{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T17:53:59Z","timestamp":1791482039678,"version":"4.3.4"},"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["T32OD011130"],"award-info":[{"award-number":["T32OD011130"]}]},{"name":"NIH","award":["R35GM133745"],"award-info":[{"award-number":["R35GM133745"]}]},{"DOI":"10.13039\/100012752","name":"Elanco Animal Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012752","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Ctenocephalides felis<\/jats:italic>\n                      is a common ectoparasite of dogs and cats and can transmit a variety of pathogens including\n                      <jats:italic>Bartonella<\/jats:italic>\n                      and\n                      <jats:italic>Rickettsia<\/jats:italic>\n                      species. These bacteria, along with the known endosymbiont\n                      <jats:italic>Wolbachia<\/jats:italic>\n                      , are well-documented members of the\n                      <jats:italic>C. felis<\/jats:italic>\n                      microbiome, but species-level information is limited. Additionally, little is known about the variation in the\n                      <jats:italic>C. felis<\/jats:italic>\n                      microbiome in fleas from different sources and when different sequencing methods are applied to the same samples.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>This study aimed to characterize the flea microbiome using both short-read (V3\/V4) and long-read (full-length) 16S rRNA gene sequencing, determine whether long-read sequencing improves species-level identification especially in known pathogenic genera, and evaluate differences in microbial composition between fleas collected from cats, dogs, and environmental traps.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Fleas were collected from cats, dogs, and traps in flea-infested homes in Florida, pooled by source, and sequenced using short- (V3\/V4) and long-read (full-length) 16S rRNA gene sequencing. Microbial prevalence and abundance were compared across sequencing approaches. Community composition was evaluated for differences between sources and houses. Candidate members of the flea microbiome were identified based on a combination of prevalence, abundance, and statistical signatures of potential contaminant origin. For\n                      <jats:italic>Rickettsia<\/jats:italic>\n                      and\n                      <jats:italic>Bartonella<\/jats:italic>\n                      , species-level taxonomic assignments were refined using a phylogenetic approach.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Wolbachia<\/jats:italic>\n                      ,\n                      <jats:italic>Rickettsia<\/jats:italic>\n                      , and\n                      <jats:italic>Bartonella<\/jats:italic>\n                      were the most prevalent and abundant taxa.\n                      <jats:italic>Spiroplasma<\/jats:italic>\n                      was identified as a fourth core member of the flea microbiome. Long-read sequencing enabled better, but not perfect, species-level classification of\n                      <jats:italic>Bartonella<\/jats:italic>\n                      and\n                      <jats:italic>Rickettsia<\/jats:italic>\n                      compared to short-read sequencing. Important relationships between specific ASVs and flea sources were identified, for example fleas from cats harbored higher abundances of\n                      <jats:italic>B. clarridgeiae<\/jats:italic>\n                      and\n                      <jats:italic>B. henselae<\/jats:italic>\n                      than fleas from traps.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0341824","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T18:34:43Z","timestamp":1769798083000},"page":"e0341824","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Pathogenic bacterial species and the microbiome of cat fleas (Ctenocephalides felis) inhabiting flea-infested homes"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2508-7929","authenticated-orcid":true,"given":"Taylor E.","family":"Gin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte O.