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

Strepis, Nikolaos; Sánchez‐Andrea, Irene; Gelder, A.H. van; Kruistum, Henri van; Shapiro, Nicole; Kyrpides, Nikos C.; Göker, Markus; Klenk, Hans‐Peter; Schaap, Peter J.; Stams, Alfons Johannes Maria; Sousa, Diana Z.

doi:10.1099/ijsem.0.001294

Cited by 29 publications

(15 citation statements)

References 46 publications

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“…Specifically for the Trichococcus group, it is patent that using protein domains or 16S rRNA genes results in different clustering of the bacteria. This corroborates with the fact that information in the 16S rRNA gene of Trichococcus species is not enough to resolve taxonomy at species level [3,4,6], and does not predict the functional relatedness of the different species. 16S rRNA gene and protein domain clustering for the other analysed LAB species is much more conserved (Fig.…”

Section: Comparison Of Protein Domains Among Trichococcus Speciessupporting

confidence: 79%

“…Type strains of existing Trichococcus species have been isolated from diverse and geographically spread ecosystems. Various species derive from waste treatment systems or contaminated sites: T. flocculiformis (activated sludge) [1], T. pasteurii (septic pit sludge) [2], T. collinsii (soil spilled with hydrocarbons) [2], T. ilyis (sulfate reducing anaerobic sludge) [3], T. shcherbakoviae (sludge from low-temperature anaerobic reactor) [4]; while others were isolated from natural environments: T. patagoniensis (guano from penguin, Patagonia) [5], T. palustris (swamp, Russia) [2], and T. paludicola and T. alkaliphilus (high elevation wetland, Tibet) [6].…”

Section: Introductionmentioning

confidence: 99%

“…Trichococcus species share a very high 16S rRNA gene sequence identity, in the range of 98-100% [2][3][4]6]. This often impairs the taxonomic classification of new strains within this genus on the basis of 16S rRNA gene sequence identity, and therefore whole genome comparison needs to be performed.…”

Section: Introductionmentioning

confidence: 99%

“…Trichococcus species are related to the lactic acid bacteria (LAB), and phylogenetically close to the genera Carnobacterium and Aerococcus [11]. Described Trichococcus species can all grow on glucose, cellobiose, D-mannose, fructose and sucrose [1][2][3][4][5][6]. However, T. pasteurii and Trichococcus strain ES5 are the only strains within the genus capable of converting glycerol to mainly 1,3-PDO [12], with comparable product yields to those of other 1,3-PDO producers, such as Clostridium butyricum and Klebsiella pneumoniae [13,14].…”

Section: Introductionmentioning

confidence: 99%

“…1,3-PDO is used as a building block in chemical industry [15], and the discovery of new efficient and resilient biocatalysts for its production are of interest for biotechnological industry. In general, Trichococcus species have a broad temperature range for growth (commonly from 4°C to 40°C) [1][2][3][4][5][6]. T. patagoniensis and T. shcherbakoviae can grow at negative temperatures and tolerate salinities up to 5% (w/v) NaCl [4,5], which is also the case for several related Carnobacterium species, such as C. funditum, C. alterfunditum and C. pleistocenium [16,17], but no other Trichococcus species.…”

Section: Introductionmentioning

confidence: 99%

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Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

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Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0°C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094 T), is able to grow on glycerol with the production of 1,3-propanediol.

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Section: Comparison Of Protein Domains Among Trichococcus Speciessupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

et al. 2020

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Jeotgalibaca

Vela¹,

Fernández‐Garayábal²

2019

Bergey's Manual of Systematics of Archaea and Bacteria

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Je.ot.ga.li.ba′ca. N.L. neut. n. jeotgalum (from Korean n. jeotgal ), traditional Korean food; L. fem. n. baca a grain or berry, and in bacteriology a coccus; N.L. fem. n. Jeotgalibaca , coccus from jeotgal. Firmicutes / Bacilli / Bacillales / Carnobacteriaceae / Jeotgalibaca Gram‐positive cocci. Oxidase‐ and catalase‐negative . Cells occur in tetrads, sarcinae, or irregular conglomerates. Non‐spore‐forming. Nonmotile. Facultative anaerobe . Chemoheterotrophic. Peptidoglycan type A4α . Major fatty acids are C 16 : 0 and C 18 : 1 ω9 c . Polar lipids include phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unidentified glycolipids, aminolipids, and phospholipids. Members of the family Carnobacteriaceae , order Lactobacillales , class Bacilli , phylum Firmicutes . Known habitats are seujeot (traditional Korean food) and joint of pigs. The full range of habitat is not known. DNA G + C content (in silico mol%) : 37.5–38.3. Type species : Jeotgalibaca dankookensis Lee, Trujillo, Kang and Ahn 2014, 1734 VP .

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Microbial community dynamics at high organic loading rates revealed by pyrosequencing during sugar refinery wastewater treatment in a UASB reactor

Zhang

Ban

2018

Front. Environ. Sci. Eng.

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

Cited by 29 publications

References 46 publications

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Jeotgalibaca

Microbial community dynamics at high organic loading rates revealed by pyrosequencing during sugar refinery wastewater treatment in a UASB reactor

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