{"id":"https://openalex.org/W7225799440","doi":"https://doi.org/10.1371/journal.pone.0362184","title":"Genetic diversity of bacterial endophytes associated with Crotalaria (Rattlepods)","display_name":"Genetic diversity of bacterial endophytes associated with Crotalaria (Rattlepods)","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225799440","doi":"https://doi.org/10.1371/journal.pone.0362184"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pone.0362184","doi":"https://doi.org/10.1371/journal.pone.0362184","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0362184","pdf_url":null,"source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pone.0362184","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116829419","display_name":"Edinah G Ongaga","orcid":"https://orcid.org/0000-0002-3502-8578","observed_orcids":["https://orcid.org/0000-0002-3502-8578"]},"institutions":[{"id":"https://openalex.org/I3132506069","display_name":"University of Embu","ror":"https://ror.org/00hzs6t60","country_code":"KE","type":"education","lineage":["https://openalex.org/I3132506069"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Edinah Ongaga","raw_affiliation_strings":["University of Embu (UoEm)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Embu (UoEm)","institution_ids":["https://openalex.org/I3132506069"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086126698","display_name":"Johnstone Omukhulu Neondo","orcid":"https://orcid.org/0000-0002-4813-8792","observed_orcids":["https://orcid.org/0000-0002-4813-8792"]},"institutions":[{"id":"https://openalex.org/I26805570","display_name":"Jomo Kenyatta University of Agriculture and Technology","ror":"https://ror.org/015h5sy57","country_code":"KE","type":"education","lineage":["https://openalex.org/I26805570"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Johnstone O. Neondo","raw_affiliation_strings":["Jomo Kenyatta University of Agriculture and Technology (JKUAT)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jomo Kenyatta University of Agriculture and Technology (JKUAT)","institution_ids":["https://openalex.org/I26805570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050395526","display_name":"Joshua Kiilu Muli","orcid":"https://orcid.org/0000-0003-1007-6722","observed_orcids":["https://orcid.org/0000-0003-1007-6722"]},"institutions":[{"id":"https://openalex.org/I3132506069","display_name":"University of Embu","ror":"https://ror.org/00hzs6t60","country_code":"KE","type":"education","lineage":["https://openalex.org/I3132506069"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Joshua Kiilu Muli","raw_affiliation_strings":["University of Embu (UoEm)"],"raw_orcid":"https://orcid.org/0000-0003-1007-6722","affiliations":[{"raw_affiliation_string":"University of Embu (UoEm)","institution_ids":["https://openalex.org/I3132506069"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049146209","display_name":"Peter K. Kamau","orcid":"https://orcid.org/0000-0001-7195-6278","observed_orcids":["https://orcid.org/0000-0001-7195-6278"]},"institutions":[{"id":"https://openalex.org/I263567798","display_name":"South Eastern Kenya University","ror":"https://ror.org/02w403504","country_code":"KE","type":"education","lineage":["https://openalex.org/I263567798"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Peter K. Kamau","raw_affiliation_strings":["South Eastern Kenya University (SEKU)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"South Eastern Kenya University (SEKU)","institution_ids":["https://openalex.org/I263567798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019664172","display_name":"Christine C. Bii","orcid":"https://orcid.org/0000-0002-5635-3871","observed_orcids":["https://orcid.org/0000-0002-5635-3871"]},"institutions":[{"id":"https://openalex.org/I2841861","display_name":"Kenya Medical Research Institute","ror":"https://ror.org/04r1cxt79","country_code":"KE","type":"facility","lineage":["https://openalex.org/I2841861"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Christine Bii","raw_affiliation_strings":["Kenya Medical Research Institute (KEMRI)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kenya Medical Research Institute (KEMRI)","institution_ids":["https://openalex.org/I2841861"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002182815","display_name":"Eddy Okoth Odari","orcid":"https://orcid.org/0000-0002-6151-9274","observed_orcids":["https://orcid.org/0000-0002-6151-9274"]},"institutions":[{"id":"https://openalex.org/I26805570","display_name":"Jomo Kenyatta University of Agriculture and Technology","ror":"https://ror.org/015h5sy57","country_code":"KE","type":"education","lineage":["https://openalex.org/I26805570"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Eddy Odari","raw_affiliation_strings":["Jomo Kenyatta University of Agriculture and Technology (JKUAT)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jomo