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 …

Prokaryotic taxonomy and nomenclature in the age of big sequence data

P Hugenholtz, M Chuvochina, A Oren… - The ISME …, 2021‏ - academic.oup.com
The classification of life forms into a hierarchical system (taxonomy) and the application of
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …

Greengenes2 unifies microbial data in a single reference tree

D McDonald, Y Jiang, M Balaban, K Cantrell… - Nature …, 2024‏ - nature.com
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …

Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

R Riesco, ME Trujillo - International Journal of Systematic …, 2024‏ - microbiologyresearch.org
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary
classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics …

The nature of the last universal common ancestor and its impact on the early Earth system

ERR Moody, S Álvarez-Carretero… - Nature Ecology & …, 2024‏ - nature.com
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth
system have been the subject of vigorous debate across diverse disciplines, often based on …

Insulin-regulated serine and lipid metabolism drive peripheral neuropathy

MK Handzlik, JM Gengatharan, KE Frizzi… - Nature, 2023‏ - nature.com
Diabetes represents a spectrum of disease in which metabolic dysfunction damages
multiple organ systems including liver, kidneys and peripheral nerves,. Although the onset …

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

X Zhou, R Baumann, X Gao, M Mendoza, S Singh… - Cell, 2022‏ - cell.com
Changes in gut microbiota have been associated with several diseases. Here, the
International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022‏ - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

RH Mills, PS Dulai, Y Vázquez-Baeza, C Sauceda… - Nature …, 2022‏ - nature.com
Ulcerative colitis (UC) is driven by disruptions in host–microbiota homoeostasis, but current
treatments exclusively target host inflammatory pathways. To understand how host …

A genomic catalog of Earth's microbiomes

S Nayfach, S Roux, R Seshadri, D Udwary… - Nature …, 2021‏ - nature.com
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …