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Abstract
Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host’s intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65–71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.
Highlights
Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner
Several intriguing features connected to the lifestyle of these organisms later opened for a deeper interest in their possible role as important symbionts[12]. They colonized primarily in the terminal part of the small intestine where many immune cells are located, they appeared at greater number around weaning which is an important period for maturation of the immune system, and, not least, they exhibited an intimate contact with the host through a specific anchoring to the intestinal cell wall
To verify the presence of an SFB 16S rRNA gene sequence in the human ileostomy sample where it was earlier detected with SFB-specific primers, we subjected the same sample to amplicon sequencing using broad-taxonomic range PCR primers
Summary
Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. Human gut shotgun metagenomic sample sets have been scanned by attempting to map reads to the SFB genomes of mice and rats, but without success[23]. We report the draft genome sequence of a tentatively human-adapted representative of the SFB group.
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