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

Abstract

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.

The genome of a steinernematid-associated Pseudomonas piscis bacterium encodes the biosynthesis of insect toxins

“…scarpo and Steinernema sp. VH1, respectively, These nematodes were isolated from soils in Murang’a and Vihiga, Kenya, respectively [19, 50]. X.…”

“…piscis pangenomes. Pangenome studies on these two species have been hampered by their few number of publicly available genomes [19, 55]. Lastly, this study has revealed P.…”

“…97, which originated from soils in the Rift Valley, Thika, and Central regions of Kenya, respectively [ 17 ]. Bacteria were indirectly isolated from each of the three, through the haemolymph of G. mellonella larvae as previously described [ 19 ]. Briefly, 8–12 larvae were infected with a nematode culture for each treatment.…”

“…To determine the characteristics of genome assemblies and their suitability for downstream genome analyses, genome assemblies were first analysed with the comprehensive genome analysis and annotation tools, on the BV-BRC platform [ 27 ]. Species delineation was conducted on TYGS [ 28 ] as previously described [ 19 ]. Briefly, genomes in fasta format were uploaded to the server for unrestricted analyses.…”

“…Bacteria were indirectly isolated from each of the three, through the haemolymph of G. mellonellalarvae as previously described(Awori et al 2023)"…”