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trey","family":"Tomlinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amiah","family":"Gray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cameron","family":"Sutherland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kamilyah","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krista","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Canfield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Herrin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0949-5698","authenticated-orcid":true,"given":"Erin","family":"Lashnits","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8752-117X","authenticated-orcid":true,"given":"Benjamin","family":"Callahan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,1,30]]},"reference":[{"key":"pone.0341824.ref001","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.vetpar.2016.07.034","article-title":"Ectoparasites of free-roaming domestic cats in the central United States","volume":"228","author":"JE Thomas","year":"2016","journal-title":"Vet Parasitol"},{"issue":"1","key":"pone.0341824.ref002","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s13071-019-3326-x","article-title":"Pathogens in fleas collected from cats and dogs: distribution and prevalence in the UK","volume":"12","author":"S Abdullah","year":"2019","journal-title":"Parasit Vectors"},{"issue":"1","key":"pone.0341824.ref003","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s13071-023-06112-5","article-title":"A nowcast model to predict outdoor flea activity in real time for the contiguous United States","volume":"17","author":"S Self","year":"2024","journal-title":"Parasit Vectors"},{"key":"pone.0341824.ref004","unstructured":"Flea Prevalence in Dogs and Cats | Today\u2019s Veterinary Practice. [cited 28 Jun 2024]. Available from: https:\/\/todaysveterinarypractice.com\/infectious-disease\/flea-prevalence-in-dogs-cats\/"},{"key":"pone.0341824.ref005","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.vetpar.2013.10.017","article-title":"Flea species infesting dogs in Florida and Bartonella spp. prevalence rates","volume":"199","author":"K Yore","year":"2014","journal-title":"Vet Parasitol"},{"key":"pone.0341824.ref006","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.vetpar.2005.03.016","article-title":"Fleas parasitizing domestic dogs in Georgia, USA: species composition and seasonal abundance","volume":"130","author":"LA Durden","year":"2005","journal-title":"Vet Parasitol"},{"key":"pone.0341824.ref007","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/S0304-4017(02)00205-4","article-title":"Prevalence of ectoparasites in a population of feral cats from north central Florida during the summer","volume":"109","author":"LH Akucewich","year":"2002","journal-title":"Vet Parasitol"},{"issue":"5","key":"pone.0341824.ref008","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1016\/S0195-5616(88)50105-5","article-title":"Flea allergy dermatitis","volume":"18","author":"VJ Scheidt","year":"1988","journal-title":"Vet Clin North Am Small Anim Pract"},{"key":"pone.0341824.ref009","doi-asserted-by":"crossref","unstructured":"2023 AAHA Management of Allergic Skin Diseases in Dogs and Cats Guidelines | Journal of the American Animal Hospital Association. [cited 14 Mar 2025]. Available from: https:\/\/meridian-allenpress-com.prox.lib.ncsu.edu\/jaaha\/article\/59\/6\/255\/496488\/2023-AAHA-Management-of-Allergic-Skin-Diseases-in","DOI":"10.5326\/JAAHA-MS-7396"},{"issue":"4","key":"pone.0341824.ref010","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3390\/insects8040118","article-title":"The biology and ecology of cat fleas and advancements in their pest management: a review","volume":"8","author":"MK Rust","year":"2017","journal-title":"Insects"},{"issue":"4","key":"pone.0341824.ref011","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.pt.2024.02.006","article-title":"Vector biology of the cat flea Ctenocephalides felis","volume":"40","author":"CO Moore","year":"2024","journal-title":"Trends Parasitol"},{"issue":"2","key":"pone.0341824.ref012","first-page":"152","article-title":"Cat-scratch disease","volume":"83","author":"SA Klotz","year":"2011","journal-title":"Am Fam Physician"},{"issue":"7","key":"pone.0341824.ref013","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1128\/jcm.30.7.1758-1762.1992","article-title":"Typhus and typhuslike rickettsiae associated with opossums and their fleas in Los Angeles County, California","volume":"30","author":"SG Williams","year":"1992","journal-title":"J Clin Microbiol"},{"issue":"6","key":"pone.0341824.ref014","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1093\/jmedent\/21.6.675","article-title":"Experimental murine typhus infection in the cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae)","volume":"21","author":"A Farhang-Azad","year":"1984","journal-title":"J Med Entomol"},{"issue":"1","key":"pone.0341824.ref015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/zph.12770","article-title":"Urban foci of murine typhus involving cat fleas (Ctenocephalides felis felis) collected from opossums in Mexico City","volume":"68","author":"V Santoyo-Col\u00edn","year":"2021","journal-title":"Zoonoses Public Health"},{"issue":"1","key":"pone.0341824.ref016","doi-asserted-by":"crossref","first-page":"41","DOI":"10.5694\/j.1326-5377.2011.tb04145.x","article-title":"First