10.5061/DRYAD.SN00Q
Lassalle, Florent
University College London
Spagnoletti, Matteo
University College London
Fumagalli, Matteo
University College London
Shaw, Liam
University College London
Dyble, Mark
University College London
University of Cambridge
Walker, Catherine
University College London
Thomas, Mark G.
University College London
Bamberg Migliano, Andrea
University College London
Balloux, Francois
University College London
Data from: Oral microbiomes from hunter-gatherers and traditional farmers
reveal shifts in commensal balance and pathogen load linked to diet
Dryad
dataset
2017
Metagenomics
hunter-gatherers
oral microbiome
2017-11-20T06:09:53Z
2017-11-20T06:09:53Z
en
https://doi.org/10.1111/mec.14435
2579962316 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Maladaptation to modern diets has been implicated in several chronic
disorders. Given the higher prevalence of disease such as dental caries
and chronic gum diseases in industrialized societies, we sought to
investigate the impact of different subsistence strategies on oral health
and physiology, as documented by the oral microbiome. To control for
confounding variables such as environment and host genetics, we sampled
saliva from three pairs of populations of hunter-gatherers and traditional
farmers living in close proximity in the Philippines. Deep shotgun
sequencing of salivary DNA generated high-coverage microbiomes along with
human genomes. Comparing these microbiomes with publicly available data
from individuals living on a Western diet revealed that abundance ratios
of core species were significantly correlated with subsistence strategy,
with hunter-gatherers and Westerners occupying either end of a gradient of
Neisseria against Haemophilus, and traditional farmers falling in between.
Species found preferentially in hunter-gatherers included microbes often
considered as oral pathogens, despite their hosts' apparent good oral
health. Discriminant analysis of gene functions revealed vitamin B5
autotrophy and urease-mediated pH regulation as candidate adaptations of
the microbiome to the hunter-gatherer and Western diets, respectively.
These results suggest that major transitions in diet selected for
different communities of commensals and likely played a role in the
emergence of modern oral pathogens.
Output of Phylosift (placement and summary files)Phylosift (Darling et
al., PeerJ, 2014) was run on sequencing read sets obtained using Illumina
technology on metagenomic DNA extracted from salivary samples of 33 human
individuals: 12 hunter-gatherers (HG) and 12 traditional farmers (TF) from
the Philippines and 9 Western individual controls (WC). Source metagenomic
read datasets are available at the ENA (www.ebi.ac.uk/ena): for HGs and
TFs (original data), under BioSample accessions ERS1202862-ERS1202885; for
WCs (previously published data): under BioSample accessions SRS013942,
SRS014468, SRS014692, SRS015055, SRS019120, SRS104275 and SRS147126, and
two other non-publicly available read data from BioProject
PRJNA231652.phylosift_results_datadryad.tar.gz
Philippines