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Volume 5, Issue 5

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

Abstract

As a proven source of potent and selective antimicrobials, 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 species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and 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, sp. BG5 and sp. VH1 were isolated. The genomes of these two, plus that of XN45 – this was previously isolated from 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 clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, sp. BG5, VH1 and 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 sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new isolates from Kenya, both of which were closely related to . The functions encoded by most species-specific genes in the clade remain unknown.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): prokaryotic pangenomics , species delineation , Steinernema endosymbionts and Xenorhabdus bacteria
Funding
This study was supported by the:
  • Hessisches Ministerium für Wissenschaft und Kunst (Award LOEWE Translational Biodiversity Genomics)
    • Principle Award Recipient: HelgeB. Bode
  • Goethe-Universität Frankfurt am Main (Award GRADE Completion Scholarship 2020)
    • Principle Award Recipient: RyanMusumba Awori
  • Deutscher Akademischer Austauschdienst (Award 91653288)
    • Principle Award Recipient: RyanMusumba Awori
  • Kenya National Research Fund (Award NRF 1st CALL/MULTIDISCIPLINARY RESEARCH/127)
    • Principle Award Recipient: NelsonO. Amugune
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-05-22
2024-04-20
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Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya
Access Microbiology 5, 000531.v4 (2023); https://doi.org/10.1099/acmi.0.000531.v4
/content/journal/acmi/10.1099/acmi.0.000531.v4
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