{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T11:24:19Z","timestamp":1788866659046,"version":"build-2803163510"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,10,9]],"date-time":"2021-10-09T00:00:00Z","timestamp":1633737600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,10,9]],"date-time":"2021-10-09T00:00:00Z","timestamp":1633737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2018-68003-27462"],"award-info":[{"award-number":["2018-68003-27462"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2018-67011-28041"],"award-info":[{"award-number":["2018-67011-28041"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Animal Sci Biotechnol"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Intestinal microbiota is critical for maintaining animal health and homeostasis. However, involvement of the fungal community, also known as the mycobiota, in animal health and disease is poorly understood. This study was aimed to examine the association between the intestinal mycobiota and the severity of necrotic enteritis (NE), an economically significant poultry disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A total of 90\u2009day-of-hatch Cobb broilers were infected with\n                      <jats:italic>Eimeria maxima<\/jats:italic>\n                      on d 10, followed by an oral challenge with\n                      <jats:italic>C. perfringens<\/jats:italic>\n                      on d 14 to induce NE, while another 10 broilers were served as mock-infected controls. On d 17, the lesions in the jejunum were scored, and the ileal digesta were subjected to DNA isolation and real-time PCR quantification of total bacterial and fungi populations. Internal transcribed spacer 2 (ITS2) amplicon sequencing was also performed to profile the ileal mycobiota composition. Changes in the ileal mycobiota in response to NE were investigated. Spearman correlation analysis was further conducted to identify the correlations between relative abundances of individual ileal fungi and the severity of NE.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      While the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population was progressively declined in more exacerbated NE, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009=\u20090.06). Compositionally, among 30 most abundant fungal amplicon sequence variants (ASVs), 11 were diminished and 7 were enriched (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.05), while 12 remained largely unchanged in NE-afflicted chickens (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&gt;\u20090.05). Multiple\n                      <jats:italic>Wallemia<\/jats:italic>\n                      and\n                      <jats:italic>Aspergillus<\/jats:italic>\n                      species were markedly diminished in NE (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.05) and also showed a significant negative correlation with NE severity (\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.05).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Dysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40104-021-00628-5","type":"journal-article","created":{"date-parts":[[2021,10,10]],"date-time":"2021-10-10T12:46:07Z","timestamp":1633869967000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Perturbations of the ileal mycobiota by necrotic enteritis in broiler chickens"],"prefix":"10.1186","volume":"12","author":[{"given":"Qing","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelsy J.","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie A.","family":"Whitmore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney N.","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4781-5816","authenticated-orcid":false,"given":"Guolong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,9]]},"reference":[{"issue":"1","key":"628_CR1","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1146\/annurev-animal-091020-075907","volume":"9","author":"RS Peixoto","year":"2021","unstructured":"Peixoto RS, Harkins DM, Nelson KE. Advances in microbiome research for animal health. Annu Rev Anim Biosci. 