301
Views
2
CrossRef citations to date
0
Altmetric
Technique

Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments

& ORCID Icon
Pages 571-577 | Received 06 Dec 2022, Accepted 14 Apr 2023, Published online: 17 May 2023

LITERATURE CITED

  • Abarenkov K, Zirk A, Piirmann T, Pöhönen R, Ivanov F, Nilsson RH, Kõljalg U. 2022a. UNITE general FASTA release for eukaryotes [Application/gzip]. UNITE Community. doi:10.15156/BIO/2483913.
  • Abarenkov K, Zirk A, Piirmann T, Pöhönen R, Ivanov F, Nilsson RH, Kõljalg U. 2022b. UNITE general FASTA release for Fungi [Application/gzip]. UNITE Community. doi:10.15156/BIO/2483911.
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389–402. doi:10.1093/nar/25.17.3389.
  • Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Tedersoo L, Bahram M. 2018. Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys. 39:29–40. doi:10.3897/mycokeys.39.28109.
  • Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10(1):189. doi:10.1186/1471-2180-10-189.
  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 13(7):581–583. doi:10.1038/nmeth.3869.
  • Cobian GM, Egan CP, Amend AS. 2019. Plant–microbe specificity varies as a function of elevation. ISME J. 13(11):2778–2788. doi:10.1038/s41396-019-0470-4.
  • Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. 2019. Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol. 10(11):1985–2001. doi:10.1111/2041-210X.13276.
  • Ettinger CL, Eisen JA. 2019. Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids. Front Microbiol. 10:2476. doi:10.3389/fmicb.2019.02476.
  • Ettinger CL, Vann LE, Eisen JA. 2021. Global diversity and biogeography of the Zostera marina mycobiome. Appl Environ Microbiol. 87(12):e02795–20. doi:10.1128/AEM.02795-20.
  • Hanson NW, Konwar KM, Hallam SJ. 2016. LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. Bioinformatics. 32(23):3535–3542. doi:10.1093/bioinformatics/btw400.
  • Ihrmark K, Bödeker ITM, Cruz-Martinez K, Friberg H, Kubartova A, Schenck J, Strid Y, Stenlid J, Brandström-Durling M, Clemmensen KE, et al. 2012. New primers to amplify the fungal ITS2 region – evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol. 82(3):666–677. doi:10.1111/j.1574-6941.2012.01437.x.
  • Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand A-C, Giraldo A, et al. 2015. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database—the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Med Mycol. 53(4):313–337. doi:10.1093/mmy/myv008.
  • Kodama Y, Shumway M, Leinonen R, on behalf of the International Nucleotide Sequence Database Collaboration. 2012. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 40(D1):D54–D56. doi:10.1093/nar/gkr854
  • McMurdie PJ, Holmes S. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 8(4):e61217. doi:10.1371/journal.pone.0061217.
  • Mims TS, Abdallah QA, Stewart JD, Watts SP, White CT, Rousselle TV, Gosain A, Bajwa A, Han JC, Willis KA, et al. 2021. The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet. Commun Biol. 4(1):281. doi:10.1038/s42003-021-01820-z.
  • Nawaz A, Purahong W, Lehmann R, Herrmann M, Totsche KU, Küsel K, Wubet T, Buscot F. 2018. First insights into the living groundwater mycobiome of the terrestrial biogeosphere. Water Res. 145:50–61. doi:10.1016/j.watres.2018.07.067.
  • Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, et al. 2019. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47(D1):D259–D264. doi:10.1093/nar/gky1022.
  • Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol. 188(1):223–241. doi:10.1111/j.1469-8137.2010.03334.x.
  • Peay KG, von Sperber C, Cardarelli E, Toju H, Francis CA, Chadwick OA, Vitousek PM. 2017. Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation–climate gradient. FEMS Microbiol Ecol. 93:5. doi:10.1093/femsec/fix045.
  • Rivers AR, Weber KC, Gardner TG, Liu S, Armstrong SD. 2018. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 7:1418. doi:10.12688/f1000research.15704.1.
  • Robinson K, Xiao Y, Johnson TJ, Chen B, Yang Q, Lyu W, Wang J, Fansler N, Becker S, Liu J, et al. 2020. Chicken intestinal mycobiome: initial characterization and its response to bacitracin methylene disalicylate. Appl Environ Microbiol. 86(13):e00304–20. doi:10.1128/AEM.00304-20.
  • Sawaswong V, Chanchaem P, Khamwut A, Praianantathavorn K, Kemthong T, Malaivijitnond S, Payungporn S. 2020. Oral-fecal mycobiome in wild and captive cynomolgus macaques (Macaca fascicularis). Fungal Genet Biol. 144:103468. doi:10.1016/j.fgb.2020.103468.
  • Tedersoo L, Anslan S. 2019. Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environ Microbiol Rep. 11(5):659–668. doi:10.1111/1758-2229.12776.
  • UNITE Community. 2019. UNITE general FASTA release for eukaryotes 2 (0.0.1) [dataset]. UNITE Community. doi:10.15156/BIO/786354.
  • Vannette RL, Leopold DR, Fukami T. 2016. Forest area and connectivity influence root-associated fungal communities in a fragmented landscape. Ecology. 97(9):2374–2383. doi:10.1002/ecy.1472.
  • Vasar M, Davison J, Sepp S-K, Öpik M, Moora M, Koorem K, Meng Y, Oja J, Akhmetzhanova AA, Al-Quraishy S, et al. 2021. Arbuscular mycorrhizal fungal communities in the soils of desert habitats. Microorganisms. 9(2):229. doi:10.3390/microorganisms9020229.
  • Wagner R, Montoya L, Gao C, Head JR, Remais J, Taylor JW. 2022. The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley. Mol Ecol. 31(19):4962–4978. doi:10.1111/mec.16640.
  • Wainwright BJ, Zahn GL, Spalding HL, Sherwood AR, Smith CM, Amend AS. 2017. Fungi associated with mesophotic macroalgae from the ’Au’au Channel, west Maui are differentiated by host and overlap terrestrial communities. PeerJ. 5:e3532. doi:10.7717/peerj.3532.
  • Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 73(16):5261–5267.
  • Yamauchi DH, Garcia Garces H, deTeixeira M, Rodrigues GFB, Ullmann LS, Garcia Garces A, Hebeler-Barbosa F, Bagagli E. 2021. Soil mycobiome is shaped by vegetation and microhabitats: a regional-scale study in Southeastern Brazil. J Fungi. 7(8):587. doi:10.3390/jof7080587.
  • Yang T, Tedersoo L, Lin X, Fitzpatrick MC, Jia Y, Liu X, Ni Y, Shi Y, Lu P, Zhu J, et al. 2020. Distinct fungal successional trajectories following wildfire between soil horizons in a cold‐temperate forest. New Phytol. 227(2):572–587. doi:10.1111/nph.16531.
  • Zahn G. 2022. gzahn/Fungal_Database_Comparison: manuscript draft 1 (v1.0.0). Zenodo. doi:10.5281/ZENODO.7406569.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.