Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Riesco, Raúl; Trujillo, Martha E.

doi:10.1099/ijsem.0.006300

Cited by 76 publications

(22 citation statements)

References 79 publications

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“…hygroscopicus NBRC 13472 T , which were 91.26 and 48%, respectively ( Table 5 ). These values were below the novel species threshold of 95% (ANI) and 70% (dDDH) ( Meier-Kolthoff et al, 2022 ; Riesco and Trujillo, 2024 ). These findings further supported that strain SCA4-21 T belongs to a novel species in the genus Streptomyces .…”

Section: Resultsmentioning

confidence: 80%

“…The overall genome-related indexes (OGRI), such as ANI and dDDH, have been widely used to replace the traditional DDH to identify different species ( Richter and Rosselló-Móra, 2009 ; Zhang et al, 2019 ; Meier-Kolthoff et al, 2022 ). The ANI and dDDH values for accepted species boundary are around 95–96 and 70%, respectively ( Riesco and Trujillo, 2024 ). In this study, ANI and dDDH values were calculated between strain SCA4-21 T and the adjacent seven strains in the phylogenetic trees of the 16S rRNA gene or MLSA.…”

Section: Discussionmentioning

confidence: 99%

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Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi

Qi,

Liu,

Zou

et al. 2024

Front. Microbiol.

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Banana wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc TR4. Here, 30 actinobacteria were isolated from soils and screened for their antagonistic activity against Foc TR4. Strain SCA4-21T was selected due to its strongest antagonistic activity against Foc TR4. Strain SCA4-21T also exhibited strong antagonistic activity against the other eight phytopathogenic fungi. The strain was identified as the genus Streptomyces according to its physiological, biochemical, and phenotypic characteristics. The phylogenetic trees of 16S rRNA sequences demonstrated that strain SCA4-21T formed a subclade with S. iranensis HM 35T and/or S. rapamycinicus NRRL B-5491T with low bootstrap values. Considering that 16S rRNAs did not provide sufficient resolution for species-level identification, the whole genome of strain SCA4-21T was sequenced. Multilocus sequence analysis (MLSA) based on five housekeeping gene alleles (atpD, gyrB, recA, rpoB, and trpB) revealed that strain SCA4-21T clustered into S. hygroscopicus subsp. hygroscopicus NBRC 13472T with 100% of bootstrap value. The analysis of the genome-based phylogeny also approved the results. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) were 91.26 and 44.30%, respectively, with values below the respective species level threshold of 95 and 70%. Hence, strain SCA 4–21T represented a novel species within the genus Streptomyces, named Streptomyces luomodiensis sp. nov. The type strain is SCA4-21T (=GDMCC4.340T = JCM36555T). By the CAZymes analysis, 348 carbohydrate-active enzymes (CAZymes) were detected, including 15 chitinases and eight β-1,3-glucanases. The fermentation broth of strain SCA4-21T, exhibiting strong antagonistic activity against Foc TR4, demonstrated high activities of chitinase and β-1,3-glucanase, which might be involved in antifungal activity. Our results showed an innovative potential biocontrol agent for managing plant fungal diseases, specifically banana fusarium wilt.

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Section: Resultsmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 99%

Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi

Qi,

Liu,

Zou

et al. 2024

Front. Microbiol.

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“…It is critical to note that the choice of reference genomes is vital for the classification and nomenclature of new species. Consequent to the International Code of Nomenclature of Prokaryotes (ICNP) and the current standard for the use of genome data for the taxonomy of prokaryotes [ 53 , 62 , 63 ], analyses for new taxa should include genomes of effectively published type strains with validly published name. Non-type strain genomes may serve only as comparative references and should not be used as references for taxa delineation.…”

Section: Discussionmentioning

confidence: 99%

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

Tian,

Teo,

Yang

et al. 2024

BMC Microbiol

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Background Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. Results Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. Conclusions Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health. Significance This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.

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“…The pairwise relatedness between strain PraFG1 T and other species belonging to the genus Psychrobacter was estimated by calculating the average nucleotide identity (ANI) using the EzBioCloud ANI calculator (www.ezbiocloud.net/tools/ani, last accessed on 26 January 2024) [21], assuming an identity below 95 % to indicate a new species according to the currently adopted standards [28]. The chromosome sequences of eight Psychrobacter strains, available on the GenBank database, were compared to the chromosome sequence of strain PraFG1 T , obtaining values ranging from 78.1 % [ P. sanguinis DSM 23635 T (NZ_CP085990)] to 72.1 % [ Psychrobacter urativorans R310.10B (NZ_CP012678)].…”

Section: Genome Featuresmentioning

confidence: 99%

Psychrobacter raelei sp. nov., isolated from a dog with peritonitis

Manzulli,

Schiavone,

Castellana

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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A strain belonging to the genus Psychrobacter, named PraFG1T, was isolated from the peritoneal effusion of a stray dog during necropsy procedures. The strain was characterized by the phylogenetic analyses based on the nucleotide sequences of 16S and 23S rRNA genes and of gyrB, which placed the strain in the genus Psychrobacter. The nucleotide sequence of the chromosome confirmed the placement, showing an average nucleotide identity of 72.1, 77.7, and 77.5 % with the closest related species, namely Psychrobacter sanguinis, Psychrobacter piechaudii, and Psychrobacter phenylpyruvicus, respectively, thus indicating a novel species. The polyphasic characterization by biochemical and fatty acid profiling as well as MALDI-TOF supported those findings. The strain was halotolerant, capable of growing within a temperature range between 4 and 37 °C, it was positive for catalase and oxidase, indole producing, nitrate reducing, and not able to use 5-keto-d-gluconic acid as a carbon source. Taken together, the data suggest that strain PraFG1T could be considered as representing a novel species, with the name Psychrobacter raelei sp. nov. (type strain PraFG1T=CIP 111873T=LMG 32233T).

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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Cited by 76 publications

References 79 publications

Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi

Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

Psychrobacter raelei sp. nov., isolated from a dog with peritonitis

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