Proposal for reclassifying Tellurirhabdus species within the genus Larkinella

Syed Raziuddin Quadri, Wesam Nofal, Muhannad Alruwaili

Abstract


Background: Members of the genera Larkinella and Tellurirhabdus are Gram-negative, aerobic, and consist of menaquinone (MK)-7 as their main isoprenoid quinone. Recent analysis suggests that both genera share similar characteristics. The taxonomic position of the genera Larkinella and Tellurirhabdus has been evaluated using genomic analysis.

Methods: The quality of the genomic sequences of Larkinella and Tellurirhabdus was assessed after they were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/). Average nucleotide identity (ANI) and average amino acid identity (AAI) data was used for evaluating their genomic relatedness.

Results: The AAI values between Larkinella and Tellurirhabdus were above the threshold value of genus delineation (>60–65 %) indicating that they are members of the same genus. The ANI values among Larkinella and Tellurirhabdus species were below 95-96% indicating they were different species.

Conclusion: We propose transferring Tellurirhabdus bombi to the genus Larkinella as Larkinella bombi comb. nov. and Tellurirhabdus rosea to the genus Larkinella as Larkinella roseola nom. nov. based on our research findings.

Keywords: Larkinella; Tellurirhabdus; Reclassification; Average amino acid identity; Average nucleotide identity


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Vancanneyt M, Nedashkovskaya OI, Snauwaert C, Mortier S, Vandemeulebroecke K, et al. Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator. International Journal of Systematic and Evolutionary Microbiology, (2006); 56(Pt 1): 237-241.

Choi J, Yang D, Chhetri G, Cha S, Seo T. Tellurirhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie Van Leeuwenhoek, (2019); 112(7): 1047-1054.

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, (2020); 70(11): 5607-5612.

Park Y, Ten LN, Lee YK, Jung HY, Kim MK. Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil. Archives of Microbiology, (2022); 204(3): 182.

Jeon J, Ten LN, Lee JJ, Lee SY, Park S, et al. Larkinella knui sp. nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology, (2018); 68(2): 582-588.

Zhou Z, Zhu L, Dong Y, Xia X, Wu S, Wang G. Larkinella punicea sp. nov., isolated from manganese mine soil. Archives of Microbiology, (2020); 202(9): 2517-2523.

Anandham R, Kwon SW, Weon HY, Kim SJ, Kim YS, et al. Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006. International Journal of Systematic and Evolutionary Microbiology, (2011); 61(Pt 1): 30-34.

Kulichevskaya IS, Zaichikova MV, Detkova EN, Dedysh SN, Zavarzin GA. Larkinella arboricola sp. nov., a new spiral-shaped bacterium of the phylum Bacteroidetes isolated from the microbial community of decomposing wood. Microbiology, (2009); 78(6): 741-746.

Park SJ, Lee JJ, Lee SY, Lee DS, Kim MK, et al.Larkinella harenae sp. nov., Isolated from Korean Beach Soil. Current Microbiology, (2017); 74(7): 798-802.

Zhang K, Narsing Rao MP, Banerjee A, Wang J, Ning S-y, et al. Description of Tellurirhabdus bombi sp. nov., Isolated from Bumblebee. Current Microbiology, (2023); 80(10): 337.

Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, (2016); 33(7): 1870-1874.

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, (1994); 22(22): 4673-4680.

Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, (1981); 17(6): 368-376.

Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, (1987); 4(4): 406-425.

Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology, (1971); 20(4): 406-416.

Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, (1985); 39(4): 783-791.

Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, (1980); 16(2): 111-120.

Nei M, Kumar S. Molecular evolution and phylogenetics. (2000) Oxford University Press, New York.

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, (2015); 25(7): 1043-1055.

Lowe TM, Eddy SR. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research, (1997); 25(5): 955-964.

Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications, (2019); 10(1): 2182.

Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Research, (2024); 52(W1): W78-W82.

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, (2010); 11119.

Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nature Methods, (2015); 12(1): 59-60.

Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Analytical Methods, (2016); 8(1): 12-24.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. BLAST+: architecture and applications. BMC Bioinformatics, (2009); 10(1): 421.

Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences of the United States of America, (2009); 106(45): 19126-19131.

Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. Journal of bacteriology, (2005); 187(18): 6258-6264.

Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Research, (2014); 42(8): e73.




DOI: http://dx.doi.org/10.62940/als.v12i2.3698

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