Abstract
Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell’s neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.’s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher’s exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or ‘phenotype’ of community assembly), it does not seem to cause the ‘mutation’ of the ‘genotype” (mechanism) of community assembly. We argue that the ‘phenotypic’ changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.
Highlights
The oral cavity is a major portal for food and air with countless microbes exchanging between human body and the environment
Both methods performed well, and Etienne formula was chosen to test the neutrality in this study, given the latter has an advantage for considering dispersal limitation
By comparing Ewens and Etienne formulae, performing the neutrality test with Etienne formula, and conducting further tests with multiple testing correction and Fisher’s exact probability test, as well as comparing the fundamental biodiversity number among three treatments, we obtained the following conclusions and postulations for further study. (i) While deterministic niche forces are predominant in driving the oral community assembly, the role of stochastic neutral dynamics cannot be ignored (in our case, approximately 23% (14 out of 61) of community samples satisfied with the neutral theory). (ii) Periodontitis does not seem to alter the assembly mechanism of oral microbial communities. (iii) periodontitis may change community composition or diversity of the oral microbiome
Summary
The oral cavity is a major portal for food and air with countless microbes exchanging between human body and the environment. At least 6 billions bacteria representing 700 species have been detected in human oral cavity [1]. Several oral infectious diseases such as caries, periodontitis, and endodontic infections are associated with oral microbiome. The oral cavity hosts far more symbiotic bacteria that play a fundamental role in maintaining the oral health. Oral microbes exist in the form of microbial community, and oral cavity is an ecosystem. The stability and dynamics of this ecosystem have far reaching influences on our oral health and diseases. The oral microbial community is subjected to frequent daily physical and biochemical disturbances, but it can maintain its long-term stability in healthy individuals [2]
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