Genomic Reconstruction and Dietary Response Assessment of Three Clostridium leptum -related Bacteria Isolated from Fecal Samples of Singapore Subjects

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Abstract
1. Clostridium leptum , a key player in gut butyrate production, has a profound impact on various facets of intestinal health. A recent clinical trial highlighted a significant increase in the relative abundance of this species in response to dietary interventions using beneficial oils. We isolated microbial strains corresponding to “ Clostridium leptum ” (at the 16S rRNA gene similarity level) and sequenced their genomes. All three genomes were successfully reconstructed, maintaining the chromosome as a single contig. Subsequent genome-wide analysis unveiled the phylogenetic diversity of the isolates, including the discovery of a new species - Gallacutalibacter singaporense . Based on the reconstructed metabolic model, we predicted the growth condition patterns of this new species and confirmed the predictions in vitro . Leveraging the assembled genomes, we dissected the components of the strong dietary intervention response signal previously ascribed to “ C. leptum ” and revealed distinct individual dynamics of all three bacteria in the clinical trial context. The transitional behavior of the novel species, in particular, revealed intriguing patterns, blazing the path to uncovering previously unrecognized interactions along the diet – gut microbiome – human health axis.

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