probable Australian cases of human infection with Rickettsia felis (cat-flea typhus)","volume":"194","author":"M Williams","year":"2011","journal-title":"Med J Aust"},{"key":"pone.0341824.ref017","first-page":"1","article-title":"Manifestations and management of Flea-Borne Rickettsioses","volume":"12","author":"MA Caravedo Martinez","year":"2021","journal-title":"Res Rep Trop Med"},{"issue":"1","key":"pone.0341824.ref018","doi-asserted-by":"crossref","first-page":"4151","DOI":"10.1038\/s41598-020-61122-y","article-title":"Domestic dogs are mammalian reservoirs for the emerging zoonosis flea-borne spotted fever, caused by Rickettsia felis","volume":"10","author":"D Ng-Nguyen","year":"2020","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0341824.ref019","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1071\/MA25008","article-title":"Global emergence of Rickettsia felis infections: the hidden threat in pets and their fleas","volume":"46","author":"LG Huggins","year":"2025","journal-title":"Microbiol Aust"},{"key":"pone.0341824.ref020","doi-asserted-by":"crossref","first-page":"7168","DOI":"10.3402\/ehtj.v4i0.7168","article-title":"Rickettsia felis, an emerging flea-transmitted human pathogen","volume":"4","author":"MY Abdad","year":"2011","journal-title":"Emerg Health Threats J"},{"issue":"9","key":"pone.0341824.ref021","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1089\/vbz.2018.2282","article-title":"Assessing cat flea microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing","volume":"18","author":"EJR Vasconcelos","year":"2018","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"5","key":"pone.0341824.ref022","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/ismej.2007.38","article-title":"Comparative microbiota of Rickettsia felis-uninfected and -infected colonized cat fleas, Ctenocephalides felis","volume":"1","author":"W Pornwiroon","year":"2007","journal-title":"ISME J"},{"key":"pone.0341824.ref023","doi-asserted-by":"crossref","first-page":"106923","DOI":"10.1016\/j.actatropica.2023.106923","article-title":"Complete bacterial profile and potential pathogens of cat fleas Ctenocephalides felis","volume":"243","author":"Y-L Wu","year":"2023","journal-title":"Acta Trop"},{"issue":"11","key":"pone.0341824.ref024","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1017\/S0031182023000835","article-title":"Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis","volume":"150","author":"CA Matthee","year":"2023","journal-title":"Parasitology"},{"issue":"3","key":"pone.0341824.ref025","doi-asserted-by":"crossref","first-page":"366","DOI":"10.3390\/pathogens12030366","article-title":"Feeding on a Bartonella henselae infected host triggers temporary changes in the Ctenocephalides felis microbiome","volume":"12","author":"C Moore","year":"2023","journal-title":"Pathogens"},{"issue":"1","key":"pone.0341824.ref026","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1186\/s13071-022-05487-1","article-title":"Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny","volume":"15","author":"C Manvell","year":"2022","journal-title":"Parasit Vectors"},{"key":"pone.0341824.ref027","unstructured":"U.S. pet ownership statistics | American Veterinary Medical Association. [cited 12 Feb 2025]. Available from: https:\/\/www.avma.org\/resources-tools\/reports-statistics\/us-pet-ownership-statistics"},{"issue":"1","key":"pone.0341824.ref028","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1186\/s13071-020-04407-5","article-title":"Parasites and vector-borne diseases disseminated by rehomed dogs","volume":"13","author":"I Wright","year":"2020","journal-title":"Parasit Vectors"},{"issue":"4","key":"pone.0341824.ref029","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1093\/jmedent\/31.4.631","article-title":"Techniques for estimating on-animal populations of Ctenocephalides felis (Siphonaptera: Pulicidae)","volume":"31","author":"MW Dryden","year":"1994","journal-title":"J Med Entomol"},{"issue":"1","key":"pone.0341824.ref030","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/s13071-016-1654-7","article-title":"Evaluation of fluralaner and afoxolaner treatments to control flea populations, reduce pruritus and minimize dermatologic lesions in naturally infested dogs in private residences in west central Florida USA","volume":"9","author":"MW Dryden","year":"2016","journal-title":"Parasit Vectors"},{"issue":"5","key":"pone.0341824.ref031","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/jmedent\/30.5.901","article-title":"Development of a trap for collecting newly emerged Ctenocephalides felis (Siphonaptera: Pulicidae) in homes","volume":"30","author":"MW Dryden","year":"1993","journal-title":"J Med