Microbial community profiling of human saliva using shotgun metagenomic sequencing.
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.
CosmosID, College Park, Maryland, United States of America; Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America.
Nur A
NA
Hasan
Battelle, Columbus, Ohio, United States of America.
Brian A
BA
Young
Battelle, Columbus, Ohio, United States of America.
Angela T
AT
Minard-Smith
CosmosID, College Park, Maryland, United States of America.
Kelly
K
Saeed
CosmosID, College Park, Maryland, United States of America.
Huai
H
Li
Battelle, Columbus, Ohio, United States of America.
Esley M
EM
Heizer
Battelle, Columbus, Ohio, United States of America.
Nancy J
NJ
McMillan
CosmosID, College Park, Maryland, United States of America.
Richard
R
Isom
CosmosID, College Park, Maryland, United States of America.
Abdul Shakur
AS
Abdullah
Battelle, Columbus, Ohio, United States of America.
Daniel M
DM
Bornman
Battelle, Columbus, Ohio, United States of America.
Seth A
SA
Faith
CosmosID, College Park, Maryland, United States of America; Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America.
Seon Young
SY
Choi
Battelle, Columbus, Ohio, United States of America.
Michael L
ML
Dickens
CosmosID, College Park, Maryland, United States of America; Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America.
Thomas A
TA
Cebula
CosmosID, College Park, Maryland, United States of America; Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America; University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
Rita R
RR
Colwell
D000328:Adult; D005260:Female; D006801:Humans; D008297:Male; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D012463:Saliva / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods*