{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T18:13:29Z","timestamp":1789668809737,"version":"4.0.1"},"reference-count":89,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2021,10,9]],"date-time":"2021-10-09T00:00:00Z","timestamp":1633737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1755051"],"award-info":[{"award-number":["IOS-1755051"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1755297"],"award-info":[{"award-number":["IOS-1755297"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n               <jats:p>The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.<\/jats:p>","DOI":"10.1093\/femsec\/fiab141","type":"journal-article","created":{"date-parts":[[2021,10,8]],"date-time":"2021-10-08T01:10:58Z","timestamp":1633655458000},"source":"Crossref","is-referenced-by-count":12,"title":["Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition"],"prefix":"10.1093","volume":"97","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6103-1885","authenticated-orcid":false,"given":"Chava L","family":"Weitzman","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Virginia Tech , Blacksburg, VA 24060, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8847-4427","authenticated-orcid":false,"given":"Bahman","family":"Rostama","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of New England , Biddeford - 04005, ME, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney A","family":"Thomason","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Virginia Tech , Blacksburg, VA 24060, USA"},{"name":"Division of Remediation, Tennessee Department of Environment and Conservation , Oak Ridge - 37830, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meghan","family":"May","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of New England , Biddeford - 04005, ME, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3514-3920","authenticated-orcid":false,"given":"Lisa K","family":"Belden","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Virginia Tech , Blacksburg, VA 24060, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9573-2914","authenticated-orcid":false,"given":"Dana M","family":"Hawley","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Virginia Tech , Blacksburg, VA 24060, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,9]]},"reference":[{"key":"2022100900061950500_bib1","first-page":"20151429","article-title":"Feeder use predicts both acquisition and transmission of a contagious pathogen in a North American songbird","volume":"282","author":"Adelman","year":"2015","journal-title":"Proc Biol Sci"},{"key":"2022100900061950500_bib2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1111\/1365-2656.12511","article-title":"Host contact and shedding patterns clarify variation in pathogen exposure and transmission in threatened tortoise Gopherus agassizii: implications for disease modelling and management","volume":"85","author":"Aiello","year":"2016","journal-title":"J Anim Ecol"},{"key":"2022100900061950500_bib3","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1038\/ismej.2015.39","article-title":"The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts","volume":"9","author":"Ainsworth","year":"2015","journal-title":"ISME J"},{"key":"2022100900061950500_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep10189","article-title":"Variation in koala microbiomes within and between individuals: effect of body region and captivity status","volume":"5","author":"Alfano","year":"2015","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib5","doi-asserted-by":"crossref","first-page":"12147","DOI":"10.1038\/s41598-018-30709-x","article-title":"Snake fungal disease alters skin bacterial and fungal diversity in an endangered rattlesnake","volume":"8","author":"Allender","year":"2018","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting linear mixed-effects models using lme4","volume":"67","author":"Bates","year":"2015","journal-title":"J Stat Softw"},{"key":"2022100900061950500_bib7","doi-asserted-by":"crossref","first-page":"6635","DOI":"10.1128\/AEM.01294-09","article-title":"The bacterially produced metabolite violacein is associated with survival of amphibians infected with a lethal fungus","volume":"75","author":"Becker","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2022100900061950500_bib8","doi-asserted-by":"crossref","first-page":"e10957","DOI":"10.1371\/journal.pone.0010957","article-title":"Cutaneous bacteria of the redback salamander prevent morbidity associated with a lethal disease","volume":"5","author":"Becker","year":"2010","journal-title":"PLoS One"},{"key":"2022100900061950500_bib9","first-page":"20142881","article-title":"Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus","volume":"282","author":"Becker","year":"2015","journal-title":"Proc Biol Sci"},{"key":"2022100900061950500_bib10","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1111\/mec.13135","article-title":"Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis","volume":"24","author":"Becker","year":"2015","journal-title":"Mol Ecol"},{"key":"2022100900061950500_bib11","doi-asserted-by":"crossref","first-page":"17287","DOI":"10.1038\/s41598-019-53599-z","article-title":"Effects of sampling strategy and DNA extraction on human skin microbiome investigations","volume":"9","author":"Bjerre","year":"2019","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib12","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2022100900061950500_bib13","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1111\/1574-6976.12035","article-title":"Interactions in the microbiome: communities of organisms and communities of genes","volume":"38","author":"Boon","year":"2014","journal-title":"FEMS Microbiol Rev"},{"key":"2022100900061950500_bib14","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":"Bradley","year":"2016","journal-title":"J Invest Dermatol"},{"key":"2022100900061950500_bib15","doi-asserted-by":"crossref","first-page":"378","DOI":"10.32614\/RJ-2017-066","article-title":"glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling","volume":"9","author":"Brooks","year":"2017","journal-title":"R J"},{"key":"2022100900061950500_bib16","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s10886-007-9352-8","article-title":"The identification of 2,4-diacetylphloroglucinol as an antifungal metabolite produced by cutaneous bacteria of the salamander Plethodon cinereus","volume":"34","author":"Brucker","year":"2008","journal-title":"J Chem Ecol"},{"key":"2022100900061950500_bib17","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1007\/s10886-008-9555-7","article-title":"Amphibian chemical defense: antifungal metabolites of the microsymbiont Janthinobacterium lividum on the salamander Plethodon cinereus","volume":"34","author":"Brucker","year":"2008","journal-title":"J Chem Ecol"},{"key":"2022100900061950500_bib18","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1007\/s00442-005-0093-5","article-title":"Dose and host characteristics influence virulence of ranavirus infections","volume":"144","author":"Brunner","year":"2005","journal-title":"Oecologia"},{"key":"2022100900061950500_bib19","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":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2022100900061950500_bib20","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1038\/ismej.2012.8","article-title":"Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms","volume":"6","author":"Caporaso","year":"2012","journal-title":"ISME J"},{"key":"2022100900061950500_bib21","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s40168-015-0143-0","article-title":"The Tasmanian devil microbiome: implications for conservation and management","volume":"3","author":"Cheng","year":"2015","journal-title":"Microbiome"},{"key":"2022100900061950500_bib22","doi-asserted-by":"crossref","first-page":"10510","DOI":"10.1002\/ece3.4518","article-title":"Ecological patterns in the skin microbiota of frogs from tropical Australia","volume":"8","author":"Christian","year":"2018","journal-title":"Ecol Evol"},{"key":"2022100900061950500_bib23","doi-asserted-by":"crossref","first-page":"3776","DOI":"10.1111\/mec.13730","article-title":"Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown","volume":"25","author":"Colston","year":"2016","journal-title":"Mol Ecol"},{"key":"2022100900061950500_bib24","first-page":"1457","article-title":"Context-dependent symbioses and their potential roles in wildlife diseases","volume":"279","author":"Daskin","year":"2012","journal-title":"Proc Biol Sci"},{"key":"2022100900061950500_bib25","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/aos.14508","article-title":"Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data","volume":"99","author":"Delbeke","year":"2021","journal-title":"Acta Ophthalmol (Copenh)"},{"key":"2022100900061950500_bib26","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1080\/03079450701286277","article-title":"Experimental evidence for transmission of Mycoplasma gallisepticum in house finches by fomites","volume":"36","author":"Dhondt","year":"2007","journal-title":"Avian Pathol"},{"key":"2022100900061950500_bib27","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1007\/s00248-020-01550-5","article-title":"Composition of the North American wood frog (Rana sylvatica) bacterial skin microbiome and seasonal variation in community structure","volume":"81","author":"Douglas","year":"2021","journal-title":"Microb Ecol"},{"key":"2022100900061950500_bib28","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1007\/PL00008847","article-title":"Dose effects and density-dependent regulation of two microparasites of Daphnia magna","volume":"122","author":"Ebert","year":"2000","journal-title":"Oecologia"},{"key":"2022100900061950500_bib29","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1111\/1365-2435.12696","article-title":"Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows","volume":"31","author":"Escall\u00f3n","year":"2017","journal-title":"Funct Ecol"},{"key":"2022100900061950500_bib30","doi-asserted-by":"crossref","first-page":"2535","DOI":"10.3389\/fmicb.2017.02535","article-title":"Temporal variation of the skin bacterial community and Batrachochytrium dendrobatidis infection in the terrestrial cryptic frog Philoria loveridgei","volume":"8","author":"Familiar\u00a0L\u00f3pez","year":"2017","journal-title":"Front Microbiol"},{"key":"2022100900061950500_bib31","first-page":"282","article-title":"Metaresearch for evaluating reproducibility in ecology and evolution","volume":"67","author":"Fidler","year":"2017","journal-title":"Bioscience"},{"key":"2022100900061950500_bib32","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/s12866-016-0738-z","article-title":"16S rRNA gene sequencing of mock microbial populations: impact of DNA extraction method, primer choice and sequencing platform","volume":"16","author":"Fouhy","year":"2016","journal-title":"BMC Microbiol"},{"key":"2022100900061950500_bib33","volume-title":"An R Companion to Applied Regression","author":"Fox","year":"2019","edition":"3rd edn"},{"key":"2022100900061950500_bib34","doi-asserted-by":"crossref","first-page":"fnz117","DOI":"10.1093\/femsle\/fnz117","article-title":"Not all animals need a microbiome","volume":"366","author":"Hammer","year":"2019","journal-title":"FEMS Microbiol Lett"},{"key":"2022100900061950500_bib35","doi-asserted-by":"crossref","first-page":"e1007891","DOI":"10.1371\/journal.ppat.1007891","article-title":"Diet\u2013microbiome\u2013disease: investigating diet's influence on infectious disease resistance through alteration of the gut microbiome","volume":"15","author":"Harris","year":"2019","journal-title":"PLoS Pathog"},{"key":"2022100900061950500_bib36","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/ismej.2009.27","article-title":"Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus","volume":"3","author":"Harris","year":"2009","journal-title":"ISME J"},{"key":"2022100900061950500_bib37","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1080\/03079457.2011.571660","article-title":"Experimental infection of domestic canaries (Serinus canaria domestica) with Mycoplasma gallisepticum: a new model system for a wildlife disease","volume":"40","author":"Hawley","year":"2011","journal-title":"Avian Pathol"},{"key":"2022100900061950500_bib38","doi-asserted-by":"crossref","first-page":"e1001570","DOI":"10.1371\/journal.pbio.1001570","article-title":"Parallel patterns of increased virulence in a recently emerged wildlife pathogen","volume":"11","author":"Hawley","year":"2013","journal-title":"PLoS Biol"},{"key":"2022100900061950500_bib39","doi-asserted-by":"crossref","first-page":"e0228982","DOI":"10.1371\/journal.pone.0228982","article-title":"Cloacal bacterial communities of tree swallows (Tachycineta bicolor): similarity within a population, but not between pair-bonded social partners","volume":"15","author":"Hernandez","year":"2020","journal-title":"PLoS One"},{"key":"2022100900061950500_bib40","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.biocon.2015.04.007","article-title":"Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis","volume":"187","author":"Holden","year":"2015","journal-title":"Biol Conserv"},{"key":"2022100900061950500_bib41","doi-asserted-by":"crossref","first-page":"5354","DOI":"10.1073\/pnas.1019378108","article-title":"Microbiota regulates immune defense against respiratory tract influenza A virus infection","volume":"108","author":"Ichinohe","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022100900061950500_bib42","doi-asserted-by":"crossref","first-page":"E5049","DOI":"10.1073\/pnas.1412752111","article-title":"The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection","volume":"111","author":"Jani","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022100900061950500_bib43","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1017\/S1464793101005875","article-title":"Publication bias in ecology and evolution: an empirical assessment using the \u2018trim and fill\u2019 method","volume":"77","author":"Jennions","year":"2002","journal-title":"Biol Rev Camb Philos