gut metagenome
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.
host
Folsomia candida VU population
isolation_source
gut tissue
collection_date
2016-03-06
geo_loc_name
Netherlands: Amsterdam
lat_lon
52.33 N 4.86 E
samp_mat_process
Dissected guts were rinsed in sterile PBS and whole springtails were rinsed three times in sterile water before processing. After the washing steps, DNA was directly isolated from two of the samples (Fc3 and Fc4) while additional steps were applied to prepare samples Fc1 and Fc2. For these two samples, we separated bacterial cells from F. candida s cells by using the method described, with modifications Proc Natl Acad Sci USA. 2012;109(27). The samples were crushed in PBS in a 1.5 ml microcentrifuge tube, using a plastic pestle. The samples were then gently vortexed, to encourage separation of cells, before being passed through 20 um and 8 um filters in succession. The filtered samples were centrifuged at 10 000 g for 30 min to harvest cells, and the pellet was resuspended in 200 ul TE buffer. For sample Fc2, an additional step with a density gradient was applied. An 80 percent Percoll solution in 0.15 mol l -1 NaCl was prepared. 1 ml of this solution was placed in a 2 ml microcentrifuge tube and spun at 20 000 g for 20 min to create a gradient. The 200 ul of TE buffer containing the cells was gently placed on top of the gradient, and the tube was centrifuged at 400 g for 20 min. Bacterial cells were then visible as a band and were collected using a pipette. The cells were centrifuged at max speed for 5 min and washed with TE buffer to remove residual Percoll solution.
samp_size
38.7 ng/uL DNA
BioSampleModel
Metagenome or environmental