{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T09:49:19Z","timestamp":1771062559517,"version":"3.50.1"},"reference-count":58,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T00:00:00Z","timestamp":1739404800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Maintaining good oral and gut health is essential for the wellbeing of animals, and fungi are key components of the oral and gut microbiota. This study aims to explore the diversity and seasonal dynamics of oral and gut fungal communities in captive giant pandas, with a focus on their potential functional roles in health and digestion.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>In the study, we collected saliva and fecal samples from 60 captive giant pandas were collected in different seasons, oral and gut fungi were analyzed using internal transcribed spacer (ITS) amplicon sequencing. We used <jats:italic>\u03b1<\/jats:italic> and <jats:italic>\u03b2<\/jats:italic> diversity analyses to examine the differences in species diversity and composition among the different seasons. Furthermore, we validated the ITS amplicon sequencing results through fungal isolation and identification.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Analyses of <jats:italic>\u03b1<\/jats:italic> and <jats:italic>\u03b2<\/jats:italic> diversity revealed both the differences and similarities between the fungal communities in the oral and gut microbiomes of giant pandas. Ascomycota and Basidiomycota were predominant in both oral and gut groups, while the dominant genera in the four seasons were <jats:italic>Cutaneotrichosporon<\/jats:italic>, and <jats:italic>unidentified_Chaetothyriales_sp<\/jats:italic>. Additionally, <jats:italic>Cladosporium<\/jats:italic> and <jats:italic>Candida<\/jats:italic> were predominant in the oral and gut fungus, respectively, across all four seasons. Notably, fungal abundance and diversity in the oral microbiome were significantly higher than in the gut microbiome, a pattern observed throughout most seasons. Several potentially pathogenic fungi, such as <jats:italic>Fusarium<\/jats:italic>, <jats:italic>Candida<\/jats:italic> and <jats:italic>Aspergillus<\/jats:italic>, were detected in healthy giant pandas, with most showing increased abundance during winter. It is worth mentioning that we found a distinct bias in the functional communities of oral and gut fungi. The abundance of saprophytic fungi in the gut is relatively high, which may be related to their role in cellulose digestion.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The abundance and diversity of fungal communities in the oral cavity and gut of giant pandas exhibit significant seasonal variations. While the oral cavity hosts a higher abundance and diversity of fungi, the species composition of fungal community composition is similar to that of the intestines. The majority of gut fungi are likely derived from the oral cavity or diet, the significant seasonal variation in gut fungal community structure further suggests that long-term resident fungi may not be present in the gut.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2025.1522289","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T07:08:30Z","timestamp":1739430510000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Analysis of fungal microbiota diversity and potential pathogenic fungi in oral secretions and gut feces of captive giant pandas"],"prefix":"10.3389","volume":"16","author":[{"given":"Xiaoping","family":"Ma","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangwen","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gen","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruiguo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongyan","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinni","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shanshan","family":"Ling","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengdong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Gu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,13]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s40168-016-0169-y","article-title":"Diet may influence the oral microbiome composition in cats","volume":"4","author":"Adler","year":"2016","journal-title":"Microbiome"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1007\/s12033-015-9878-x","article-title":"Heterogeneous expression and functional characterization of cellulose-degrading enzymes from aspergillus Niger for enzymatic hydrolysis of alkali pretreated bamboo biomass","volume":"57","author":"Ali","year":"2015","journal-title":"Mol. Biotechnol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.4103\/njcp.njcp_32_17","article-title":"A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods","volume":"20","author":"Anukam","year":"2017","journal-title":"Niger. J. Clin. Pract."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/978-3-319-31248-4_4","article-title":"The Oral microbiota","volume":"902","author":"Arweiler","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"e00092-18","DOI":"10.1128\/mSphere.00092-18","article-title":"Investigating colonization of the healthy adult gastrointestinal tract by Fungi","volume":"3","author":"Auchtung","year":"2018","journal-title":"mSphere"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1089\/dna.2009.0874","article-title":"The oral microbiota: living with a permanent guest","volume":"28","author":"Avila","year":"2009","journal-title":"DNA Cell Biol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"252","DOI":"10.17294\/2330-0698.1705","article-title":"Oral fungal microbiota: to thrush and beyond","volume":"6","author":"Baumgardner","year":"2019","journal-title":"J. Patient Cent. Res. Rev."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nmeth.2276","article-title":"Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing","volume":"10","author":"Bokulich","year":"2013","journal-title":"Nat. Methods"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"R33","DOI":"10.1152\/ajpregu.00387.2012","article-title":"Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle","volume":"304","author":"Carey","year":"2013","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"377","DOI":"10.4067\/s0716-10182018000400377","article-title":"Factors related to oral candidiasis in HIV children and adolescents, species characterization and antifungal susceptibility","volume":"35","author":"Castillo-Martinez","year":"2018","journal-title":"Rev. Chilena Infectol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1111\/j.1834-7819.2010.01219.x","article-title":"Invasive oral aspergillosis in a patient with acute myeloid leukaemia","volume":"55","author":"Cho","year":"2010","journal-title":"Aust. Dent. J."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1056\/NEJMe1307415","article-title":"Inhibition of leukocyte trafficking in inflammatory bowel disease","volume":"369","author":"Cominelli","year":"2013","journal-title":"N. Engl. J. Med."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/gm467","article-title":"The human mycobiome in health and disease","volume":"5","author":"Cui","year":"2013","journal-title":"Genome Med."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"718222","DOI":"10.3389\/fmolb.2021.718222","article-title":"Relationships between Oral microecosystem and respiratory diseases","volume":"8","author":"Dong","year":"2021","journal-title":"Front. Mol. Biosci."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/BF02670897","article-title":"Microprep protocol for extraction of DNA from tomato and other herbaceous plants","volume":"13","author":"Fulton","year":"1995","journal-title":"Plant Mol. Biol. Report."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1007\/s13238-018-0548-1","article-title":"Oral microbiomes: more and more importance in oral cavity and whole body","volume":"9","author":"Gao","year":"2018","journal-title":"Protein Cell"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e1000713","DOI":"10.1371\/journal.ppat.1000713","article-title":"Characterization of the oral fungal microbiome (mycobiome) in healthy individuals","volume":"6","author":"Ghannoum","year":"2010","journal-title":"PLoS Pathog."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1101\/gr.112730.110","article-title":"Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons","volume":"21","author":"Haas","year":"2011","journal-title":"Genome Res."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e40888","DOI":"10.1371\/journal.pone.0040888","article-title":"Molecular detection of eukaryotes in a single human stool sample from Senegal","volume":"7","author":"Hamad","year":"2012","journal-title":"PLoS One"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1002\/zoo.20280","article-title":"Seasonal shifts in giant panda feeding behavior: relationships to bamboo plant part consumption","volume":"29","author":"Hansen","year":"2010","journal-title":"Zoo Biol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e66019","DOI":"10.1371\/journal.pone.0066019","article-title":"Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents","volume":"8","author":"Hoffmann","year":"2013","journal-title":"PLoS One"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"145316","DOI":"10.1016\/j.scitotenv.2021.145316","article-title":"Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas","volume":"770","author":"Jin","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.jcpa.2011.08.001","article-title":"Dental abnormalities in eight captive giant pandas (Ailuropoda melanoleuca) in China","volume":"146","author":"Jin","year":"2012","journal-title":"J. Comp. Pathol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1086\/323550","article-title":"Role of Candida in antibiotic-associated diarrhea","volume":"184","author":"Krause","year":"2001","journal-title":"J. Infect. Dis."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1007\/s10096-023-04736-0","article-title":"The first report of Apiotrichum mycotoxinivorans isolation from human cerebrospinal fluid","volume":"43","author":"Li","year":"2023","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"7874","DOI":"10.18632\/aging.103108","article-title":"Microbiome succession with increasing age in three oral sites","volume":"12","author":"Liu","year":"2020","journal-title":"Aging (Albany NY)"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1053\/jinf.2002.1056","article-title":"Invasive infection due to Penicillium species other than P. marneffei","volume":"45","author":"Lyratzopoulos","year":"2002","journal-title":"J. Infect."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/s41598-020-79642-y","article-title":"Assessment of the pulmonary adaptive immune response to Cladosporium cladosporioides infection using an experimental mouse model","volume":"11","author":"Ma","year":"","journal-title":"Sci. Rep."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1364486","DOI":"10.3389\/fmicb.2024.1364486","article-title":"Analysis of fungal diversity in the gut feces of wild takin (Budorcas taxicolor)","volume":"15","author":"Ma","year":"","journal-title":"Front. Microbiol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"708077","DOI":"10.3389\/fvets.2021.708077","article-title":"Skin Mycobiota of the captive Giant panda (Ailuropoda melanoleuca) and the distribution of opportunistic dermatomycosis-associated Fungi in different seasons","volume":"8","author":"Ma","year":"","journal-title":"Front. Vet. Sci."