue number	10
DOIs	https://doi.org/10.1099/ijsem.0.001294
Publication status	Published - 2016

Keywords

Citrate
DDH
Fermentation
Genome blast distance phylogeny
Genomics
Trichococcus

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10.1099/ijsem.0.001294Licence: Publisher

Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, A. H. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. J. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. Z. (Creator), Wageningen University, 10 Apr 2016
https://www.ebi.ac.uk/ena/data/view/PRJEB12706
Dataset
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, A. H. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. J. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. Z. (Creator), Wageningen University, 10 Apr 2016
https://www.ebi.ac.uk/ena/data/view/PRJEB12708
Dataset
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, A. H. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. J. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. Z. (Creator), Wageningen University, 10 Apr 2016
https://www.ebi.ac.uk/ena/data/view/PRJEB12705
Dataset

Cite this

Strepis, N., Sánchez-Andrea, I., van Gelder, T., van Kruistum, H., Shapiro, N., Kyrpides, N., Göker, M., Klenk, H. P., Schaap, P., Stams, F., & Sousa, D. Z. (2016). Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. International Journal of Systematic and Evolutionary Microbiology, 66(10), 3957-3963. https://doi.org/10.1099/ijsem.0.001294

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title = "Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses",

abstract = "Trichococcus species share high similarity of their 16S rRNA gene sequences (> 99%). Digital DNA-DNA hybridization values (dDDH) among all described Trichococcus species (T. flocculiformis DSM 2094T, T. pasteurii DSM 2381T, T. collinsii DSM 14526T, T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus. The dDDH values showed a low DNA relatedness between strain R210T and all other Trichococcus spp. (23-32 %). Cells of strain R210T were motile, slightly curved rods with sizes 0.63-1.40 x 0.48-0.90 μm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30°C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol. The genomic DNA G+C content of strain R210T was 47.9%. Based on morphological, physiological, biochemical characteristics of strain R210T and along with measured dDDH values for all Trichococcus spp. we propose to separate this isolate into a new taxon on species level within Trichococcus genus. The name Trichococcus ilyis is proposed. The type strain of Trichococcus ilyis is R210T (=DSM 22150T =JCM 31247T).",

keywords = "Citrate, DDH, Fermentation, Genome blast distance phylogeny, Genomics, Trichococcus",

author = "Nikolaos Strepis and Irene S{\'a}nchez-Andrea and {van Gelder}, Ton and {van Kruistum}, Henri and Nicole Shapiro and Nikos Kyrpides and Markus G{\"o}ker and H.P. Klenk and Peter Schaap and Fons Stams and Sousa, {Diana Z.}",

year = "2016",

doi = "10.1099/ijsem.0.001294",

language = "English",

volume = "66",

pages = "3957--3963",

journal = "International Journal of Systematic and Evolutionary Microbiology",

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}

Strepis, N, Sánchez-Andrea, I, van Gelder, T, van Kruistum, H, Shapiro, N, Kyrpides, N, Göker, M, Klenk, HP, Schaap, P, Stams, F & Sousa, DZ 2016, 'Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses', International Journal of Systematic and Evolutionary Microbiology, vol. 66, no. 10, pp. 3957-3963. https://doi.org/10.1099/ijsem.0.001294

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. / Strepis, Nikolaos; Sánchez-Andrea, Irene; van Gelder, Ton et al.
In: International Journal of Systematic and Evolutionary Microbiology, Vol. 66, No. 10, 2016, p. 3957-3963.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

AU - Strepis, Nikolaos

AU - Sánchez-Andrea, Irene

AU - van Gelder, Ton

AU - van Kruistum, Henri

AU - Shapiro, Nicole

AU - Kyrpides, Nikos

AU - Göker, Markus

AU - Klenk, H.P.

AU - Schaap, Peter

AU - Stams, Fons

AU - Sousa, Diana Z.

PY - 2016

Y1 - 2016

N2 - Trichococcus species share high similarity of their 16S rRNA gene sequences (> 99%). Digital DNA-DNA hybridization values (dDDH) among all described Trichococcus species (T. flocculiformis DSM 2094T, T. pasteurii DSM 2381T, T. collinsii DSM 14526T, T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus. The dDDH values showed a low DNA relatedness between strain R210T and all other Trichococcus spp. (23-32 %). Cells of strain R210T were motile, slightly curved rods with sizes 0.63-1.40 x 0.48-0.90 μm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30°C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol. The genomic DNA G+C content of strain R210T was 47.9%. Based on morphological, physiological, biochemical characteristics of strain R210T and along with measured dDDH values for all Trichococcus spp. we propose to separate this isolate into a new taxon on species level within Trichococcus genus. The name Trichococcus ilyis is proposed. The type strain of Trichococcus ilyis is R210T (=DSM 22150T =JCM 31247T).

AB - Trichococcus species share high similarity of their 16S rRNA gene sequences (> 99%). Digital DNA-DNA hybridization values (dDDH) among all described Trichococcus species (T. flocculiformis DSM 2094T, T. pasteurii DSM 2381T, T. collinsii DSM 14526T, T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus. The dDDH values showed a low DNA relatedness between strain R210T and all other Trichococcus spp. (23-32 %). Cells of strain R210T were motile, slightly curved rods with sizes 0.63-1.40 x 0.48-0.90 μm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30°C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol. The genomic DNA G+C content of strain R210T was 47.9%. Based on morphological, physiological, biochemical characteristics of strain R210T and along with measured dDDH values for all Trichococcus spp. we propose to separate this isolate into a new taxon on species level within Trichococcus genus. The name Trichococcus ilyis is proposed. The type strain of Trichococcus ilyis is R210T (=DSM 22150T =JCM 31247T).

KW - Citrate

KW - DDH

KW - Fermentation

KW - Genome blast distance phylogeny

KW - Genomics

KW - Trichococcus

U2 - 10.1099/ijsem.0.001294

DO - 10.1099/ijsem.0.001294

M3 - Article

SN - 1466-5026

VL - 66

SP - 3957

EP - 3963

JO - International Journal of Systematic and Evolutionary Microbiology

JF - International Journal of Systematic and Evolutionary Microbiology

IS - 10

ER -

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

Abstract

Keywords

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Datasets

Comparative genomic and physiological analysis of Trichococcus species

Comparative genomic and physiological analysis of Trichococcus species

Comparative genomic and physiological analysis of Trichococcus species

Cite this