A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

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.

The role of metal binding in the function of the human salivary antimicrobial peptide histatin-5

“…By comparison, little is known about the potentially harmonious relationship between histatins and microbes that normally colonise healthy oral and oropharyngeal tissues. We showed here that Hst5 does not kill oral streptococci, which represent the most abundant microbial taxon in healthy human oral cavity [73][74][75][76] and oropharynx 77 . This lack of an anti-streptococcal effect contrasts with the potent antibacterial effects of Hst5 against ESKAPE pathogens 11 , although the latter are worth revisiting, to verify that they are not associated with artificial experimental conditions that do not mimic the saliva.…”

“…Streptococci do not use nutrient Cu, and so these bacteria will only benefit from the action of histatins as Cu-buffering agents. This idea is not inconsistent with the relative dominance of Streptococcus species in the human oral cavity 74,75 and oropharynx 77 . However, other resident oral microbes, such as commensal Neisseria species and even C. albicans, need nutrient Cu for respiration and energy production.…”

“…does not kill oral streptococci, which represent the most abundant taxon in a healthy oral cavity [71][72][73][74] and oropharynx [75]. This lack of an anti-streptococcal effect contrasts with the potent antibacterial effects of Hst5 against several ESKAPE pathogens [12], although the latter are worth revisiting to ensure that they are not associated with artificial experimental conditions that do not mimic the saliva.…”

The Effects of Smoking on Human Pharynx Microbiota Composition and Stability

“…These included Streptococcus mitis , Streptococcus salivarius , and Streptococcus parasanguinis , which were also the most dominant OTUs in the healthy samples from nonsmoking participants. Further details on the microbial composition of nonsmokers can be found in our previous publication ( 42 ). For plots showing the temporal changes in the community composition for all participants over the course of the study period at the phylum, family, and OTU levels, refer to Fig.…”

Salivary Antimicrobial Peptide Histatin-5 Does Not Display Zn(II)-Dependent or -Independent Activity against Streptococci

“…The healthy human oral cavity and oropharynx are colonized by a mixture of microbial species, with Streptococcus as the most abundant taxon. − Some species, such as S. gordonii and S.…”