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 …

Disentangling host–microbiota complexity through hologenomics

A Alberdi, SB Andersen, MT Limborg, RR Dunn… - Nature Reviews …, 2022 - nature.com
Research on animal–microbiota interactions has become a central topic in biological
sciences because of its relevance to basic eco-evolutionary processes and applied …

The person-to-person transmission landscape of the gut and oral microbiomes

M Valles-Colomer, A Blanco-Míguez, P Manghi… - Nature, 2023 - nature.com
The human microbiome is an integral component of the human body and a co-determinant
of several health conditions,. However, the extent to which interpersonal relations shape the …

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver… - Nature …, 2023 - nature.com
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

[HTML][HTML] Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation

A Iljazovic, U Roy, EJC Gálvez, TR Lesker, B Zhao… - Mucosal …, 2021 - Elsevier
Diverse microbial signatures within the intestinal microbiota have been associated with
intestinal and systemic inflammatory diseases, but whether these candidate microbes …

MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis

Y El Morr, M Fürstenheim, M Mestdagh… - Science …, 2024 - science.org
Intestinal inflammation shifts microbiota composition and metabolism. How the host monitors
and responds to such changes remains unclear. Here, we describe a protective mechanism …

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

C Chen, Y Zhou, H Fu, X **
BS Beresford-Jones, SC Forster, MD Stares, G Notley… - Cell host & …, 2022 - cell.com
Human health and disease have increasingly been shown to be impacted by the gut
microbiota, and mouse models are essential for investigating these effects. However, the …

Critical assessment of metagenome interpretation: the second round of challenges

F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker… - Nature …, 2022 - nature.com
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus
of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II …