Soc"},{"key":"2022100900061950500_bib44","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1007\/s00360-012-0645-z","article-title":"Diversity and function of the avian gut microbiota","volume":"182","author":"Kohl","year":"2012","journal-title":"J Comp Physiol B"},{"key":"2022100900061950500_bib45","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1111\/mec.13921","article-title":"Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission","volume":"26","author":"Kohl","year":"2017","journal-title":"Mol Ecol"},{"key":"2022100900061950500_bib46","doi-asserted-by":"crossref","first-page":"79","DOI":"10.7589\/0090-3558-40.1.79","article-title":"Experimental infection of house finches with Mycoplasma gallisepticum","volume":"40","author":"Kollias","year":"2004","journal-title":"J Wildl Dis"},{"key":"2022100900061950500_bib47","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1038\/jid.2011.417","article-title":"Skin microbiome: looking back to move forward","volume":"132","author":"Kong","year":"2012","journal-title":"J Invest Dermatol"},{"key":"2022100900061950500_bib48","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/s41559-019-0798-1","article-title":"Community richness of amphibian skin bacteria correlates with bioclimate at the global scale","volume":"3","author":"Kueneman","year":"2019","journal-title":"Nat Ecol Evol"},{"key":"2022100900061950500_bib49","doi-asserted-by":"crossref","first-page":"e1005855","DOI":"10.1371\/journal.ppat.1005855","article-title":"Impact of microbiota on resistance to ocular Pseudomonas aeruginosa-induced keratitis","volume":"12","author":"Kugadas","year":"2016","journal-title":"PLoS Pathog"},{"key":"2022100900061950500_bib50","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1643\/0045-8511(2007)2007[630:CCBFTE]2.0.CO;2","article-title":"Common cutaneous bacteria from the eastern red-backed salamander can inhibit pathogenic fungi","volume":"2007","author":"Lauer","year":"2007","journal-title":"Copeia"},{"key":"2022100900061950500_bib51","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/ismej.2007.110","article-title":"Diversity of cutaneous bacteria with antifungal activity isolated from female four-toed salamanders","volume":"2","author":"Lauer","year":"2008","journal-title":"ISME J"},{"key":"2022100900061950500_bib52","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1111\/vop.12599","article-title":"Initial description of the core ocular surface microbiome in dogs: bacterial community diversity and composition in a defined canine population","volume":"22","author":"Leis","year":"2019","journal-title":"Vet Ophthalmol"},{"key":"2022100900061950500_bib53","doi-asserted-by":"crossref","first-page":"e0247392","DOI":"10.1371\/journal.pone.0247392","article-title":"The porcine corneal surface bacterial microbiome: a distinctive niche within the ocular surface","volume":"16","author":"Leis","year":"2021","journal-title":"PLoS One"},{"key":"2022100900061950500_bib54","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1007\/s10393-017-1261-x","article-title":"Host responses to pathogen priming in a natural songbird host","volume":"14","author":"Leon","year":"2017","journal-title":"Ecohealth"},{"key":"2022100900061950500_bib55","doi-asserted-by":"crossref","first-page":"fiaa168","DOI":"10.1093\/femsec\/fiaa168","article-title":"Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment","volume":"96","author":"Loudon","year":"2020","journal-title":"FEMS Microbiol Ecol"},{"key":"2022100900061950500_bib56","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1111\/imm.12231","article-title":"The microbiome and regulation of mucosal immunity","volume":"142","author":"McDermott","year":"2014","journal-title":"Immunology"},{"key":"2022100900061950500_bib57","doi-asserted-by":"crossref","first-page":"20190592","DOI":"10.1098\/rstb.2019.0592","article-title":"Pathogen resistance may be the principal evolutionary advantage provided by the microbiome","volume":"375","author":"McLaren","year":"2020","journal-title":"Philos Trans R Soc B Biol Sci"},{"key":"2022100900061950500_bib58","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.kijoms.2017.11.004","article-title":"Detection of Sphingomonas paucimobilis and antibacterial activity of Prosopis farcta extracts on it","volume":"4","author":"Mustafa","year":"2018","journal-title":"Karbala Int J Mod Sci"},{"key":"2022100900061950500_bib59","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1007\/s00248-021-01706-x","article-title":"Inhibition of Batrachochytrium dendrobatidis infection by skin bacterial communities in wild amphibian populations","volume":"82","author":"Nava-Gonz\u00e1lez","year":"2021","journal-title":"Microb