Robust Demarcation of the Family () and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2020 Feb 4

PMID 32010063

Citations 22

Authors

Radhey S Gupta

Sudip Patel

Affiliations

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Abstract

The family / is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily , the evolutionary history of this family, containing the potent mosquitocidal species , remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family / and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available / and representative species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family / or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family / based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family /, namely gen. nov., gen. nov., and gen. nov., as well as the transfer of 25 misclassified species from the families / and into these three genera and in , , , and genera. These amendments establish a coherent taxonomy and evolutionary history for the family /, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family within the emended family .

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References

Gao B, Gupta R . Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev. 2012; 76(1):66-112. PMC: 3294427. DOI: 10.1128/MMBR.05011-11. View

Kong D, Wang Y, Zhao B, Li Y, Song J, Zhai Y . Lysinibacillus halotolerans sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol. 2014; 64(Pt 8):2593-2598. DOI: 10.1099/ijs.0.061465-0. View

Thompson C, Chimetto L, Edwards R, Swings J, Stackebrandt E, Thompson F . Microbial genomic taxonomy. BMC Genomics. 2013; 14:913. PMC: 3879651. DOI: 10.1186/1471-2164-14-913. View

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

Parte A . LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 2013; 42(Database issue):D613-6. PMC: 3965054. DOI: 10.1093/nar/gkt1111. View

De Maayer P, Aliyu H, Cowan D . Reorganising the order Bacillales through phylogenomics. Syst Appl Microbiol. 2018; 42(2):178-189. DOI: 10.1016/j.syapm.2018.10.007. View

Yu J, Guan X, Liu C, Xiang W, Yu Z, Liu X . Erratum to: Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5). Antonie Van Leeuwenhoek. 2016; 110(1):173. DOI: 10.1007/s10482-016-0773-7. View

Rahi P, Kurli R, Khairnar M, Jagtap S, Pansare A, Dastager S . Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone. Int J Syst Evol Microbiol. 2017; 67(7):2289-2295. DOI: 10.1099/ijsem.0.001943. View

Kimura M . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16(2):111-20. DOI: 10.1007/BF01731581. View

10.

Cheng M, Zhang H, Zhang J, Hu G, Zhang J, He J . Lysinibacillus fluoroglycofenilyticus sp. nov., a bacterium isolated from fluoroglycofen contaminated soil. Antonie Van Leeuwenhoek. 2014; 107(1):157-64. DOI: 10.1007/s10482-014-0313-2. View

11.

Azmatunnisa M, Rahul K, Lakshmi K, Sasikala C, Ramana C . Lysinibacillus acetophenoni sp. nov., a solvent-tolerant bacterium isolated from acetophenone. Int J Syst Evol Microbiol. 2015; 65(Pt 6):1741-1748. DOI: 10.1099/ijs.0.000170. View

12.

Ouoba L, Vouidibio Mbozo A, Thorsen L, Anyogu A, Nielsen D, Kobawila S . Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo. Int J Syst Evol Microbiol. 2015; 65(11):4256-4262. DOI: 10.1099/ijsem.0.000570. View

13.

Burkett-Cadena M, Sastoque L, Cadena J, Dunlap C . Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant. Antonie Van Leeuwenhoek. 2019; 112(8):1161-1167. DOI: 10.1007/s10482-019-01248-w. View

14.

Berry C . The bacterium, Lysinibacillus sphaericus, as an insect pathogen. J Invertebr Pathol. 2011; 109(1):1-10. DOI: 10.1016/j.jip.2011.11.008. View

15.

Dobritsa A, Linardopoulou E, Samadpour M . Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov. Int J Syst Evol Microbiol. 2017; 67(10):3846-3853. DOI: 10.1099/ijsem.0.002202. View

16.

Luo X, Zhang J, Li D, Xin Y, Xin D, Fan L . Planomicrobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol. 2014; 64(Pt 8):2700-2705. DOI: 10.1099/ijs.0.055426-0. View

17.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

18.

Konstantinidis K, Tiedje J . Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005; 187(18):6258-64. PMC: 1236649. DOI: 10.1128/JB.187.18.6258-6264.2005. View

19.

Yoon J, Kang S, Lee S, Oh K, Oh T . Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus. Int J Syst Evol Microbiol. 2009; 60(Pt 4):754-758. DOI: 10.1099/ijs.0.013136-0. View

20.

Yilmaz P, Parfrey L, Yarza P, Gerken J, Pruesse E, Quast C . The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2013; 42(Database issue):D643-8. PMC: 3965112. DOI: 10.1093/nar/gkt1209. View