Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya.

Autor:	Awori RM; Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.; Elakistos Biosciences, PO Box 19301-00100, Nairobi, Kenya., Waturu CN; Horticulture Research Institute, Kenya Agricultural and Livestock Research Organisation, PO Box 220 Thika., Pidot SJ; Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia., Amugune NO; Department of Biology, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya., Bode HB; Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany.; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
Jazyk:	angličtina
Zdroj:	Access microbiology [Access Microbiol] 2023 May 22; Vol. 5 (5). Date of Electronic Publication: 2023 May 22 (Print Publication: 2023).
DOI:	10.1099/acmi.0.000531.v4
Abstrakt:	As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown. Competing Interests: The authors declare no competing financial interest. R.M.A. is a proprietor of Elakistos Biosciences. (© 2023 The Authors.)
Databáze:	MEDLINE
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