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.
| Language | English |
|---|---|
| Article number | 7308 |
| Pages | 1-13 |
| Number of pages | 13 |
| Journal | Scientific Reports |
| Volume | 9 |
| DOIs | |
| Publication status | Published - 13 May 2019 |
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Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida. / Agamennone, Valeria; Le, Ngoc Giang; van Straalen, Nico M; Brouwer, Abraham; Roelofs, Dick.
In: Scientific Reports, Vol. 9, 7308, 13.05.2019, p. 1-13.Research output: Contribution to Journal › Article › Academic › peer-review
TY - JOUR
T1 - Antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the soil-living invertebrate Folsomia candida
AU - Agamennone, Valeria
AU - Le, Ngoc Giang
AU - van Straalen, Nico M
AU - Brouwer, Abraham
AU - Roelofs, Dick
PY - 2019/5/13
Y1 - 2019/5/13
N2 - 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.
AB - 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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UR - http://www.scopus.com/inward/citedby.url?scp=85065743830&partnerID=8YFLogxK
U2 - 10.1038/s41598-019-43828-w
DO - 10.1038/s41598-019-43828-w
M3 - Article
VL - 9
SP - 1
EP - 13
JO - Scientific Reports
T2 - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 7308
ER -