Page 82 - Read Online

Renzi et al. Microbiome Res Rep 2024;3:2 https://dx.doi.org/10.20517/mrr.2023.27 Page 13 of 16

to microbial isolate. Crit Rev Microbiol 2018;44:212-29. DOI PubMed
45. Borges FM, de Paula TO, Sarmiento MRA, et al. Fungal diversity of human gut microbiota among eutrophic, overweight, and obese
individuals based on aerobic culture-dependent approach. Curr Microbiol 2018;75:726-35. DOI
46. Hamad I, Ranque S, Azhar EI, et al. Culturomics and amplicon-based metagenomic approaches for the study of fungal population in
human gut microbiota. Sci Rep 2017;7:16788. DOI PubMed PMC
47. Huseyin CE, Rubio RC, O’Sullivan O, Cotter PD, Scanlan PD. The fungal frontier: a comparative analysis of methods used in the
study of the human gut mycobiome. Front Microbiol 2017;8:1432. DOI PubMed PMC
48. Aimanianda V, Clavaud C, Simenel C, Fontaine T, Delepierre M, Latgé JP. Cell wall beta-(1,6)-glucan of Saccharomyces cerevisiae:
structural characterization and in situ synthesis. J Biol Chem 2009;284:13401-12. DOI PubMed PMC
49. Valiante V, Macheleidt J, Föge M, Brakhage AA. The Aspergillus fumigatus cell wall integrity signaling pathway: drug target,
compensatory pathways, and virulence. Front Microbiol 2015;6:325. DOI PubMed PMC
50. Gow NAR, Latge JP, Munro CA. The fungal cell wall: structure, biosynthesis, and function. Microbiol Spectr 2017;5. DOI PubMed
51. Machová E, Kvapilová K, Kogan G, Sandula J. Effect of ultrasonic treatment on the molecular weight of carboxymethylated chitin-
glucan complex from Aspergillus niger. Ultrason Sonochem 1999;5:169-72. DOI PubMed
52. Mendonça A, Carvalho-Pereira J, Franco-Duarte R, Sampaio P. Correction to: optimization of a quantitative PCR methodology for
detection of Aspergillus spp. and Rhizopus arrhizus. Mol Diagn Ther 2022;26:527. DOI PubMed PMC
53. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007;449:804-
10. DOI PubMed
54. Stefanini I, Dapporto L, Legras JL, et al. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad
Sci U S A 2012;109:13398-403. DOI PubMed PMC
55. Abdelrhman KF, Bacci G, Mancusi C, Mengoni A, Serena F, Ugolini A. A first insight into the gut microbiota of the sea turtle caretta
caretta. Front Microbiol 2016;7:1060. DOI PubMed PMC
56. Abdelrhman KF, Bacci G, Marras B, et al. Exploring the bacterial gut microbiota of supralittoral talitrid amphipods. Res Microbiol
2017;168:74-84. DOI
57. Ramazzotti M, Bacci G. Chapter 5 - 16S rRNA-based taxonomy profiling in the metagenomics era. In: Nagarajan M, editor.
Metagenomics. Academic Press; 2018. p. 103-19. DOI
58. Arranz V, Pearman WS, Aguirre JD, Liggins L. MARES, a replicable pipeline and curated reference database for marine eukaryote
metabarcoding. Sci Data 2020;7:209. DOI PubMed PMC
59. Frøslev TG, Kjøller R, Bruun HH, et al. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity
estimates. Nat Commun 2017;8:1188. DOI PubMed PMC
60. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina
amplicon data. Nat Methods 2016;13:581-3. DOI PubMed PMC
61. Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and
identification of fungi. Nat Rev Microbiol 2019;17:95-109. DOI PubMed
62. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH. Intraspecific ITS variability in the kingdom fungi as expressed in
the international sequence databases and its implications for molecular species identification. Evol Bioinform Online 2008;4:193-201.
DOI PubMed PMC
63. Ali NABM, Mac Aogáin M, Morales RF, Tiew PY, Chotirmall SH. Optimisation and benchmarking of targeted amplicon sequencing
for mycobiome analysis of respiratory specimens. Int J Mol Sci 2019;20:4991. DOI PubMed PMC
64. Bokulich NA, Mills DA. Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-
throughput profiling of fungal communities. Appl Environ Microbiol 2013;79:2519-26. DOI PubMed PMC
65. Tedersoo L, Lindahl B. Fungal identification biases in microbiome projects. Environ Microbiol Rep 2016;8:774-9. DOI PubMed
66. Franco-Duarte R, Fernandes I, Gulis V, Cássio F, Pascoal C. ITS rDNA barcodes clarify molecular diversity of aquatic
hyphomycetes. Microorganisms 2022;10:1569. DOI PubMed PMC
67. Bradshaw MJ, Aime MC, Rokas A, et al. Extensive intragenomic variation in the internal transcribed spacer region of fungi. iScience
2023;26:107317. DOI PubMed PMC
68. 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;10:189. DOI PubMed PMC
69. Mbareche H, Veillette M, Bilodeau G, Duchaine C. Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based
sequencing of bioaerosols. PeerJ 2020;8:e8523. DOI PubMed PMC
70. Hoggard M, Vesty A, Wong G, et al. Characterizing the human mycobiota: a comparison of small subunit rRNA, ITS1, ITS2, and
large subunit rRNA genomic targets. Front Microbiol 2018;9:2208. DOI PubMed PMC
71. Peterson SW, Kurtzman CP. Ribosomal RNA sequence divergence among sibling species of yeasts. Syst Appl Microbiol
1991;14:124-9. DOI
72. Kurtzman CP, Robnett CJ. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S)
ribosomal DNA partial sequences. Antonie Van Leeuwenhoek 1998;73:331-71. DOI PubMed
73. Tang J, Iliev ID, Brown J, Underhill DM, Funari VA. Mycobiome: approaches to analysis of intestinal fungi. J Immunol Methods
2015;421:112-21. DOI PubMed PMC
74. Filippis F, Laiola M, Blaiotta G, Ercolini D. Different amplicon targets for sequencing-based studies of fungal diversity. Appl