Dr. Jessica Mark Welch's research group investigates the organizational structure and functional roles of the human oral microbiome, focusing on how these complex bacterial communities impact overall health. Utilizing a dual approach of advanced imaging and DNA sequencing, her team co-developed CLASI-FISH (Combinatorial Labeling and Spectral Imaging – Fluorescence In Situ Hybridization) to visualize multiple bacterial species simultaneously, leading to the discovery of highly structured consortia like "hedgehogs" in dental plaque and "bacterial high-rises" on the tongue. On the genomic front, they employ bioinformatics tools like Anvi'o to construct pangenomes and metapangenomes, mapping the genetic capabilities and distribution of bacteria across the mouth. Dr. Mark Welch also co-curates the Human Oral Microbiome Database (HOMD) and works to cultivate and sequence currently uncultivable oral species, aiming to ultimately manipulate these communities for therapeutic benefit.
Summarizing the Research of Jessica Mark Welch, PhD
Research Focus (Introduction): The core goal is to understand the structure and function of the hundreds of bacterial species comprising the oral microbiome, recognizing its broad impact on both oral and systemic human health.
Imaging Methodology (CLASI-FISH): Dr. Mark Welch and Gary Borisy developed CLASI-FISH (Combinatorial Labeling and Spectral Imaging – Fluorescence In Situ Hybridization) to image and identify multiple types of bacterial cells simultaneously at the genus or species level.
Key Imaging Discoveries (Oral Architecture): Using CLASI-FISH, the team discovered highly organized, complex bacterial structures:
"Hedgehogs": Spiny, characteristic clusters of bacterial filaments found in dental plaque samples.
"Bacterial High-Rises": Complex microbial "apartment buildings" or consortia found on the surface of the tongue.
Genomic Methodology (Pangenomes/Metapangenomes): The research utilizes DNA sequencing and the Anvi’o software environment to construct pangenomes (distinguishing "core" genes present in all members from "accessory" genes) and metapangenomes (comparing pangenomes with metagenome data from different individuals and oral sites).
Key Takeaway (Functional Goal): The metapangenome analysis aims to understand bacterial localization—why different species live where they do—and how to manipulate the community to encourage health-promoting bacteria.
Database Contribution (HOMD): Dr. Mark Welch co-curates the Human Oral Microbiome Database (HOMD) with colleagues, providing researchers with high-quality, curated information about oral bacteria, their genomes, and their distribution.
Future Work (Uncultivables): A current focus is sequencing the genomes of currently "uncultivable" oral bacterial species to significantly broaden and deepen the available genomic information for the oral microbiome community.