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

L Tedersoo, M Bahram, L Zinger, RH Nilsson… - Molecular …, 2022 - Wiley Online Library
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 …

Mycobiome diversity: high-throughput sequencing and identification of fungi

RH Nilsson, S Anslan, M Bahram… - Nature Reviews …, 2019 - nature.com
Fungi are major ecological players in both terrestrial and aquatic environments by cycling
organic matter and channelling nutrients across trophic levels. High-throughput sequencing …

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

R Lücking, MC Aime, B Robbertse, AN Miller… - IMA fungus, 2020 - Springer
True fungi (Fungi) and fungus-like organisms (eg Mycetozoa, Oomycota) constitute the
second largest group of organisms based on global richness estimates, with around 3 …

Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity …

M Chiarello, M McCauley, S Villéger, CR Jackson - PloS one, 2022 - journals.plos.org
Advances in the analysis of amplicon sequence datasets have introduced a methodological
shift in how research teams investigate microbial biodiversity, away from sequence identity …

[HTML][HTML] Airborne environmental DNA for terrestrial vertebrate community monitoring

C Lynggaard, MF Bertelsen, CV Jensen, MS Johnson… - Current Biology, 2022 - cell.com
Biodiversity monitoring at the community scale is a critical element of assessing and
studying species distributions, ecology, diversity, and movements, and it is key to …

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

BJ Callahan, J Wong, C Heiner, S Oh… - Nucleic acids …, 2019 - academic.oup.com
Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S
rRNA gene fragments is widely used to profile microbial communities. New long-read …

Diversity and ecology of protists revealed by metabarcoding

F Burki, MM Sandin, M Jamy - Current Biology, 2021 - cell.com
Protists are the dominant eukaryotes in the biosphere where they play key functional roles.
While protists have been studied for over a century, it is the high-throughput sequencing of …

[HTML][HTML] ITS alchemy: on the use of ITS as a DNA marker in fungal ecology

H Kauserud - Fungal Ecology, 2023 - Elsevier
High throughput sequencing of PCR amplicons derived from environmental DNA (aka DNA
metabarcoding) has become an integral part of fungal ecology, enabling in-depth …

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

C Pauvert, M Buée, V Laval, V Edel-Hermann… - Fungal Ecology, 2019 - Elsevier
Fungal communities associated with plants and soil influence plant fitness and ecosystem
functioning. They are frequently studied by metabarcoding approaches targeting the …

Promises and pitfalls of using high‐throughput sequencing for diet analysis

A Alberdi, O Aizpurua, K Bohmann… - Molecular ecology …, 2019 - Wiley Online Library
The application of high‐throughput sequencing‐based approaches to DNA extracted from
environmental samples such as gut contents and faeces has become a popular tool for …