A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

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 …

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 …

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 …

Machine learning for microbiologists

F Asnicar, AM Thomas, A Passerini… - Nature Reviews …, 2024 - nature.com
Abstract Machine learning is increasingly important in microbiology where it is used for tasks
such as predicting antibiotic resistance and associating human microbiome features with …

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

S Pan, C Zhu, XM Zhao, LP Coelho - Nature communications, 2022 - nature.com
Metagenomic binning is the step in building metagenome-assembled genomes (MAGs)
when sequences predicted to originate from the same genome are automatically grouped …

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

C Chen, Y Zhou, H Fu, X Xiong, S Fang, H Jiang… - Nature …, 2021 - nature.com
Gut microbiota plays an important role in pig health and production. Still, availability of
sequenced genomes and functional information for most pig gut microbes remains limited …

Mucins and the microbiome

GC Hansson - Annual review of biochemistry, 2020 - annualreviews.org
Generating the barriers that protect our inner surfaces from bacteria and other challenges
requires large glycoproteins called mucins. These come in two types, gel-forming and …

Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman… - Nature …, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …