{
  "abstract": "Bacterial wilt caused by Ralstonia solanacearum species complex is a major constraint in tomato production in Kenya, resulting in yield losses of up to 100% in heavily infested fields. This study used high-throughput shotgun metagenomic sequencing approach to characterize the rhizosphere microbiomes of tomato plants in three of the major production areas in Kenya (Kirinyaga, Kiambu, and Laikipia counties) focusing on detecting Ralstonia phage sequences. Soil samples were collected from the rhizosphere of bacterial wilt-infected tomato plants, and microbial DNA was extracted using a modified phenol-chloroform protocol and sequenced using Illumina NovaSeq platform. Taxonomic profiling revealed diverse microbial communities dominated by Actinobacteria and Proteobacteria. Four Ralstonia species were confirmed (R. insidiosa, R. pickettii, R. mannitolilytica and R. wenshanensis). Sequences similar to the R. solanacearum species complex were also detected but were too short for species-level confirmation. Metagenomic analysis detected sequences matching four previously described Ralstonia phages (RSL1, RSIBR3, Anchaing, and Cimandef). Functional annotation demonstrated abundant metabolic pathways, energy production systems, and stress response mechanisms, indicating highly adaptive microbial communities in the tomato rhizosphere. This study provides baseline data on rhizosphere microbiome composition in Kenyan tomato production systems and identifies Ralstonia phage sequences that could guide future isolation and host-range studies. If future work shows that these phages are active against Ralstonia, they could contribute to locally adapted biocontrol approaches that reduce reliance on chemical pesticides.",
  "abstract_shown": true,
  "affiliations": [
    "Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya",
    "Biological Sciences, Machakos University, Machakos, Kenya",
    "Health Sciences, Machakos University, Machakos, Kenya",
    "Agricultural Sciences, Machakos University, Machakos, Kenya"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Derleen Bosibori Mogire",
      "orcid": "0009-0009-5089-3779"
    },
    {
      "affs": [
        0
      ],
      "name": "Johnstone Neondo",
      "orcid": "0000-0002-4813-8792"
    },
    {
      "affs": [
        1
      ],
      "name": "Christabel Muhonja"
    },
    {
      "affs": [
        2
      ],
      "name": "Consolate Awuor"
    },
    {
      "affs": [
        3
      ],
      "name": "Daniel Mureithi"
    },
    {
      "affs": [
        0
      ],
      "name": "Stephen Ogada"
    },
    {
      "affs": [
        0
      ],
      "name": "Tofick Barasa Wekesa"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dy9bwd0ez6t32.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0362106",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13734573/",
  "id": "dy9bwd0ez6t32",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0362106",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Agricultural Soil Science"
    ],
    [
      "heading",
      "Agriculture"
    ],
    [
      "heading",
      "Bacterial Pathogens"
    ],
    [
      "heading",
      "Bacteriophages"
    ],
    [
      "heading",
      "Biology and Life Sciences"
    ],
    [
      "heading",
      "Earth Sciences"
    ],
    [
      "heading",
      "Ecology"
    ],
    [
      "heading",
      "Ecology and Environmental Sciences"
    ],
    [
      "heading",
      "Eukaryota"
    ],
    [
      "heading",
      "Fruits"
    ],
    [
      "heading",
      "Genetics"
    ],
    [
      "heading",
      "Genomics"
    ],
    [
      "heading",
      "Medical Microbiology"
    ],
    [
      "heading",
      "Medicine and Health Sciences"
    ],
    [
      "heading",
      "Metagenomics"
    ],
    [
      "heading",
      "Microbial Genomics"
    ],
    [
      "heading",
      "Microbial Pathogens"
    ],
    [
      "heading",
      "Microbiology"
    ],
    [
      "heading",
      "Microbiome"
    ],
    [
      "heading",
      "Organisms"
    ],
    [
      "heading",
      "Pathogens"
    ],
    [
      "heading",
      "Pathology and Laboratory Medicine"
    ],
    [
      "heading",
      "Plant Bacterial Pathogens"
    ],
    [
      "heading",
      "Plant Ecology"
    ],
    [
      "heading",
      "Plant Pathogens"
    ],
    [
      "heading",
      "Plant Pathology"
    ],
    [
      "heading",
      "Plant Science"
    ],
    [
      "heading",
      "Plant-Environment Interactions"
    ],
    [
      "heading",
      "Plants"
    ],
    [
      "heading",
      "Ralstonia"
    ],
    [
      "heading",
      "Research Article"
    ],
    [
      "heading",
      "Rhizosphere"
    ],
    [
      "heading",
      "Soil Science"
    ],
    [
      "heading",
      "Tomatoes"
    ],
    [
      "heading",
      "Viruses"
    ],
    [
      "plos",
      "/Biology and life sciences/Agriculture/Agricultural soil science"
    ],
    [
      "plos",
      "/Biology and life sciences/Ecology/Plant ecology/Plant-environment interactions/Rhizosphere"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Metagenomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Microbial genomics/Microbiome"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Ralstonia"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbiome"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Microbial genomics/Microbiome"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Eukaryota/Plants/Fruits/Tomatoes"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Bacteriophages"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant ecology/Plant-environment interactions/Rhizosphere"
    ],
    [
      "plos",
      "/Biology and life sciences/Plant science/Plant pathology/Plant pathogens/Plant bacterial pathogens"
    ],
    [
      "plos",
      "/Earth sciences/Soil science/Agricultural soil science"
    ],
    [
      "plos",
      "/Ecology and environmental sciences/Ecology/Plant ecology/Plant-environment interactions/Rhizosphere"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Ralstonia"
    ]
  ],
  "openalex": null,
  "pdf_url": null,
  "pmcid": "PMC13734573",
  "pmid": "42981365",
  "published": "2026-11-04",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/dy9bwd0ez6t32.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T12:20:11Z",
      "native_id": "10.1371/journal.pone.0362106",
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      "url": "https://doi.org/10.1371/journal.pone.0362106"
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    {
      "first_seen": "2026-11-08T12:24:01Z",
      "native_id": "PMC13734573",
      "source": "pmc",
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  "subjects": [
    {
      "field": "biology",
      "origin": "plos:ecology",
      "subfield": "ecology"
    },
    {
      "field": "biology",
      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
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    {
      "field": "biology",
      "origin": "heading:Plant Science",
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    },
    {
      "field": "medicine",
      "origin": "heading:Medicine and Health Sciences",
      "subfield": "general"
    }
  ],
  "title": "Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils",
  "title_text": "Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:24:01Z",
  "url": "https://research.draconitic.com/paper/dy9bwd0ez6t32",
  "venue": "PLOS One",
  "versions": []
}