Ecol"},{"key":"2022100900061950500_bib60","doi-asserted-by":"crossref","first-page":"e80074","DOI":"10.1371\/journal.pone.0080074","article-title":"Vaginal pH and microbicidal lactic acid when lactobacilli dominate the microbiota","volume":"8","author":"O'Hanlon","year":"2013","journal-title":"PLoS One"},{"key":"2022100900061950500_bib61","article-title":"vegan: community ecology package","author":"Oksanen","year":"2018"},{"key":"2022100900061950500_bib62","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1111\/1365-2435.12133","article-title":"Defensive symbiosis in the real world: advancing ecological studies of heritable, protective bacteria in aphids and beyond","volume":"28","author":"Oliver","year":"2014","journal-title":"Funct Ecol"},{"key":"2022100900061950500_bib63","doi-asserted-by":"crossref","first-page":"4268","DOI":"10.1167\/iovs.18-24651","article-title":"Identification and visualization of a distinct microbiome in ocular surface conjunctival tissue","volume":"59","author":"Ozkan","year":"2018","journal-title":"Invest Opthalmol Vis Sci"},{"key":"2022100900061950500_bib64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-10494-9","article-title":"Temporal stability and composition of the ocular surface microbiome","volume":"7","author":"Ozkan","year":"2017","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib65","doi-asserted-by":"crossref","first-page":"5143","DOI":"10.1038\/s41598-018-23296-4","article-title":"Methodology challenges in studying human gut microbiota: effects of collection, storage, DNA extraction and next generation sequencing technologies","volume":"8","author":"Panek","year":"2018","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib66","article-title":"R: a language and environment for statistical computing","author":"R Development Core Team","year":"2015","journal-title":"GBIFORG"},{"key":"2022100900061950500_bib68","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1098\/rspb.2001.1816","article-title":"Dose\u2013dependent infection rates of parasites produce the Allee effect in epidemiology","volume":"269","author":"Regoes","year":"2002","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"2022100900061950500_bib67","doi-asserted-by":"crossref","first-page":"e1002767","DOI":"10.1371\/journal.pcbi.1002767","article-title":"The role of exposure history on HIV acquisition: insights from repeated low-dose challenge studies","volume":"8","author":"Regoes","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"2022100900061950500_bib69","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1128\/AAC.3.4.488","article-title":"Evaluation of cefazolin, a new cephalosporin antibiotic","volume":"3","author":"Reller","year":"1973","journal-title":"Antimicrob Agents Chemother"},{"key":"2022100900061950500_bib70","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.ijfoodmicro.2004.06.003","article-title":"Production of antimicrobial metabolites by strains of Lactobacillus or Lactococcus co-cultured with Bacillus cereus in milk","volume":"98","author":"R\u00f8ssland","year":"2005","journal-title":"Int J Food Microbiol"},{"key":"2022100900061950500_bib71","author":"RStudio Team","year":"2020","journal-title":"RStudio: Integrated Development Environment for R"},{"key":"2022100900061950500_bib72","doi-asserted-by":"crossref","first-page":"4081","DOI":"10.4049\/jimmunol.1403169","article-title":"No vacancy: how beneficial microbes cooperate with immunity to provide colonization resistance to pathogens","volume":"194","author":"Sassone-Corsi","year":"2015","journal-title":"J Immunol"},{"key":"2022100900061950500_bib73","doi-asserted-by":"crossref","first-page":"4726","DOI":"10.1128\/IAI.00319-08","article-title":"Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection","volume":"76","author":"Sekirov","year":"2008","journal-title":"Infect Immun"},{"key":"2022100900061950500_bib74","doi-asserted-by":"crossref","first-page":"e133","DOI":"10.1038\/cti.2017.6","article-title":"Microbiome effects on immunity, health and disease in the lung","volume":"6","author":"Shukla","year":"2017","journal-title":"Clin Transl Immunol"},{"key":"2022100900061950500_bib75","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.vetmic.2010.06.012","article-title":"The effect of inoculation dose of a highly pathogenic avian influenza virus strain H5N1 on the infectiousness of chickens","volume":"147","author":"Spekreijse","year":"2011","journal-title":"Vet Microbiol"},{"key":"2022100900061950500_bib76","doi-asserted-by":"crossref","first-page":"5732","DOI":"10.1002\/ece3.3148","article-title":"Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)","volume":"7","author":"Springer","year":"2017","journal-title":"Ecol