Date of Award
Summer 2026
Language
English
Embargo Period
5-29-2027
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
College/School/Department
Department of Biological Sciences
Program
Biology
First Advisor
Alex Valm
Committee Members
Melinda Larsen, ChangHwan Lee, Claudia Marques
Keywords
Oral Biofilms, Microbial Ecology, Spatial Biology, Bioimage Analysis, Generative AI, Microscopy
Subject Categories
Biology | Microbiology
Abstract
The mechanisms that generate complex spatial architecture and high taxonomic diversity in oral biofilms, in the transition from health to disease, remain poorly understood. While modern sequencing-based methods provide high-resolution compositional data, they lack micron-scale spatial information that is critical for understanding structure-function relationships. This dissertation investigates the hypothesis that plaque-derived, multispecies coaggregates act as foundational agents of colonization, functioning as autonomous, self-contained units that stochastically seed this complex biogeography on nascent surfaces. To address this, a novel “dental plaque on a chip” model was developed to culture species-rich biofilms from human donors in a system amenable to high-resolution, multispectral imaging. By comparing biofilms initiated from intact versus enzymatically de-aggregated plaque, this work establishes that the physical integrity of these coaggregates is essential for the development of complex community structure. The disruption of aggregates diminished spatial heterogeneity and was linked to a disproportionate depletion of obligate anaerobes. Live-cell imaging demonstrated that these aggregates create and sustain protected, anoxic microenvironments, functioning as agentic units that transport a pre-formed, niche-protective architecture. The analytical demands of this research motivated the parallel development of MicroVisionAI, a system that generates ImageJ/Fiji macros from natural language aiming to democratize advanced bioimage analysis. This integrated body of work establishes a new model for oral biofilm assembly driven by agent-based nucleation and lays the groundwork for a novel diagnostic paradigm where the emergent architectural features of microbial communities serve as quantitative
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Lemus, Alex A., "Multispecies Aggregates as Foundational Agents of Emergent Multiscale Architecture in the Human Oral Microbiome" (2026). Electronic Theses & Dissertations (2024 - present). 488.
https://scholarsarchive.library.albany.edu/etd/488