Entomol"},{"issue":"3","key":"pone.0341824.ref032","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1645\/21-60","article-title":"Using surface washing to remove the environmental component from flea microbiome analysis","volume":"108","author":"R Sridhar","year":"2022","journal-title":"J Parasitol"},{"issue":"1","key":"pone.0341824.ref033","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"A Klindworth","year":"2012","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"pone.0341824.ref034","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M Martin","year":"2011","journal-title":"EMBnet J"},{"issue":"7","key":"pone.0341824.ref035","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"BJ Callahan","year":"2016","journal-title":"Nat Methods"},{"issue":"4","key":"pone.0341824.ref036","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"PJ McMurdie","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"pone.0341824.ref037","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"NM Davis","year":"2018","journal-title":"Microbiome"},{"issue":"2","key":"pone.0341824.ref038","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.tim.2018.11.003","article-title":"Contamination in low microbial biomass microbiome studies: issues and recommendations","volume":"27","author":"R Eisenhofer","year":"2019","journal-title":"Trends Microbiol"},{"issue":"12","key":"pone.0341824.ref039","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.2217\/fmb.13.108","article-title":"Microbiology and epidemiology of Halomonas species","volume":"8","author":"KK Kim","year":"2013","journal-title":"Future Microbiol"},{"issue":"1","key":"pone.0341824.ref040","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13073-017-0397-1","article-title":"Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae","volume":"9","author":"C Runcharoen","year":"2017","journal-title":"Genome Med"},{"issue":"16","key":"pone.0341824.ref041","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Q Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"pone.0341824.ref042","article-title":"Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2","author":"MR McLaren","year":"2021","journal-title":"Zenodo"},{"key":"pone.0341824.ref043","unstructured":"Seemann T. tseemann\/barrnap. 2024. Available from: https:\/\/github.com\/tseemann\/barrnap"},{"issue":"4","key":"pone.0341824.ref044","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pone.0341824.ref045","doi-asserted-by":"crossref","unstructured":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies | Bioinformatics | Oxford Academic. [cited 26 Oct 2024]. Available from: https:\/\/academic.oup.com\/bioinformatics\/article\/30\/9\/1312\/238053","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"pone.0341824.ref046","doi-asserted-by":"crossref","unstructured":"Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation | Nucleic Acids Research | Oxford Academic. [cited 26 Oct 2024]. Available from: https:\/\/academic.oup.com\/nar\/article\/49\/W1\/W293\/6246398","DOI":"10.1093\/nar\/gkab301"},{"key":"pone.0341824.ref047","unstructured":"Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, et al. vegan: Community Ecology Package. 2024. Available from: https:\/\/cran.r-project.org\/web\/packages\/vegan\/index.html"},{"key":"pone.0341824.ref048","unstructured":"BioRender. [cited 22 Jan 2025]. Available from: https:\/\/app.biorender.com\/citation\/679184ca319add0b1340b5da"},{"key":"pone.0341824.ref049","first-page":"1","article-title":"RAWGraphs: A Visualisation Platform to Create Open Outputs","author":"M Mauri","year":"2017","journal-title":"Proceedings of the 12th Biannual Conference on Italian SIGCHI Chapter. New York, NY, USA: Association for Computing Machinery"},{"issue":"1","key":"pone.0341824.ref050","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/s13071-024-06292-8","article-title":"A case of mistaken identity: a systematic review, meta-analysis, and reinvestigation of hemotropic Mycoplasma spp. infection in Ctenocephalides felis (cat flea)","volume":"17","author":"CO Moore","year":"2024","journal-title":"Parasit Vectors"},{"key":"pone.0341824.ref051","article-title":"Spiroplasmas: evolution, adaptation and diversity","volume":"7","author":"GE Gasparich","year":"2002","journal-title":"Front Biosci"},{"issue":"3","key":"pone.0341824.ref052","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/j.ttbdis.2019.02.001","article-title":"Phylogenetics of the Spiroplasma ixodetis endosymbiont reveals past transfers between ticks and other arthropods","volume":"10","author":"F Binetruy","year":"2019","journal-title":"Ticks Tick Borne Dis"},{"issue":"1","key":"pone.0341824.ref053","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3390\/tropicalmed6010037","article-title":"Molecular Evidence of a