Evol"},{"key":"2022100900061950500_bib77","doi-asserted-by":"crossref","first-page":"326","DOI":"10.7589\/0090-3558-41.2.326","article-title":"Re-exposure of captive house finches that recovered from Mycoplasma gallisepticum infection","volume":"41","author":"Sydenstricker","year":"2005","journal-title":"J Wildl Dis"},{"key":"2022100900061950500_bib78","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/nature18847","article-title":"The microbiome and innate immunity","volume":"535","author":"Thaiss","year":"2016","journal-title":"Nature"},{"key":"2022100900061950500_bib79","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1111\/1462-2920.13625","article-title":"Eye of the Finch: characterization of the ocular microbiome of house finches in relation to mycoplasmal conjunctivitis","volume":"19","author":"Thomason","year":"2017","journal-title":"Environ Microbiol"},{"key":"2022100900061950500_bib80","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-16393-3","article-title":"Resident microbiome disruption with antibiotics enhances virulence of a colonizing pathogen","volume":"7","author":"Thomason","year":"2017","journal-title":"Sci Rep"},{"key":"2022100900061950500_bib81","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S0031182001008083","article-title":"The effect of parasite dose on disease severity in the rodent malaria Plasmodium chabaudi","volume":"123","author":"Timms","year":"2001","journal-title":"Parasitology"},{"key":"2022100900061950500_bib82","doi-asserted-by":"crossref","first-page":"e05224","DOI":"10.7554\/eLife.05224","article-title":"Social networks predict gut microbiome composition in wild baboons","volume":"4","author":"Tung","year":"2015","journal-title":"eLife"},{"key":"2022100900061950500_bib83","doi-asserted-by":"crossref","first-page":"e33188","DOI":"10.1371\/journal.pone.0033188","article-title":"Symbionts as major modulators of insect health: lactic acid bacteria and honeybees","volume":"7","author":"V\u00e1squez","year":"2012","journal-title":"PLoS One"},{"key":"2022100900061950500_bib84","doi-asserted-by":"crossref","first-page":"e0139848","DOI":"10.1371\/journal.pone.0139848","article-title":"Community structure and function of amphibian skin microbes: an experiment with bullfrogs exposed to a chytrid fungus","volume":"10","author":"Walke","year":"2015","journal-title":"PLoS One"},{"key":"2022100900061950500_bib85","doi-asserted-by":"crossref","first-page":"e1005796","DOI":"10.1371\/journal.ppat.1005796","article-title":"Harnessing the microbiome to prevent fungal infections: lessons from amphibians","volume":"12","author":"Walke","year":"2016","journal-title":"PLoS Pathog"},{"key":"2022100900061950500_bib86","doi-asserted-by":"crossref","first-page":"8413","DOI":"10.1038\/ncomms9413","article-title":"Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health","volume":"6","author":"Wei","year":"2015","journal-title":"Nat Commun"},{"key":"2022100900061950500_bib87","doi-asserted-by":"crossref","first-page":"181068","DOI":"10.1098\/rsos.181068","article-title":"Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises","volume":"5","author":"Weitzman","year":"2018","journal-title":"R Soc Open Sci"},{"key":"2022100900061950500_bib88","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1093\/infdis\/jit597","article-title":"Resident microbiota affect Bordetella pertussis infectious dose and host specificity","volume":"209","author":"Weyrich","year":"2014","journal-title":"J Infect Dis"},{"key":"2022100900061950500_bib89","doi-asserted-by":"crossref","first-page":"e00910","DOI":"10.1128\/mSystems.00910-19","article-title":"Sex bias in gut microbiome transmission in newly paired marmosets (Callithrix jacchus)","volume":"5","author":"Zhu","year":"2020","journal-title":"mSystems"}],"container-title":["FEMS Microbiology Ecology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/femsec\/advance-article-pdf\/doi\/10.1093\/femsec\/fiab141\/40540621\/fiab141.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsec\/article-pdf\/97\/11\/fiab141\/40787711\/fiab141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsec\/article-pdf\/97\/11\/fiab141\/40787711\/fiab141.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,9]],"date-time":"2022-10-09T00:07:36Z","timestamp":1665274056000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsec\/article\/doi\/10.1093\/femsec\/fiab141\/6385755"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,9]]},"references-count":89,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2021,10,20]]}},"URL":"https:\/\/doi.org\/10.1093\/femsec\/fiab141","relation":{},"ISSN":["1574-6941"],"issn-type":[{"value":"1574-6941","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,11]]},"published":{"date-parts":[[2021,10,9]]},"article-number":"fiab141"}}