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Abstract
The microbiome associated with an animal’s gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia’s metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
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1 VU University Amsterdam, Department of Ecological Science, Amsterdam, The Netherlands (GRID:grid.12380.38) (ISNI:0000 0004 1754 9227); Department of Microbiology and Systems Biology, TNO, Zeist, The Netherlands (GRID:grid.4858.1) (ISNI:0000 0001 0208 7216)
2 VU University Amsterdam, Department of Ecological Science, Amsterdam, The Netherlands (GRID:grid.12380.38) (ISNI:0000 0004 1754 9227); Vietnam Academy of Science and Technology, Institute of Biotechnology, Hanoi, Vietnam (GRID:grid.267849.6) (ISNI:0000 0001 2105 6888)
3 VU University Amsterdam, Department of Ecological Science, Amsterdam, The Netherlands (GRID:grid.12380.38) (ISNI:0000 0004 1754 9227)
4 BioDetection Systems, Amsterdam, The Netherlands (GRID:grid.450522.4) (ISNI:0000 0004 0646 8536)