Best practices in metabarcoding of fungi: From experimental design to results

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

NATURVETENSKAP Biologi Biokemi och molekylärbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology hsv//eng
NATURVETENSKAP Biologi Ekologi hsv//swe
NATURAL SCIENCES Biological Sciences Ecology hsv//eng
biodiversity
bioinformatics
community ecology
experiment setup
molecular identification
statistical analyses
internal transcribed spacer
sequence-based identification
ribosomal-rna
ectomycorrhizal fungi
microbial communities
bayesian
classifier
global change
its2 region
data sets
soil DNA
Biochemistry & Molecular Biology
Environmental Sciences & Ecology
Evolutionary Biology

Bahram, M.Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för ekologi,Department of Ecology,University of Tartu (författare)
Zinger, L. (författare)
Nilsson, R. Henrik,1976Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xnihen (författare)
Kennedy, P. G. (författare)
Yang, T. (författare)
Anslan, S. (författare)
Mikryukov, V. (författare)
Sveriges lantbruksuniversitetInstitutionen för ekologi (creator_code:org_t)
Sveriges lantbruksuniversitet

Av författaren/redakt...: Tedersoo, L.; Bahram, M.; Zinger, L.; Nilsson, R. Henr ...; Kennedy, P. G.; Yang, T.; visa fler...; Anslan, S.; Mikryukov, V.; visa färre...

Om ämnet

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.