Broad Range of Pathogenic Bacteria in Ctenocephalides spp.: Should We Re-Examine the Role of Fleas in the Transmission of Pathogens?","volume":"6","author":"G Dougas","year":"2021","journal-title":"Trop Med Infect Dis"},{"issue":"7","key":"pone.0341824.ref054","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0220463","article-title":"The feline cutaneous and oral microbiota are influenced by breed and environment","volume":"14","author":"CE Older","year":"2019","journal-title":"PLoS One"},{"key":"pone.0341824.ref055","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1016\/j.jid.2016.01.023","article-title":"Longitudinal Evaluation of the Skin Microbiome and Association with Microenvironment and Treatment in Canine Atopic Dermatitis","volume":"136","author":"CW Bradley","year":"2016","journal-title":"J Investig Dermatol"},{"issue":"3","key":"pone.0341824.ref056","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.01500-21","article-title":"Phylogenomic analyses of snodgrassella isolates from honeybees and bumblebees reveal taxonomic and functional diversity","volume":"7","author":"L Cornet","year":"2022","journal-title":"mSystems"},{"issue":"12","key":"pone.0341824.ref057","doi-asserted-by":"crossref","DOI":"10.1093\/femsec\/fiv134","article-title":"Evaluation of the bacterial microbiome of two flea species using different DNA-isolation techniques provides insights into flea host ecology","volume":"91","author":"AL Lawrence","year":"2015","journal-title":"FEMS Microbiol Ecol"},{"issue":"1","key":"pone.0341824.ref058","article-title":"An ANI gap within bacterial species that advances the definitions of intra-species units","volume":"15","author":"LM Rodriguez-R","year":"2024","journal-title":"mBio"},{"issue":"1","key":"pone.0341824.ref059","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1038\/s41467-019-13036-1","article-title":"Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis","volume":"10","author":"JS Johnson","year":"2019","journal-title":"Nat Commun"},{"issue":"19","key":"pone.0341824.ref060","doi-asserted-by":"crossref","first-page":"5962","DOI":"10.1128\/AEM.01282-13","article-title":"Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity","volume":"79","author":"D-L Sun","year":"2013","journal-title":"Appl Environ Microbiol"},{"issue":"9","key":"pone.0341824.ref061","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nrmicro3330","article-title":"Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences","volume":"12","author":"P Yarza","year":"2014","journal-title":"Nat Rev Microbiol"},{"key":"pone.0341824.ref062","doi-asserted-by":"crossref","first-page":"106765","DOI":"10.1016\/j.micpath.2024.106765","article-title":"The polymicrobial nature of the oral cavity and claws of cats diagnosed by mass spectrometry and next-generation sequencing","volume":"193","author":"FVR Portilho","year":"2024","journal-title":"Microbial Pathogenesis"},{"issue":"5","key":"pone.0341824.ref063","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1017\/S0031182017001263","article-title":"Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives","volume":"145","author":"M Kosoy","year":"2018","journal-title":"Parasitology"},{"issue":"7","key":"pone.0341824.ref064","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/S0966-842X(03)00143-4","article-title":"Gene-sequence-based criteria for species definition in bacteriology: the Bartonella paradigm","volume":"11","author":"B La Scola","year":"2003","journal-title":"Trends Microbiol"},{"issue":"24","key":"pone.0341824.ref065","doi-asserted-by":"crossref","first-page":"7828","DOI":"10.1128\/AEM.01303-08","article-title":"Cross-kingdom amplification using bacteria-specific primers: complications for studies of coral microbial ecology","volume":"74","author":"JP Galkiewicz","year":"2008","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"pone.0341824.ref066","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1128\/AEM.64.2.795-799.1998","article-title":"Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA","volume":"64","author":"JR Marchesi","year":"1998","journal-title":"Appl Environ Microbiol"},{"issue":"11","key":"pone.0341824.ref067","doi-asserted-by":"crossref","first-page":"6801","DOI":"10.1128\/AEM.69.11.6801-6807.2003","article-title":"Design and evaluation of PCR primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis","volume":"69","author":"I Lopez","year":"2003","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"pone.0341824.ref068","doi-asserted-by":"crossref","first-page":"258","DOI":"10.3390\/pathogens9040258","article-title":"A host-specific blocking primer combined with optimal DNA extraction improves the detection capability of a metabarcoding protocol for canine vector-borne bacteria","volume":"9","author":"LG