A longitudinal study of the human oropharynx microbiota over time reveals a common core and significant variations with self-reported disease

Bach, L. L. , Ram, A., Ijaz, U. Z. , Evans, T. J. and Lindström, J. (2021) A longitudinal study of the human oropharynx microbiota over time reveals a common core and significant variations with self-reported disease. Frontiers in Microbiology, 11, 573969. (doi: 10.3389/fmicb.2020.573969) (PMID:33552004) (PMCID:PMC7861042)

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Abstract

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean=204.55 OTUs, sd=35.64), evenness (19.83, sd=9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd=0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modelling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Evans, Professor Tom and Lindstrom, Dr Jan and Bach, Dr Lydia and Ijaz, Dr Umer
Authors: Bach, L. L., Ram, A., Ijaz, U. Z., Evans, T. J., and Lindström, J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:Frontiers in Microbiology
Publisher:Frontiers Media
ISSN:1664-302X
ISSN (Online):1664-302X
Copyright Holders:Copyright © 2021 Bach, Ram, Ijaz, Evans and Lindström
First Published:First published in Frontiers in Microbiology 11: 573969
Publisher Policy:Reproduced under a Creative Commons License
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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
190536Integrated Health - Polyomics and Systems Biomedicine (ISSF Bid)Anna DominiczakWellcome Trust (WELLCOTR)097821/Z/11/ZInstitute of Cardiovascular & Medical Sciences
301229Evolutionary ecology and dynamics of pharyngeal microbial communities in humansJan LindstromLeverhulme Trust (LEVERHUL)RPG-2017-279Institute of Biodiversity, Animal Health and Comparative Medicine