Title: Ecology and evolution within the oral microbiome
Abstract: Bacteria inhabit every known ecosystem, from deep-sea hydrothermal vents to plant surfaces. The human body represents one such microbially-dominated ecosystem with the identity and function of human-associated microbiota being intimately connected with human health. However, few specifics are known about the processes governing the distribution and composition of host-associated microbial communities, challenging efforts to alter or maintain certain host-associated bacterial communities. Thus, studying the ecology and evolution of human-associated bacteria is critical both for improving human health and more broadly for better understanding microbial community organization and function. In this dissertation, I use the healthy human oral microbiome as a model system to investigate the processes shaping bacterial populations from an ecological and evolutionary perspective. Altogether, these investigations reveal genomic signatures indicative of fine-scale adaptation to diverse oral niches.
In my first chapter, I employ a metapangenomic approach to combine Human Microbiome Project (HMP) metagenomes with pangenomes from public genomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes revealed distinct genomic groups based on shared genome content. H. parainfluenzae genomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified genes encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup, suggesting a metabolic adaptation to the tongue habitat. For the genus Rothia, while most R. mucilaginosa were restricted to the tongue as expected, two genomes represented a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, I identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous. These findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results also illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.
In my second chapter, I address the process of how bacteria adapt over time, namely whether adaptation occurs principally by gene-centric or genome-centric processes. I sequenced 81 metagenomes, shotgun sequencing of total community DNA, from the tongues of 17 healthy volunteers at four to seven timepoints obtained over intervals of days to weeks. I obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes for 55 bacterial genera. Decomposing MAGs by metagenomic nucleotide variants revealed MAG-defined bacterial populations were composed of up to five detectable subpopulations. Bacterial subpopulations were generally stable over time, yet some swept from low abundance to dominance over a period of days, a pattern suggestive of genome-centric adaptation. At the gene level, the vast majority of genes in each MAG were tightly coupled over time based on their frequency in the metagenomes of different mouths. Some genes were uncoupled but their frequencies did not change directionally, nor did nonsynonymous codon variants become fixed within these uncoupled genes, suggesting transient effects. Altogether, these results demonstrate that both gene- and genome-wide processes occur on daily timescales but likely with different ecological ramifications. I suggest a model where genome-wide selection of ecotypes is the dominant mode of adaptation with short-term changes in gene frequency also occurring within the populations.
My third chapter examines individuality in the tongue microbiome from a genome-centric perspective to reveal the genomic and functional differences of bacterial populations occurring in only a single mouth. The v4 region of the 16S rRNA gene was sequenced from all 81 samples obtained in Chapter 2 and analyzed to obtain amplicon sequence variants (ASVs) for 50 bacterial genera. Sixteen out of 287 ASVs were found to be endemic, i.e., they were abundant in a single mouth but absent elsewhere. Linking MAG and haplotype data revealed that the endemic ASVs represent genetically distinct populations, differing in tens to hundreds of genes encoding diverse functions related to mobile elements, defense, carbon metabolism, and the cell envelope. Approximately 1% of the entire set of almost 700,000 genes were individual-specific, and their predicted functions revealed phage- and defense-related genes were enriched relative to genes not restricted to a single mouth. These genomic and functional differences suggest individual-specific populations occupy similar but distinct niches across individuals.
Committee: Colleen Cavanaugh (Advisor), Otto Cordero (MIT CEE), Peter Girguis (Chair), Naomi Pierce