Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties

The Clostridium genus is highly heterogeneous, encompassing numerous species and strains, many of which remain to be isolated and characterized to better understand their relationship to host physiology. This study aimed to isolate and characterize novel bacterial species within the Clostridium genus and explore their potential links to host health. Under microaerophilic conditions, we isolated and characterized three bacterial isolates belonging to a new anaerobic Clostridium species, designating Clostridium sp. DSM 115107 (Clostridium filamentum ETTB3) as the type strain. C. filamentum ETTB isolates are rod- to filament-shaped, Gram-positive bacteria and exhibit poor growth when cultured on rich media such as LYBHI. Genome sequencing and phylogenetic analysis revealed that C. filamentum ETTB belongs to the Clostridium genus and clusters closely with Clostridium saudiense JCC. Interestingly, C. filamentum ETTB has a significantly smaller genome compared to C. saudiense JCC containing a reduced repertoire of genes involved in carbohydrate degradation and amino acid synthesis and a larger number of genes related to cell motility, including an additional copy of the fliC gene. Unlike C. saudiense, C. filamentum ETTB adopted a filamentous morphology when in contact with Caco-2 cells and stimulate the TLR5 pathway in Caco-2 cells. Metagenomics analysis revealed that C. filamentum ETTB is present in both industrialized and non-industrialized populations, although the relative abundance varying considerably between and within individuals. Our study identifies a novel bacterial strain adapted for the human gut that has the potential to influence host immune response by activating TLR5 pathway.