2021;9(1):289\u2013311. https:\/\/doi.org\/10.1146\/annurev-animal-091020-075907.","journal-title":"Annu Rev Anim Biosci"},{"issue":"1","key":"628_CR2","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/s41579-020-0433-9","volume":"19","author":"Y Fan","year":"2021","unstructured":"Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19(1):55\u201371. https:\/\/doi.org\/10.1038\/s41579-020-0433-9.","journal-title":"Nat Rev Microbiol"},{"issue":"6","key":"628_CR3","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1016\/j.immuni.2019.05.023","volume":"50","author":"XV Li","year":"2019","unstructured":"Li XV, Leonardi I, Iliev ID. Gut mycobiota in immunity and inflammatory disease. Immunity. 2019;50(6):1365\u201379. https:\/\/doi.org\/10.1016\/j.immuni.2019.05.023.","journal-title":"Immunity."},{"issue":"4","key":"628_CR4","doi-asserted-by":"publisher","first-page":"e00648","DOI":"10.1128\/IAI.00648-20","volume":"89","author":"W Santus","year":"2021","unstructured":"Santus W, Devlin JR, Behnsen J. Crossing kingdoms: how the mycobiota and fungal-bacterial interactions impact host health and disease. Infect Immun. 2021;89(4):e00648\u201320.","journal-title":"Infect Immun"},{"issue":"1","key":"628_CR5","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s40168-021-01024-x","volume":"9","author":"X Wu","year":"2021","unstructured":"Wu X, Xia Y, He F, Zhu C, Ren W. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. Microbiome. 2021;9(1):60. https:\/\/doi.org\/10.1186\/s40168-021-01024-x.","journal-title":"Microbiome."},{"issue":"6414","key":"628_CR6","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1126\/science.aat0537","volume":"362","author":"GHW Tso","year":"2018","unstructured":"Tso GHW, Reales-Calderon JA, Tan ASM, Sem X, Le GTT, Tan TG, et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science. 2018;362(6414):589\u201395. https:\/\/doi.org\/10.1126\/science.aat0537.","journal-title":"Science."},{"issue":"3","key":"628_CR7","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/j.chom.2019.02.004","volume":"25","author":"TY Shao","year":"2019","unstructured":"Shao TY, Ang WXG, Jiang TT, Huang FS, Andersen H, Kinder JM, et al. Commensal Candida albicans positively calibrates systemic Th17 immunological responses. Cell Host Microbe. 2019;25(3):404\u201317.e6.","journal-title":"Cell Host Microbe"},{"issue":"6","key":"628_CR8","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1136\/gutjnl-2015-310746","volume":"66","author":"H Sokol","year":"2017","unstructured":"Sokol H, Leducq V, Aschard H, Pham HP, Jegou S, Landman C, et al. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039\u201348. https:\/\/doi.org\/10.1136\/gutjnl-2015-310746.","journal-title":"Gut."},{"issue":"3","key":"628_CR9","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/j.chom.2019.01.007","volume":"25","author":"JJ Limon","year":"2019","unstructured":"Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, et al. Malassezia is associated with Crohn\u2018s disease and exacerbates colitis in mouse models. Cell Host Microbe. 2019;25(3):377\u201388.e6.","journal-title":"Cell Host Microbe"},{"issue":"9","key":"628_CR10","doi-asserted-by":"publisher","first-page":"e1007260","DOI":"10.1371\/journal.ppat.1007260","volume":"14","author":"JH Skalski","year":"2018","unstructured":"Skalski JH, Limon JJ, Sharma P, Gargus MD, Nguyen C, Tang J, et al. Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. PLoS Pathog. 