Current understanding of the human microbiome

JA Gilbert, MJ Blaser, JG Caporaso, JK Jansson… - Nature medicine, 2018 - nature.com
Our understanding of the link between the human microbiome and disease, including
obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding …

The progress of gut microbiome research related to brain disorders

S Zhu, Y Jiang, K Xu, M Cui, W Ye, G Zhao… - Journal of …, 2020 - Springer
There is increasing evidence showing that the dynamic changes in the gut microbiota can
alter brain physiology and behavior. Cognition was originally thought to be regulated only by …

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 …

Characterization of the gut microbiome using 16S or shotgun metagenomics

J Jovel, J Patterson, W Wang, N Hotte… - Frontiers in …, 2016 - frontiersin.org
The advent of next generation sequencing (NGS) has enabled investigations of the gut
microbiome with unprecedented resolution and throughput. This has stimulated the …

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

MGI Langille, J Zaneveld, JG Caporaso… - Nature …, 2013 - nature.com
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of
microbial communities but does not provide direct evidence of a community's functional …

[HTML][HTML] Monitoring antibiotic resistance genes in wastewater environments: the challenges of filling a gap in the One-Health cycle

A Miłobedzka, C Ferreira, I Vaz-Moreira… - Journal of Hazardous …, 2022 - Elsevier
Antibiotic resistance (AR) is a global problem requiring international cooperation and
coordinated action. Global monitoring must rely on methods available and comparable …

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

PJ McMurdie, S Holmes - PloS one, 2013 - journals.plos.org
Background The analysis of microbial communities through DNA sequencing brings many
challenges: the integration of different types of data with methods from ecology, genetics …

The ecologist's field guide to sequence‐based identification of biodiversity

S Creer, K Deiner, S Frey, D Porazinska… - Methods in ecology …, 2016 - Wiley Online Library
The past 100 years of ecological research has seen substantial progress in understanding
the natural world and likely effects of change, whether natural or anthropogenic. Traditional …

[HTML][HTML] Conducting a microbiome study

JK Goodrich, SC Di Rienzi, AC Poole, O Koren… - Cell, 2014 - cell.com
Human microbiome research is an actively develo** area of inquiry, with ramifications for
our lifestyles, our interactions with microbes, and how we treat disease. Advances depend …

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

N Fierer, JW Leff, BJ Adams, UN Nielsen… - Proceedings of the …, 2012 - pnas.org
For centuries ecologists have studied how the diversity and functional traits of plant and
animal communities vary across biomes. In contrast, we have only just begun exploring …