Perspectives and benefits of high-throughput long-read sequencing in microbial ecology

L Tedersoo, M Albertsen, S Anslan… - Applied and …, 2021‏ - journals.asm.org
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important
insights into microbial ecology and function. Yet, in many instances short-read HTS …

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 …

Revisions to the classification, nomenclature, and diversity of eukaryotes

SM Adl, D Bass, CE Lane, J Lukeš… - Journal of Eukaryotic …, 2019‏ - Wiley Online Library
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk.
Microbiol. 59 (5)] and retains an emphasis on protists. Changes since have improved the …

Warming reshaped the microbial hierarchical interactions

Y Zhou, B Sun, B ** of
microbial diversity and modified microbial interactions. Here, we examined the effects of 5 …

An introduction to next generation sequencing bioinformatic analysis in gut microbiome studies

B Gao, L Chi, Y Zhu, X Shi, P Tu, B Li, J Yin, N Gao… - Biomolecules, 2021‏ - mdpi.com
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than
the human host and plays an essential role in human health and disease pathogenesis …

Functional trait‐based approaches as a common framework for aquatic ecologists

S Martini, F Larras, A Boyé, E Faure… - Limnology and …, 2021‏ - Wiley Online Library
Aquatic ecologists face challenges in identifying the general rules of the functioning of
ecosystems. A common framework, including freshwater, marine, benthic, and pelagic …

Diat. barcode, an open-access curated barcode library for diatoms

F Rimet, E Gusev, M Kahlert, MG Kelly… - Scientific Reports, 2019‏ - nature.com
Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton
and which make a major contribution to the productivity of oceans and freshwaters. They …

Perspectives from ten years of protist studies by high‐throughput metabarcoding

L Santoferrara, F Burki, S Filker… - Journal of Eukaryotic …, 2020‏ - Wiley Online Library
During the last decade, high‐throughput metabarcoding became routine for analyzing
protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists …

Does intraspecific variation in rDNA copy number affect analysis of microbial communities?

A Lavrinienko, T Jernfors, JJ Koskimäki, AM Pirttilä… - Trends in …, 2021‏ - cell.com
Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to
profile microbial communities. However, the rDNA is dynamic and can exhibit substantial …

Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

FW Lefler, DE Berthold… - Journal of …, 2023‏ - Wiley Online Library
Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe,
playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and …