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 …

[HTML][HTML] Harnessing the plant microbiome to promote the growth of agricultural crops

J Zhang, J Cook, JT Nearing, J Zhang… - Microbiological …, 2021 - Elsevier
The rhizosphere microbiome is composed of diverse microbial organisms, including
archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a …

The oral microbiome–an update for oral healthcare professionals

M Kilian, ILC Chapple, M Hannig, PD Marsh… - British dental …, 2016 - nature.com
For millions of years, our resident microbes have coevolved and coexisted with us in a
mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome …

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

R Ranjan, A Rani, A Metwally, HS McGee… - … and biophysical research …, 2016 - Elsevier
The human microbiome has emerged as a major player in regulating human health and
disease. Translational studies of the microbiome have the potential to indicate clinical …

[HTML][HTML] Human genetics shape the gut microbiome

JK Goodrich, JL Waters, AC Poole, JL Sutter, O Koren… - Cell, 2014 - cell.com
Host genetics and the gut microbiome can both influence metabolic phenotypes. However,
whether host genetic variation shapes the gut microbiome and interacts with it to affect host …

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 …

Gut microbiota from twins discordant for obesity modulate metabolism in mice

VK Ridaura, JJ Faith, FE Rey, J Cheng, AE Duncan… - Science, 2013 - science.org
Introduction Establishing whether specific structural and functional configurations of a
human gut microbiota are causally related to a given physiologic or disease phenotype is …

The human microbiome: at the interface of health and disease

I Cho, MJ Blaser - Nature Reviews Genetics, 2012 - nature.com
Interest in the role of the microbiome in human health has burgeoned over the past decade
with the advent of new technologies for interrogating complex microbial communities. The …

Defining the human microbiome

LK Ursell, JL Metcalf, LW Parfrey, R Knight - Nutrition reviews, 2012 - academic.oup.com
Rapidly develo** sequencing methods and analytical techniques are enhancing our
ability to understand the human microbiome, and, indeed, how the microbiome and its …

Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents

C Hoffmann, S Dollive, S Grunberg, J Chen, H Li… - PloS one, 2013 - journals.plos.org
Diet influences health as a source of nutrients and toxins, and by sha** the composition of
resident microbial populations. Previous studies have begun to map out associations …