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 …

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

AE Pérez-Cobas, L Gomez-Valero… - Microbial …, 2020 - microbiologyresearch.org
Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …

Commensal fungi in health and disease

JJ Limon, JH Skalski, DM Underhill - Cell host & microbe, 2017 - cell.com
Fungi are increasingly being recognized as common members of the microbiomes found on
nearly all mucosal surfaces, and interest is growing in understanding how these organisms …

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 …

Crossing kingdoms: how the mycobiota and fungal-bacterial interactions impact host health and disease

W Santus, JR Devlin, J Behnsen - Infection and Immunity, 2021 - Am Soc Microbiol
The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria.
These surfaces and the luminal compartments they form indeed predominantly harbor …

First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin

K Koskinen, MR Pausan, AK Perras, M Beck, C Bang… - MBio, 2017 - Am Soc Microbiol
Human-associated archaea remain understudied in the field of microbiome research,
although in particular methanogenic archaea were found to be regular commensals of the …

Mycobiome in the gut: a multiperspective review

VK Chin, VC Yong, PP Chong… - Mediators of …, 2020 - Wiley Online Library
Human gut is home to a diverse and complex microbial ecosystem encompassing bacteria,
viruses, parasites, fungi, and other microorganisms that have an undisputable role in …

[HTML][HTML] What is new and relevant for sequencing-based microbiome research? A mini-review

AM Fricker, D Podlesny, WF Fricke - Journal of advanced research, 2019 - Elsevier
Microbiome research has transformed the scientific landscape, as reflected by the
exponential increase in microbiome-related publications from many different disciplines …

The impact of DNA extraction methods on stool bacterial and fungal microbiota community recovery

K Fiedorová, M Radvanský, E Němcová… - Frontiers in …, 2019 - frontiersin.org
Our understanding of human gut microbiota in health and disease depends on accurate and
reproducible microbial data acquisition. The critical step in this process is to apply an …