Kenyatta University of Agriculture and Technology (JKUAT)","institution_ids":["https://openalex.org/I26805570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076590299","display_name":"Nancy L. M. Budambula","orcid":"https://orcid.org/0000-0001-8093-2702","observed_orcids":["https://orcid.org/0000-0001-8093-2702"]},"institutions":[{"id":"https://openalex.org/I3132506069","display_name":"University of Embu","ror":"https://ror.org/00hzs6t60","country_code":"KE","type":"education","lineage":["https://openalex.org/I3132506069"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Nancy L. M. Budambula","raw_affiliation_strings":["University of Embu (UoEm)"],"raw_orcid":"https://orcid.org/0000-0001-8093-2702","affiliations":[{"raw_affiliation_string":"University of Embu (UoEm)","institution_ids":["https://openalex.org/I3132506069"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2382,"currency":"USD","value_usd":2382},"apc_paid":{"value":2382,"currency":"USD","value_usd":2382},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"11","first_page":"e0362184","last_page":"e0362184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.9185000061988831,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.9185000061988831,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.03999999910593033,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12934","display_name":"Plant and fungal interactions","score":0.02280000038444996,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9025999903678894},{"id":"https://openalex.org/C134387633","wikidata":"https://www.wikidata.org/wiki/Q11395","display_name":"Domestication","level":2,"score":0.70660001039505},{"id":"https://openalex.org/C2776110052","wikidata":"https://www.wikidata.org/wiki/Q311148","display_name":"Crotalaria","level":2,"score":0.6353999972343445},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.6086999773979187},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.5332000255584717},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.5246999859809875},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.4645000100135803},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.38920000195503235},{"id":"https://openalex.org/C2777461220","wikidata":"https://www.wikidata.org/wiki/Q589029","display_name":"Germplasm","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C203519979","wikidata":"https://www.wikidata.org/wiki/Q865360","display_name":"Jaccard index","level":3,"score":0.36559998989105225},{"id":"https://openalex.org/C157369684","wikidata":"https://www.wikidata.org/wiki/Q34740","display_name":"Genus","level":2,"score":0.33500000834465027},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.329800009727478},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.3255999982357025},{"id":"https://openalex.org/C207812311","wikidata":"https://www.wikidata.org/wiki/Q426560","display_name":"Ribosomal DNA","level":4,"score":0.2994999885559082},{"id":"https://openalex.org/C53565203","wikidata":"https://www.wikidata.org/wiki/Q17146659","display_name":"Species richness","level":2,"score":0.2985999882221222},{"id":"https://openalex.org/C2778926719","wikidata":"https://www.wikidata.org/wiki/Q3762368","display_name":"Alteromonas","level":3,"score":0.2906000018119812},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.28299999237060547},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.2809000015258789},{"id":"https://openalex.org/C26589402","wikidata":"https://www.wikidata.org/wiki/Q7068267","display_name":"Nucleotide diversity","level":5,"score":0.2806999981403351},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.27570000290870667},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.2669000029563904},{"id":"https://openalex.org/C2781463711","wikidata":"https://www.wikidata.org/wiki/Q131143","display_name":"Pseudomonas","level":3,"score":0.2637999951839447},{"id":"https://openalex.org/C2779246796","wikidata":"https://www.wikidata.org/wiki/Q7131869","display_name":"Pantoea","level":4,"score":0.2612000107765198},{"id":"https://openalex.org/C2779825944","wikidata":"https://www.wikidata.org/wiki/Q7097792","display_name":"Operational taxonomic unit","level":4,"score":0.2540999948978424},{"id":"https://openalex.org/C62648534","wikidata":"https://www.wikidata.org/wiki/Q706937","display_name":"Species diversity","level":2,"score":0.25279998779296875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2513999938964844},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1371/journal.pone.0362184","doi":"https://doi.org/10.1371/journal.pone.0362184","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0362184","pdf_url":null,"source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1371/journal.pone.0362184","doi":"https://doi.org/10.1371/journal.pone.0362184","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0362184","pdf_url":null,"source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS One","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W592426295","https://openalex.org/W1999034231","https://openalex.org/W2025403656","https://openalex.org/W2025730106","https://openalex.org/W2036897871","https://openalex.org/W2054600557","https://openalex.org/W2080283023","https://openalex.org/W2082117651","https://openalex.org/W2133057003","https://openalex.org/W2174530374","https://openalex.org/W2330205313","https://openalex.org/W2401404581","https://openalex.org/W2592687664","https://openalex.org/W2792756568","https://openalex.org/W2883941526","https://openalex.org/W2885546258","https://openalex.org/W2923759160","https://openalex.org/W2952463830","https://openalex.org/W2982117376","https://openalex.org/W3016385513","https://openalex.org/W3032170404","https://openalex.org/W3045890286","https://openalex.org/W3048805481","https://openalex.org/W3049266533","https://openalex.org/W3106439484","https://openalex.org/W4210666862","https://openalex.org/W4220694443","https://openalex.org/W4294739458","https://openalex.org/W4390841531","https://openalex.org/W4392378556","https://openalex.org/W4396704842","https://openalex.org/W4408921836","https://openalex.org/W7163023102"],"related_works":[],"abstract_inverted_index":{"Crotalaria":[0,37,41,211,283],"is":[1],"a":[2],"diverse":[3],"legume":[4],"genus":[5,237],"valued":[6],"for":[7],"its":[8,14],"ecological":[9],"and":[10,27,35,66,92,110,165,198,242,285],"agronomic":[11],"roles.":[12],"However,":[13],"associated":[15],"endophytic":[16,82,167,268,278],"microbiome":[17],"remains":[18],"minimally":[19],"characterized.":[20],"This":[21,270],"study":[22,271],"examined":[23],"the":[24,47,60,176,210,215,225,234,273],"genetic":[25],"diversity":[26,158,280,295],"community":[28,147],"structure":[29],"of":[30,70,131,138,175,277,293],"bacterial":[31,83,168,256,279],"endophytes":[32],"inhabiting":[33],"domesticated":[34,65,153,164,240,252],"wild":[36,67,135,142,166,243,262,287],"species.":[38],"Twenty-nine":[39],"healthy":[40],"plant":[42],"samples":[43,124,136,143,154],"were":[44,108,207,258],"analyzed":[45],"using":[46,59,77,94],"culture-independent":[48],"16S":[49,71],"rRNA":[50],"gene":[51,74],"amplicon":[52,114],"sequencing":[53],"approach.":[54],"Genomic":[55],"DNA":[56],"was":[57,75,88,214,224,248],"extracted":[58],"Phenol-Chloroform":[61],"method":[62],"from":[63],"both":[64,239],"samples.":[68,212],"Sequencing":[69],"ribosomal":[72],"RNA":[73],"performed":[76],"Illumina":[78],"MiSeq":[79],"to":[80,152,260],"profile":[81],"communities.":[84],"The":[85],"sequence":[86,106,115,120],"data":[87],"imported":[89],"into":[90,112],"R":[91,181,186],"processed":[93],"Divisive":[95],"Amplicon":[96],"Denoising":[97],"Algorithm":[98],"2":[99,182,187],"(DADA2)":[100],"pipeline.":[101],"In":[102],"total,":[103],"1,546,153":[104],"high-quality":[105],"reads":[107],"obtained":[109],"grouped":[111],"611":[113],"variants":[116],"(ASVs)":[117],"at":[118],"97%":[119],"similarity":[121],"threshold.":[122],"Domesticated":[123],"exhibited":[125],"higher":[126],"observed":[127,177],"species":[128,284],"richness":[129],"(median":[130,137,149,155],"39":[132],"ASVs)":[133],"than":[134],"36":[139],"ASVs),":[140],"while":[141,254],"showed":[144,160],"greater":[145],"microbial":[146,294],"evenness":[148],"~1.08)":[150],"compared":[151],"~0.93).":[156],"Beta":[157],"analyses":[159],"clear":[161],"separation":[162],"between":[163],"communities,":[169],"with":[170,230,296],"domestication":[171],"status":[172],"explaining":[173],"most":[174,226,235],"variations":[178],"(PERMANOVA:":[179],"Bray-Curtis":[180],"=":[183,188,201],"0.826;":[184],"Jaccard":[185],"0.846),":[189],"but":[190],"PERMANOVA":[191],"detected":[192,208],"no":[193],"statistically":[194],"significant":[195],"difference":[196],"(Bray-Curtis":[197],"Jaccard;":[199],"p":[200],"0.067).":[202],"Overall,":[203],"five":[204],"bacteria":[205],"phyla":[206],"in":[209,238,251,281],"Pseudomonadota":[213],"dominant":[216],"phylum":[217],"(64.27%)":[218],"followed":[219],"by":[220],"Cyanobacteriota":[221],"(35.5%).":[222],"Enterobacteriaceae":[223],"abundant":[227,236],"family":[228],"(81.06%)":[229],"Enterobacter":[231],"emerging":[232],"as":[233,289],"(38.3%)":[241],"(89.4%)":[244],"accessions.":[245],"Notably,":[246],"Pseudomonas":[247],"relatively":[249],"enriched":[250],"plants":[253],"several":[255],"genera":[257],"restricted":[259],"either":[261],"or":[263],"cultivated":[264],"hosts,":[265],"indicating":[266],"habitat-associated":[267],"specialization.":[269],"provides":[272],"first":[274],"comprehensive":[275],"assessment":[276],"Kenyan":[282],"highlights":[286],"germplasm":[288],"an":[290],"important":[291],"reservoir":[292],"potential":[297],"biotechnological":[298],"value.":[299]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}