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"117866","DOI":"10.1016\/j.envres.2023.117866","article-title":"An overview on the current status and future prospects in aspergillus cellulase production","volume":"244","author":"Ma","year":"","journal-title":"Environ. Res."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Magoc","year":"2011","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1038\/s41396-019-0551-4","article-title":"Biodiversity of protists and nematodes in the wild nonhuman primate gut","volume":"14","author":"Mann","year":"2020","journal-title":"ISME J."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1007\/s11046-017-0231-8","article-title":"Cutaneotrichosporon (Trichosporon) debeurmannianum: a rare yeast isolated from blood and urine samples","volume":"183","author":"Nath","year":"2018","journal-title":"Mycopathologia"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/s10266-009-0118-3","article-title":"Antifungal drug resistance of oral fungi","volume":"98","author":"Niimi","year":"2010","journal-title":"Odontology"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1128\/CMR.00014-07","article-title":"Fusarium infections in immunocompromised patients","volume":"20","author":"Nucci","year":"2007","journal-title":"Clin. Microbiol. Rev."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1080\/00365520801935434","article-title":"Fungi and inflammatory bowel diseases: alterations of composition and diversity","volume":"43","author":"Ott","year":"2008","journal-title":"Scand. J. Gastroenterol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.mib.2019.04.007","article-title":"Candida albicans dwelling in the mammalian gut","volume":"52","author":"Perez","year":"2019","journal-title":"Curr. Opin. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"a019810","DOI":"10.1101\/cshperspect.a019810","article-title":"The human mycobiome","volume":"5","author":"Seed","year":"2014","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","article-title":"Fungal microbiota dysbiosis in IBD","volume":"66","author":"Sokol","year":"2017","journal-title":"Gut"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.3389\/fmicb.2016.01227","article-title":"Age and gender affect the composition of fungal population of the Human gastrointestinal tract","volume":"7","author":"Strati","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S1130-1406(08)70032-9","article-title":"Infecci\u00f3n por Rhodotorula. Revisi\u00f3n de 128 casos","volume":"25","author":"Tuon","year":"2008","journal-title":"Rev. Iberoam. Micol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1007\/s00203-018-1505-3","article-title":"Insights into the human oral microbiome","volume":"200","author":"Verma","year":"2018","journal-title":"Arch. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1093\/molbev\/msu278","article-title":"Giant pandas are not an evolutionary cul-de-sac: evidence from multidisciplinary research","volume":"32","author":"Wei","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"5660","DOI":"10.1111\/mec.12096","article-title":"Black and white and read all over: the past, present and future of giant panda genetics","volume":"21","author":"Wei","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/2049-2618-1-6","article-title":"CloVR-ITS: automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota","volume":"1","author":"White","year":"2013","journal-title":"Microbiome"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.simyco.2015.07.001","article-title":"Alternariasection Alternaria: Species, formae speciales or pathotypes?","volume":"82","author":"Woudenberg","year":"2015","journal-title":"Stud. Mycol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e00022","DOI":"10.1128\/mBio.00022-15","article-title":"The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations","volume":"6","author":"Xue","year":"2015","journal-title":"MBio"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.3389\/fmicb.2018.01717","article-title":"Metagenomic analysis of Bacteria, Fungi, bacteriophages, and helminths in the gut of Giant pandas","volume":"9","author":"Yang","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"707548","DOI":"10.3389\/fmicb.2021.707548","article-title":"Contrasting vaginal bacterial communities between estrus and non-estrus of Giant pandas (Ailuropoda melanoleuca)","volume":"12","author":"Yue","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1186\/1471-2164-8-315","article-title":"Giant panda BAC library construction and assembly of a 650-kb contig spanning major histocompatibility complex class II region","volume":"8","author":"Zeng","year":"2007","journal-title":"BMC Genomics"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"551038","DOI":"10.3389\/fmicb.2020.551038","article-title":"Succession of gut microbial structure in twin Giant pandas during the dietary change stage and its role in polysaccharide metabolism","volume":"11","author":"Zhan","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1038\/s41396-018-0051-y","article-title":"Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose","volume":"12","author":"Zhang","year":"2018","journal-title":"ISME J."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"4945","DOI":"10.7150\/thno.55209","article-title":"Candida albicans disorder is associated with gastric carcinogenesis","volume":"11","author":"Zhong","year":"2021","journal-title":"Theranostics"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"106703","DOI":"10.1016\/j.envint.2021.106703","article-title":"Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome","volume":"155","author":"Zhu","year":"2021","journal-title":"Environ. 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