2018;14(9):e1007260. https:\/\/doi.org\/10.1371\/journal.ppat.1007260.","journal-title":"PLoS Pathog"},{"issue":"2","key":"628_CR11","doi-asserted-by":"publisher","first-page":"46","DOI":"10.3390\/microorganisms6020046","volume":"6","author":"J Zajc","year":"2018","unstructured":"Zajc J, Gunde-Cimerman N. The genus Wallemia-from contamination of food to health threat. Microorganisms. 2018;6(2):46. https:\/\/doi.org\/10.3390\/microorganisms6020046.","journal-title":"Microorganisms."},{"issue":"4","key":"628_CR12","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1136\/gutjnl-2018-317178","volume":"68","author":"OO Coker","year":"2019","unstructured":"Coker OO, Nakatsu G, Dai RZ, Wu WKK, Wong SH, Ng SC, et al. Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer. Gut. 2019;68(4):654\u201362. https:\/\/doi.org\/10.1136\/gutjnl-2018-317178.","journal-title":"Gut."},{"issue":"5","key":"628_CR13","doi-asserted-by":"publisher","first-page":"e01250","DOI":"10.1128\/mBio.01250-16","volume":"7","author":"G Hoarau","year":"2016","unstructured":"Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, et al. Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn\u2018s disease. mBio. 2016;7(5):e01250\u201316.","journal-title":"mBio"},{"issue":"13","key":"628_CR14","doi-asserted-by":"publisher","first-page":"e00304","DOI":"10.1128\/AEM.00304-20","volume":"86","author":"K Robinson","year":"2020","unstructured":"Robinson K, Xiao Y, Johnson TJ, Chen B, Yang Q, Lyu W, et al. Chicken intestinal mycobiome: initial characterization and its response to bacitracin methylene disalicylate. Appl Environ Microbiol. 2020;86(13):e00304\u201320.","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"628_CR15","doi-asserted-by":"publisher","first-page":"e02171","DOI":"10.1128\/mBio.02171-19","volume":"10","author":"TL Ward","year":"2019","unstructured":"Ward TL, Weber BP, Mendoza KM, Danzeisen JL, Llop K, Lang K, et al. Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression. mBio. 2019;10(5):e02171\u201319.","journal-title":"mBio"},{"issue":"7","key":"628_CR16","first-page":"16","volume":"31","author":"B Wade","year":"2015","unstructured":"Wade B, Keyburn A. The true cost of necrotic enteritis. World Poult. 2015;31(7):16\u20137.","journal-title":"World Poult"},{"issue":"3","key":"628_CR17","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1080\/03079457.2016.1152625","volume":"45","author":"G Antonissen","year":"2016","unstructured":"Antonissen G, Eeckhaut V, Van Driessche K, Onrust L, Haesebrouck F, Ducatelle R, et al. Microbial shifts associated with necrotic enteritis. Avian Pathol. 2016;45(3):308\u201312. https:\/\/doi.org\/10.1080\/03079457.2016.1152625.","journal-title":"Avian Pathol"},{"issue":"1","key":"628_CR18","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/1297-9716-43-74","volume":"43","author":"B Shojadoost","year":"2012","unstructured":"Shojadoost B, Vince AR, Prescott JF. The successful experimental induction of necrotic enteritis in chickens by Clostridium perfringens: a critical review. Vet Res. 2012;43(1):74. https:\/\/doi.org\/10.1186\/1297-9716-43-74.","journal-title":"Vet Res"},{"issue":"3\u20134","key":"628_CR19","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.vetmic.2009.09.065","volume":"142","author":"KK Cooper","year":"2010","unstructured":"Cooper KK, Songer JG. Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis. Vet Microbiol. 2010;142(3\u20134):323\u20138. https:\/\/doi.org\/10.1016\/j.vetmic.2009.09.065.","journal-title":"Vet Microbiol"},{"issue":"5","key":"628_CR20","doi-asserted-by":"publisher","first-page":"1947","DOI":"10.1007\/s00436-012-3041-4","volume":"111","author":"R Al-Badri","year":"2012","unstructured":"Al-Badri R, Barta JR. The kinetics of oocyst shedding and sporulation in two immunologically distinct strains of Eimeria maxima, GS and M6. Parasitol Res. 2012;111(5):1947\u201352. https:\/\/doi.org\/10.1007\/s00436-012-3041-4.","journal-title":"Parasitol Res"},{"key":"628_CR21","doi-asserted-by":"publisher","first-page":"199","DOI":"10.3389\/fvets.2018.00199","volume":"5","author":"JD Latorre","year":"2018","unstructured":"Latorre JD, Adhikari B, Park SH, Teague KD, Graham LE, Mahaffey BD, et al. Evaluation of the epithelial barrier function and ileal microbiome in an established necrotic enteritis challenge model in broiler chickens. Front Vet Sci. 2018;5:199. https:\/\/doi.org\/10.3389\/fvets.2018.00199.","journal-title":"Front Vet Sci"},{"issue":"3","key":"628_CR22","doi-asserted-by":"publisher","first-page":"e00019","DOI":"10.1128\/MMBR.00019-17","volume":"81","author":"GC diCenzo","year":"2017","unstructured":"diCenzo GC, Finan TM. The divided bacterial genome: structure, function, and evolution. Microbiol Mol Biol Rev. 2017;81(3):e00019\u20137.","journal-title":"Microbiol Mol Biol Rev"},{"key":"628_CR23","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/bs.adgen.2016.01.003","volume":"94","author":"HH De Fine Licht","year":"2016","unstructured":"De Fine Licht HH, Hajek AE, Eilenberg J, Jensen AB. Utilizing genomics to study entomopathogenicity in the fungal phylum entomophthoromycota: a review of current genetic resources. Adv Genet. 2016;94:41\u201365. https:\/\/doi.org\/10.1016\/bs.adgen.2016.01.003.","journal-title":"Adv Genet"},{"key":"628_CR24","first-page":"315","volume-title":"PCR protocols: a guide to methods and applications","author":"TJ White","year":"1990","unstructured":"White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York: Academic Press; 1990. p. 315\u201322."},{"issue":"8","key":"628_CR25","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852\u20137. https:\/\/doi.org\/10.1038\/s41587-019-0209-9.","journal-title":"Nat Biotechnol"},{"issue":"2","key":"628_CR26","first-page":"e00191","volume":"2","author":"A Amir","year":"2017","unstructured":"Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems. 2017;2(2):e00191\u201316.","journal-title":"mSystems"},{"issue":"12","key":"628_CR27","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1038\/nmeth.2658","volume":"10","author":"JN Paulson","year":"2013","unstructured":"Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10(12):1200\u20132. https:\/\/doi.org\/10.1038\/nmeth.2658.","journal-title":"Nat Methods"},{"issue":"4","key":"628_CR28","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.","journal-title":"PLoS One"},{"issue":"12","key":"628_CR29","doi-asserted-by":"publisher","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","volume":"71","author":"C Lozupone","year":"2005","unstructured":"Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71(12):8228\u201335. https:\/\/doi.org\/10.1128\/AEM.71.12.8228-8235.2005.","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"628_CR30","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. https:\/\/doi.org\/10.1186\/gb-2011-12-6-r60.","journal-title":"Genome Biol"},{"key":"628_CR31","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: elegant graphics for data analysis. 2nd ed","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2: elegant graphics for data analysis. 2nd ed. New York: Springer; 2016. https:\/\/doi.org\/10.1007\/978-3-319-24277-4."},{"issue":"1","key":"628_CR32","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/s40168-019-0721-7","volume":"7","author":"X Wang","year":"2019","unstructured":"Wang X, Tsai T, Deng F, Wei X, Chai J, Knapp J, et al. Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria. Microbiome. 2019;7(1):109. https:\/\/doi.org\/10.1186\/s40168-019-0721-7.","journal-title":"Microbiome."},{"issue":"1","key":"628_CR33","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s40104-020-00542-2","volume":"12","author":"J Liu","year":"2021","unstructured":"Liu J, Stewart SN, Robinson K, Yang Q, Lyu W, Whitmore MA, et al. Linkage between the intestinal microbiota and residual feed intake in broiler chickens. J Anim Sci Biotechnol. 