Current challenges and best-practice protocols for microbiome analysis

R Bharti, DG Grimm - Briefings in bioinformatics, 2021 - academic.oup.com
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …

Tara Oceans: towards global ocean ecosystems biology

S Sunagawa, SG Acinas, P Bork, C Bowler… - Nature Reviews …, 2020 - nature.com
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate
change, is crucial. Here, we review the work of Tara Oceans, an international …

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 …

Gut microbial carbohydrate metabolism contributes to insulin resistance

T Takeuchi, T Kubota, Y Nakanishi, H Tsugawa… - Nature, 2023 - nature.com
Insulin resistance is the primary pathophysiology underlying metabolic syndrome and type 2
diabetes,. Previous metagenomic studies have described the characteristics of gut …

Unravelling the collateral damage of antibiotics on gut bacteria

L Maier, CV Goemans, J Wirbel, M Kuhn, C Eberl… - Nature, 2021 - nature.com
Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the
composition of gut microbiota and causing dysbiosis and disease. Despite this well-known …

[HTML][HTML] A faecal microbiota signature with high specificity for pancreatic cancer

E Kartal, TSB Schmidt, E Molina-Montes… - Gut, 2022 - gut.bmj.com
Background Recent evidence suggests a role for the microbiome in pancreatic ductal
adenocarcinoma (PDAC) aetiology and progression. Objective To explore the faecal and …

Expanding known viral diversity in the healthy infant gut

SA Shah, L Deng, J Thorsen, AG Pedersen… - Nature …, 2023 - nature.com
The gut microbiome is shaped through infancy and impacts the maturation of the immune
system, thus protecting against chronic disease later in life. Phages, or viruses that infect …

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

J Wirbel, PT Pyl, E Kartal, K Zych, A Kashani… - Nature medicine, 2019 - nature.com
Association studies have linked microbiome alterations with many human diseases.
However, they have not always reported consistent results, thereby necessitating cross …

[HTML][HTML] Biosynthetic potential of the global ocean microbiome

L Paoli, HJ Ruscheweyh, CC Forneris, F Hubrich… - Nature, 2022 - nature.com
Natural microbial communities are phylogenetically and metabolically diverse. In addition to
underexplored organismal groups, this diversity encompasses a rich discovery potential for …

Towards the biogeography of prokaryotic genes

LP Coelho, R Alves, ÁR Del Río, PN Myers… - Nature, 2022 - nature.com
Microbial genes encode the majority of the functional repertoire of life on earth. However,
despite increasing efforts in metagenomic sequencing of various habitats,–, little is known …