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 modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.
Highlights
About half of the approximately 60 trillion cells found within our bodies are of human origin, the rest comprises bacterial cells known as the microbiota (Sender et al, 2016)
Serratia is commonly reported to be associated with a variety of human infections (Elston and Magnuson, 1965). These findings are supported by the non-metric multidimensional scaling plot (NMDS) plot, with the sample obtained in week 14 clustering away from the main centroid, showing differences in community composition associated with increased abundance of OTU 14 (Figure 3C)
While the human oral microbiome has been extensively studied, less attention has been paid to the oropharyngeal microbiome and, to our knowledge, replicated time series data from a group of generally healthy participants has not been available until now
Summary
About half of the approximately 60 trillion cells found within our bodies are of human origin, the rest comprises bacterial cells known as the microbiota (Sender et al, 2016) These microbial communities inhabit a wide number of habitats on the human body, such as the oral cavity, skin, vagina, or mucosal gut surface, providing important functions such as resisting pathogen invasion, regulating metabolism, and supporting the host’s immune system (Dethlefsen et al, 2007; Parfrey et al, 2011). It has become apparent that, rather than being caused by single organisms, many of these infections are linked to communities of organisms, often occurring in complex biofilms (Hall-Stoodley et al, 2004; Jenkinson and Lamont, 2005; Bai et al, 2019) This has resulted in a shift of focus away from single species to considering that increasing understanding of human health and disease requires the characterization of the microbial community. We set out to define the general microbial community and phylogeny of the most prevalent taxa in the human oropharynx, its temporal dynamics and variability in community structure and to describe the core microbiome shared across baseline-healthy participants
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