Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, et al. Investigating colonization of the healthy adult gastrointestinal tract by fungi. MSphere. 2018;3(2):1–16. https://doi.org/10.1128/mSphere.00092-18.
Article
Google Scholar
Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, et al. Characterization of the oral fungal microbiome (Mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1): e1000713. https://doi.org/10.1371/journal.ppat.1000713.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fujimura KE, Sitarik AR, Havstad S, Lin DL, Levan S, Fadrosh D, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med. 2016;22(10):1187–91. https://doi.org/10.1038/nm.4176.
Article
CAS
PubMed
PubMed Central
Google Scholar
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’s disease. MBio. 2016;7(5):1–11. https://doi.org/10.1128/mBio.01250-16.
Article
Google Scholar
Sokol H, Leducq V, Aschard H, Pham H-P, Jegou S, Landman C, et al. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039–48. https://doi.org/10.1136/gutjnl-2015-310746.
Article
CAS
PubMed
Google Scholar
Honkanen J, Vuorela A, Muthas D, Orivuori L, Luopajärvi K, Tejesvi MVG, et al. Fungal dysbiosis and intestinal inflammation in children with beta-cell autoimmunity. Front Immunol. 2020;11:1–14. https://doi.org/10.3389/fimmu.2020.00468.
Article
CAS
Google Scholar
Ward TL, Knights D, Gale CA. Infant fungal communities: current knowledge and research opportunities. BMC Med. 2017;15(1):30. https://doi.org/10.1186/s12916-017-0802-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ezeonu IM, Ntun NW, Ugwu KO. Intestinal candidiasis and antibiotic usage in children: case study of Nsukka, South Eastern Nigeria. Afr Health Sci. 2018;17(4):1178. https://doi.org/10.4314/ahs.v17i4.27.
Article
Google Scholar
Coates EW. distinctive distribution of pathogens associated with peritonitis in neonates with focal intestinal perforation compared with necrotizing enterocolitis. Pediatrics. 2005;116(2):e241–6. https://doi.org/10.1542/peds.2004-2537.
Article
PubMed
Google Scholar
Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, et al. The gut mycobiome of the human microbiome project healthy cohort. Microbiome. 2017;5(1):153. https://doi.org/10.1186/s40168-017-0373-4.
Article
PubMed
PubMed Central
Google Scholar
Strati F, Di Paola M, Stefanini I, Albanese D, Rizzetto L, Lionetti P, et al. Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front Microbiol. 2016;7:1–16. https://doi.org/10.3389/fmicb.2016.01227.
Article
Google Scholar
James SA, Phillips S, Telatin A, Baker D, Ansorge R, Clarke P, et al. Preterm infants harbour a rapidly changing mycobiota that includes candida pathobionts. J Fungi. 2020;6(4):273. https://doi.org/10.3390/jof6040273.
Article
Google Scholar
Willis KA, Purvis JH, Myers ED, Aziz MM, Karabayir I, Gomes CK, et al. Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. FASEB J. 2019;33(11):12825–37. https://doi.org/10.1096/fj.201901436RR.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schei K, Avershina E, Øien T, Rudi K, Follestad T, Salamati S, et al. Early gut mycobiota and mother-offspring transfer. Microbiome. 2017;5(1):107. https://doi.org/10.1186/s40168-017-0319-x.
Article
PubMed
PubMed Central
Google Scholar
Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med. 2013;5(7):63. https://doi.org/10.1186/gm467.
Article
PubMed
PubMed Central
Google Scholar
Kabwe MH, Vikram S, Mulaudzi K, Jansson JK, Makhalanyane TP. The gut mycobiota of rural and urban individuals is shaped by geography. BMC Microbiol. 2020;20(1):257. https://doi.org/10.1186/s12866-020-01907-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
NelVanZyl K, Whitelaw AC, Hesseling AC, Seddon JA, Demers AM, Newton-Foot M. Association between clinical and environmental factors and the gut microbiota profiles in young South African children. Sci Rep. 2021;11(1):15895. https://doi.org/10.1038/s41598-021-95409-5.
Article
CAS
Google Scholar
Zou R, Wang Y, Duan M, Guo M, Zhang Q, Zheng H. Dysbiosis of gut fungal microbiota in children with autism spectrum disorders. J Autism Dev Disord. 2021;51(1):267–75. https://doi.org/10.1007/s10803-020-04543-y.
Article
PubMed
Google Scholar
Mahnic A, Rupnik M. Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort. PLoS ONE. 2018;13(12): e0209209. https://doi.org/10.1371/journal.pone.0209209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Zhan H, Xu W, Yan S, Ng SC. The role of gut mycobiome in health and diseases. Therap Adv Gastroenterol. 2021;14:1–18. https://doi.org/10.1177/17562848211047130.
Article
CAS
Google Scholar
Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, et al. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci Transl Med. 2017;9(390):aal4069. https://doi.org/10.1126/scitranslmed.aal4069.
Article
Google Scholar
Iyer N, Vaishnava S. Vitamin A at the interface of host–commensal–pathogen interactions. PLOS Pathog. 2019;15(6): e1007750. https://doi.org/10.1371/journal.ppat.1007750.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huda MN, Ahmad SM, Kalanetra KM, Taft DH, Alam MJ, Khanam A, et al. Neonatal vitamin A supplementation and vitamin A status are associated with gut microbiome composition in Bangladeshi infants in early infancy and at 2 years of age. J Nutr. 2019;149(6):1075–88. https://doi.org/10.1093/jn/nxz034.
Article
PubMed
PubMed Central
Google Scholar
Hallen-Adams HE, Suhr MJ. Fungi in the healthy human gastrointestinal tract. Virulence. 2017;8(3):352–8. https://doi.org/10.1080/21505594.2016.1247140.
Article
CAS
PubMed
Google Scholar
Suhr MJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials–a mycologists perspective. Mycologia. 2015;107(6):1057–73. https://doi.org/10.3852/15-147.
Article
CAS
PubMed
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63. https://doi.org/10.1038/nature12820.
Article
CAS
PubMed
Google Scholar
Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer A-C, et al. Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome. 2020;8(1):133. https://doi.org/10.1186/s40168-020-00899-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mirhakkak MH, Schäuble S, Klassert TE, Brunke S, Brandt P, Loos D, et al. Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. ISME J. 2021;15(5):1257–70. https://doi.org/10.1038/s41396-020-00848-z.
Article
CAS
PubMed
Google Scholar
Rao C, Coyte KZ, Bainter W, Geha RS, Martin CR, Rakoff-Nahoum S. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature. 2021;591(7851):633–8. https://doi.org/10.1038/s41586-021-03241-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 2010;10(1):189. https://doi.org/10.1186/1471-2180-10-189.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nel Van Zyl K, Whitelaw AC, Newton-Foot M. The effect of storage conditions on microbial communities in stool. PLoS One. 2020;15(1):e0227486. https://doi.org/10.1371/journal.pone.0227486.
Article
CAS
PubMed
PubMed Central
Google Scholar
Illumina, Inc. Fungal sequencing and classification with the ITS Metagenomics Protocol [Internet]. San Diego: Illumina, Inc.; 2019 [Cited 2022 Aug 16]. Available from: https://emea.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/its-metagenomics-app-note-1270-2018-001-web.pdf.
Illumina, Inc. Fungal Metagenomic Sequencing Demonstrated Protocol [Internet]. Illumina, Inc.; 2019 [Cited 2022 Aug 16]. Available from: https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/metagenomic/fungal-metagenomic-demonstrated-protocol-1000000064940-01.pdf.
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):852–7. https://doi.org/10.1038/s41587-019-0209-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rivers AR, Weber KC, Gardner TG, Liu S, Armstrong SD. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Res. 2018;7:1418. https://doi.org/10.12688/f1000research.15704.1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3. https://doi.org/10.1038/nmeth.3869.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine learning in python. J Mach Learn Res. 2011;12(85):2825–30.
Google Scholar
Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6(1):90. https://doi.org/10.1186/s40168-018-0470-z.
Article
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10. https://doi.org/10.14806/ej.17.1.200.
Article
Google Scholar
Shannon CE, Weaver W W. The mathematical theory of communication. Champaign, Illinois: The University of Illinois Press; 1949.
Google Scholar
Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J Am Stat Assoc. 1952;47(260):583–621. https://doi.org/10.1080/01621459.1952.10483441.
Article
Google Scholar
Spearman C. The proof and measurement of association between two things. Am J Psychol. 1904;15(1):72–101.
Article
Google Scholar
Bray JR, Curtis JT. an ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957;27(4):325–49. https://doi.org/10.2307/1942268.
Article
Google Scholar
Jaccard P. Nouvelles recherches sur la distribution florale. Bull la Société vaudoise des Sci Nat. 1908;44:223–70.
Google Scholar
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26(1):32–46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x.
Article
Google Scholar
Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O’Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and HW. Vegan: Community Ecology Package. 2018.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57(1):289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x.
Article
Google Scholar
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Heal Dis. 2015;26:27663. https://doi.org/10.3402/mehd.v26.27663.
Article
Google Scholar
Watts SC, Ritchie SC, Inouye M, Holt KE. FastSpar: rapid and scalable correlation estimation for compositional data. Bioinformatics. 2019;35(6):1064–6. https://doi.org/10.1093/bioinformatics/bty734.
Article
CAS
PubMed
Google Scholar
Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9): e1002687. https://doi.org/10.1371/journal.pcbi.1002687.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei T, Simko V. Corrplot: visualization of a correlation matrix. 2016.
Google Scholar