2021;12(1):22. https:\/\/doi.org\/10.1186\/s40104-020-00542-2.","journal-title":"J Anim Sci Biotechnol"},{"key":"628_CR34","first-page":"1727","volume":"7","author":"J Hu","year":"2016","unstructured":"Hu J, Nie Y, Chen J, Zhang Y, Wang Z, Fan Q, et al. Gradual changes of gut microbiota in weaned miniature piglets. Front Microbiol. 2016;7:1727.","journal-title":"Front Microbiol"},{"issue":"1","key":"628_CR35","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/s12866-017-1024-4","volume":"17","author":"SH Subramanya","year":"2017","unstructured":"Subramanya SH, Sharan NK, Baral BP, Hamal D, Nayak N, Prakash PY, et al. Diversity, in-vitro virulence traits and antifungal susceptibility pattern of gastrointestinal yeast flora of healthy poultry, Gallus gallus domesticus. BMC Microbiol. 2017;17(1):113. https:\/\/doi.org\/10.1186\/s12866-017-1024-4.","journal-title":"BMC Microbiol"},{"issue":"3","key":"628_CR36","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1637\/11780-121117-Reg.1","volume":"62","author":"I Sokol","year":"2018","unstructured":"Sokol I, Gawel A, Bobrek K. The prevalence of yeast and characteristics of the isolates from the digestive tract of clinically healthy turkeys. Avian Dis. 2018;62(3):286\u201390. https:\/\/doi.org\/10.1637\/11780-121117-Reg.1.","journal-title":"Avian Dis"},{"issue":"1","key":"628_CR37","first-page":"47","volume":"8","author":"SS Ghaemmaghami","year":"2016","unstructured":"Ghaemmaghami SS, Modirsaneii M, Khosravi AR, Razzaghi-Abyaneh M. Study on mycoflora of poultry feed ingredients and finished feed in Iran. Iran J Microbiol. 2016;8(1):47\u201354.","journal-title":"Iran J Microbiol"},{"issue":"5","key":"628_CR38","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1007\/s11046-006-0070-5","volume":"162","author":"GR Oliveira","year":"2006","unstructured":"Oliveira GR, Ribeiro JM, Fraga ME, Cavaglieri LR, Direito GM, Keller KM, et al. Mycobiota in poultry feeds and natural occurrence of aflatoxins, fumonisins and zearalenone in the Rio de Janeiro state, Brazil. Mycopathologia. 2006;162(5):355\u201362. https:\/\/doi.org\/10.1007\/s11046-006-0070-5.","journal-title":"Mycopathologia"},{"issue":"3","key":"628_CR39","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/ecco-jcc\/jjv209","volume":"10","author":"G Liguori","year":"2016","unstructured":"Liguori G, Lamas B, Richard ML, Brandi G, da Costa G, Hoffmann TW, et al. Fungal dysbiosis in mucosa-associated microbiota of Crohn\u2018s disease patients. J Crohns Colitis. 2016;10(3):296\u2013305. https:\/\/doi.org\/10.1093\/ecco-jcc\/jjv209.","journal-title":"J Crohns Colitis"},{"issue":"4","key":"628_CR40","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1007\/s00248-017-1105-9","volume":"75","author":"J Li","year":"2018","unstructured":"Li J, Chen D, Yu B, He J, Zheng P, Mao X, et al. Fungi in gastrointestinal tracts of human and mice: from community to functions. Microb Ecol. 2018;75(4):821\u20139. https:\/\/doi.org\/10.1007\/s00248-017-1105-9.","journal-title":"Microb Ecol"},{"issue":"2","key":"628_CR41","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.chom.2017.07.002","volume":"22","author":"JJ Limon","year":"2017","unstructured":"Limon JJ, Skalski JH, Underhill DM. Commensal fungi in health and disease. Cell Host Microbe. 2017;22(2):156\u201365. https:\/\/doi.org\/10.1016\/j.chom.2017.07.002.","journal-title":"Cell Host Microbe"},{"issue":"12","key":"628_CR42","doi-asserted-by":"publisher","first-page":"e0169116","DOI":"10.1371\/journal.pone.0169116","volume":"11","author":"S Jan\u010di\u010d","year":"2016","unstructured":"Jan\u010di\u010d S, Frisvad JC, Kocev D, Gostin\u010dar C, D\u017eeroski S, Gunde-Cimerman N. Production of secondary metabolites in extreme environments: food- and airborne Wallemia spp. produce toxic metabolites at hypersaline conditions. PLoS One. 2016;11(12):e0169116.","journal-title":"PLoS One"},{"issue":"8","key":"628_CR43","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.7164\/antibiotics.46.1312","volume":"46","author":"I Takahashi","year":"1993","unstructured":"Takahashi I, Maruta R, Ando K, Yoshida M, Iwasaki T, Kanazawa J, et al. UCA1064-B, a new antitumor antibiotic isolated from Wallemia sebi: production, isolation and structural determination. J Antibiot (Tokyo). 