The gut microbiome of a springtail: who’s there and what are they doing?

Background

Folsomia candida is a soil invertebrate and an important model organism in ecotoxicology and ecogenomics. The genome of F. candida contains some of the genes involved in the production of a beta-lactam antibiotic (Roelofs et al., 2012; Suring et al., unpublished). Since only fungi and bacteria are known to produce antibiotics, these genes probably originated from some microorganism through a horizontal gene transfer (HGT) event. The microbial community of F. candida, living in close association with this animal, most likely constitutes the source of these antibiotic-producing genes. In this project, we want to investigate the bacterial community of F. candida, with a specific focus on antibacterial resistance and the production of antibacterial compounds. The objective of this work is to increase our knowledge of the microbial community of F. candida and of its unexplored reservoir of genes and functions.

Approach

We are interested in screening the bacterial community of F. candida for the presence of antibacterial resistance and for its potential to produce antibacterial compounds. There is an approach that enables us to address both issues at the same time. Antibacterial -producing organisms need to evolve resistance to the same compounds they produce. Therefore, by screening for antibacterial resistance we would select potential antibacterial-producing microorganisms (Thaker et al., 2013). Once these microorganisms are available in the form of bacterial cultures, we can characterize them, screen them for the presence of antibacterial biosynthetic genes and perform enzymatic studies (Vilanova et al., 2012), in order to confirm the presence or absence of antibacterial genes and functions.

In short, we will isolate antibacterial-resistant cultivable members of the bacterial community of F. candida, and we will investigate the potential of such bacteria to produce antibacterial compounds.

The activities involved in this internship will include:

  • prepare extracts of springtails and identify antibacterial-resistant bacteria
  • establish and maintain bacterial cultures on agar plates and in liquid medium
  • apply molecular methods to identify genes of interest: PCR, cloning, sequencing

Supervision and contact information

Dr. ir. Dick Roelofs
Room H147 (W&N building, Vrije Universiteit)
E-mail:  dick.roelofs@vu.nl
Phone: +31 (0)20 – 59 87078

References

Roelofs D., Timmermans M.J.T.N., Hensbergen P., van Leeuwen H., Koopman J., Faddeeva A., Suring W., de Boer T.E., Mariën J., Boer R., Bovenberg R., van Straalen N.M., 2012. A functional isopenicillin N synthase in an animal genome. Molecular Biology and Evolution, 30 (3): 541-548.

Thaker M.N., Wang W., Spanogiannopoulos P., Waglechner N., King A.M., Medina R., Wright G.D, 2013. Identifying producers of antibacterial compounds by screening for antibiotic resistance. Nature Biotechnology, 31 (10): 922-927.

Vilanova C., Marco G., Domínguez-Escribà L., Genovés S., Sentandreu V., Bataller E., Ramón D., Porcar M., 2012. Bacteria from acidic to strongly alkaline insect midguts: potential sources of extreme cellulolytic enzymes. Biomass and bioenergy, 45: 288-294.