Huggins","year":"2020","journal-title":"Pathogens"},{"key":"pone.0341824.ref069","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1186\/s13071-015-0958-3","article-title":"Inhibition of the endosymbiont \u201cCandidatus Midichloria mitochondrii\u201d during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia","volume":"8","author":"AW Gofton","year":"2015","journal-title":"Parasit Vectors"},{"issue":"6","key":"pone.0341824.ref070","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1016\/j.cvsm.2022.06.006","article-title":"Bartonellosis in dogs and cats, an update","volume":"52","author":"R Taber","year":"2022","journal-title":"Vet Clin North Am Small Anim Pract"},{"issue":"1","key":"pone.0341824.ref071","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1186\/s13071-018-3152-6","article-title":"Bartonella infections in cats and dogs including zoonotic aspects","volume":"11","author":"A \u00c1lvarez-Fern\u00e1ndez","year":"2018","journal-title":"Parasit Vectors"},{"issue":"7","key":"pone.0341824.ref072","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1128\/jcm.35.7.1813-1818.1997","article-title":"Bartonella clarridgeiae, a newly recognized zoonotic pathogen causing inoculation papules, fever, and lymphadenopathy (cat scratch disease)","volume":"35","author":"DL Kordick","year":"1997","journal-title":"J Clin Microbiol"},{"key":"pone.0341824.ref073","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/B978-1-4377-0795-3.00052-1","article-title":"Bartonellosis","author":"JE Sykes","year":"2014","journal-title":"Canine and Feline Infectious Diseases. Elsevier"},{"issue":"26","key":"pone.0341824.ref074","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1056\/NEJM199712253372603","article-title":"Molecular epidemiology of bartonella infections in patients with bacillary angiomatosis-peliosis","volume":"337","author":"JE Koehler","year":"1997","journal-title":"N Engl J Med"},{"issue":"8","key":"pone.0341824.ref075","doi-asserted-by":"crossref","first-page":"3462","DOI":"10.1128\/JCM.42.8.3462-3468.2004","article-title":"Bartonella koehlerae, a new cat-associated agent of culture-negative human endocarditis","volume":"42","author":"B Avidor","year":"2004","journal-title":"J Clin Microbiol"},{"key":"pone.0341824.ref076","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.micinf.2017.11.002","article-title":"Chlamydiales, Anaplasma and Bartonella: persistence and immune escape of intracellular bacteria","volume":"20","author":"A Scherler","year":"2018","journal-title":"Microbes Infect"},{"key":"pone.0341824.ref077","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s40475-016-0070-6","article-title":"Rickettsia felis, an emerging flea-borne Rickettsiosis","volume":"3","author":"LD Brown","year":"2016","journal-title":"Curr Trop Med Rep"},{"issue":"1","key":"pone.0341824.ref078","first-page":"96","article-title":"Vertical transmission of Rickettsia felis in the cat flea (Ctenocephalides felis Bouch\u00e9)","volume":"27","author":"Jr Wedincamp J","year":"2002","journal-title":"J Vector Ecol"},{"key":"pone.0341824.ref079","unstructured":"Bartonella Infection in Animals: Carriership, Reservoir Potential, Pathogenicity, and Zoonotic Potential for Human Infection | Clinical Microbiology Reviews. [cited 12 Nov 2025]. Available from: https:\/\/journals-asm-org.prox.lib.ncsu.edu\/doi\/10.1128\/cmr.13.3.428"},{"issue":"1","key":"pone.0341824.ref080","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1186\/s13071-019-3517-5","article-title":"Surface sterilization methods impact measures of internal microbial diversity in ticks","volume":"12","author":"F Binetruy","year":"2019","journal-title":"Parasit Vectors"},{"issue":"4","key":"pone.0341824.ref081","doi-asserted-by":"crossref","first-page":"1933","DOI":"10.1111\/tbed.14180","article-title":"A multipronged next-generation sequencing metabarcoding approach unearths hyperdiverse and abundant dog pathogen communities in Cambodia","volume":"69","author":"LG Huggins","year":"2022","journal-title":"Transbound Emerg Dis"},{"issue":"1","key":"pone.0341824.ref082","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s40168-017-0267-5","article-title":"Optimizing methods and dodging pitfalls in microbiome research","volume":"5","author":"D Kim","year":"2017","journal-title":"Microbiome"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341824","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T18:34:55Z","timestamp":1769798095000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0341824"}},"subtitle":[],"editor":[{"given":"Beza","family":"Ramasindrazana","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,30]]},"references-count":82,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0341824","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,30]]}}}