1993;46(8):1312\u20134. https:\/\/doi.org\/10.7164\/antibiotics.46.1312.","journal-title":"J Antibiot (Tokyo)"},{"key":"628_CR44","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1002\/9781119421481.ch25","volume-title":"Diseases of poultry","author":"MJ Dykstra","year":"2013","unstructured":"Dykstra MJ, Charlton BR, Chin RP, Barnes HJ. Fungal infections. In: Swayne DE, Glisson JR, McDougald LR, Nolan LK, Suarez DL, Nair VL, editors. Diseases of poultry. 13th ed. Oxford: Wiley-Blackwell; 2013. p. 1075\u201396. https:\/\/doi.org\/10.1002\/9781119421481.ch25.","edition":"13"},{"key":"628_CR45","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/B978-0-12-821005-5.00015-6","volume-title":"New and future developments in microbial biotechnology and bioengineering","author":"N Ashtekar","year":"2021","unstructured":"Ashtekar N, Anand G, Prakash PY, Rajeshkumar KC. Aspergillus terreus: taxonomy, biology, and bioactive secondary metabolites with potential applications. In: Singh J, Gehlot P, editors. New and future developments in microbial biotechnology and bioengineering. Amsterdam: Elsevier; 2021. p. 215\u201323. https:\/\/doi.org\/10.1016\/B978-0-12-821005-5.00015-6."},{"issue":"2","key":"628_CR46","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1016\/j.rvsc.2011.09.005","volume":"93","author":"Y Garc\u00eda-Hern\u00e1ndez","year":"2012","unstructured":"Garc\u00eda-Hern\u00e1ndez Y, Rodr\u00edguez Z, Brand\u00e3o LR, Rosa CA, Nicoli JR, El\u00edas Iglesias A, et al. Identification and in vitro screening of avian yeasts for use as probiotic. Res Vet Sci. 2012;93(2):798\u2013802. https:\/\/doi.org\/10.1016\/j.rvsc.2011.09.005.","journal-title":"Res Vet Sci"},{"issue":"6","key":"628_CR47","doi-asserted-by":"publisher","first-page":"1766","DOI":"10.1111\/jam.13297","volume":"121","author":"AP Magnoli","year":"2016","unstructured":"Magnoli AP, Rodriguez MC, Poloni VL, Rojo MC, Combina M, Chiacchiera SM, et al. Novel yeast isolated from broilers\u2018 feedstuff, gut and faeces as aflatoxin B1 adsorbents. J Appl Microbiol. 2016;121(6):1766\u201376. https:\/\/doi.org\/10.1111\/jam.13297.","journal-title":"J Appl Microbiol"},{"key":"628_CR48","doi-asserted-by":"publisher","first-page":"201","DOI":"10.3389\/fcimb.2020.00201","volume":"10","author":"M Spatz","year":"2020","unstructured":"Spatz M, Richard ML. Overview of the potential role of Malassezia in gut health and disease. Front Cell Infect Microbiol. 2020;10:201. https:\/\/doi.org\/10.3389\/fcimb.2020.00201.","journal-title":"Front Cell Infect Microbiol"},{"key":"628_CR49","doi-asserted-by":"publisher","first-page":"118","DOI":"10.3389\/fcimb.2017.00118","volume":"7","author":"C Duarte-Oliveira","year":"2017","unstructured":"Duarte-Oliveira C, Rodrigues F, Gon\u00e7alves SM, Goldman GH, Carvalho A, Cunha C. The cell biology of the Trichosporon-host interaction. Front Cell Infect Microbiol. 2017;7:118.","journal-title":"Front Cell Infect Microbiol"},{"key":"628_CR50","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.mmcr.2017.01.002","volume":"15","author":"M Ekhtiari","year":"2017","unstructured":"Ekhtiari M, Farahyar S, Falahati M, Razmjou E, Ashrafi-Khozani M, Ghasemi Z, et al. The first report of onychomycosis caused by Cryptococcus friedmannii (Naganishia friedmannii) a basidiomycetous yeast. Med Mycol Case Rep. 2017;15:25\u20137. https:\/\/doi.org\/10.1016\/j.mmcr.2017.01.002.","journal-title":"Med Mycol Case Rep"},{"issue":"2","key":"628_CR51","doi-asserted-by":"publisher","first-page":"70","DOI":"10.3390\/pathogens8020070","volume":"8","author":"W Kruger","year":"2019","unstructured":"Kruger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Fungal-bacterial interactions in health and disease. Pathogens. 2019;8(2):70. https:\/\/doi.org\/10.3390\/pathogens8020070.","journal-title":"Pathogens."},{"key":"628_CR52","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.procbio.2020.12.018","volume":"102","author":"M Lin","year":"2020","unstructured":"Lin M, Feng L, Cheng Z, Wang K. Effect of ethanol or lactic acid on short chain fatty acid production and microbial community in short-term sequentially transfers by ruminal fermented with wheat straw in vitro. Process Biochem. 2020;102:369\u201375.","journal-title":"Process Biochem"},{"issue":"5","key":"628_CR53","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1016\/S1286-4579(00)00313-0","volume":"2","author":"S Boris","year":"2000","unstructured":"Boris S, Barb\u00e9s C. Role played by lactobacilli in controlling the population of vaginal pathogens. Microbes Infect. 2000;2(5):543\u20136. https:\/\/doi.org\/10.1016\/S1286-4579(00)00313-0.","journal-title":"Microbes Infect"},{"issue":"7","key":"628_CR54","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1038\/nm.3871","volume":"21","author":"D Fan","year":"2015","unstructured":"Fan D, Coughlin LA, Neubauer MM, Kim J, Kim MS, Zhan X, et al. Activation of HIF-1\u03b1 and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat Med. 2015;21(7):808\u201314. https:\/\/doi.org\/10.1038\/nm.3871.","journal-title":"Nat Med"},{"issue":"8","key":"628_CR55","doi-asserted-by":"publisher","first-page":"e104739","DOI":"10.1371\/journal.pone.0104739","volume":"9","author":"D Stanley","year":"2014","unstructured":"Stanley D, Wu SB, Rodgers N, Swick RA, Moore RJ. Differential responses of cecal microbiota to fishmeal, Eimeria and Clostridium perfringens in a necrotic enteritis challenge model in chickens. PLoS One. 2014;9(8):e104739. https:\/\/doi.org\/10.1371\/journal.pone.0104739.","journal-title":"PLoS One"},{"issue":"5","key":"628_CR56","doi-asserted-by":"publisher","first-page":"e0205784","DOI":"10.1371\/journal.pone.0205784","volume":"14","author":"WY Yang","year":"2019","unstructured":"Yang WY, Lee Y, Lu H, Chou CH, Wang C. Analysis of gut microbiota and the effect of lauric acid against necrotic enteritis in Clostridium perfringens and Eimeria side-by-side challenge model. PLoS One. 2019;14(5):e0205784. https:\/\/doi.org\/10.1371\/journal.pone.0205784.","journal-title":"PLoS One"}],"container-title":["Journal of Animal Science and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40104-021-00628-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40104-021-00628-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40104-021-00628-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,10]],"date-time":"2021-10-10T12:46:14Z","timestamp":1633869974000},"score":1,"resource":{"primary":{"URL":"https:\/\/jasbsci.biomedcentral.com\/articles\/10.1186\/s40104-021-00628-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,9]]},"references-count":56,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["628"],"URL":"https:\/\/doi.org\/10.1186\/s40104-021-00628-5","relation":{},"ISSN":["2049-1891"],"issn-type":[{"value":"2049-1891","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,9]]},"assertion":[{"value":"14 May 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 October 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All animal procedures were approved by the Institutional Animal Care and Use Committee of Oklahoma State University under protocol number AG-16-10.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"107"}}