Unveiling the prokaryotic diversity and multipartite symbiotic relationships in the termite gut microbiota

The gut of termites is a complex ecosystem that hosts diverse prokaryotic communities. Many Bacteria and Archaea within this ecosystem engage in ancient symbiotic relationships with cellulolytic flagellates, which are essential for lignocellulose digestion and take part in intricate metabolic interactions. Due to difficulties cultivating these microbes, my doctoral research focused on culture-independent approaches, including deep sequencing of gut sections and flagellate suspensions, as well as metagenomic studies and fluorescence in situ hybridization (FISH). I developed the latest version of the Dictyopteran gut microbiota reference Database (DictDb), which serves as an updated 16S rRNA gene reference for automated classification of 16S amplicons. Key findings from this research include a taxonomic revision of methanogenic Archaea colonizing arthropod guts, the analysis of the diversity and host colonization patterns of filamentous Lachnospiraceae (Arthromitus), and improved classification of termite-specific lineages. Notable taxa identified and expanded upon include the primarily flagellate-associated Azobacteroidaceae (Bacteroidota), the highly diverse homoacetogenic Breznakiellaceae (Spirochaetota), the cellulolytic Fibromonas (Fibrobacterota), the rare Elusimicrobium (Elusimicrobiota), the termite-specific Bifidobacteriaceae (Actinomycetota), and the putative energy parasites of the Opitutales (Verrucomicrobiota). Among the termite gut metagenome-assembled genomes (MAGs) recovered in a recent study, I identified four new genera within the family Bifidobacteriaceae: Ancillula, Opitulatrix, Servula, and Nutricula, expanding on the first report of protist-associated Actinomycetota. The new species exhibit diverse biosynthetic capabilities. Members of Opitulatrix have largely lost the ability to produce amino acids and cofactors, relying on nutrients from their flagellate hosts, while Ancillula retains significant biosynthetic capacity. Most termite-specific Bifidobacteriaceae retain an export system for threonine and serine (ThrE), providing evidence of nutrient exchange with their flagellate hosts. Furthermore, the observed genome erosion in this clade is balanced by horizontal gene transfer events within the termite gut microbiota, supporting the hypothesis of convergent evolution among termite gut flagellate symbionts.