Microbiome research at icipe

The bodies of all animals are inhabited by various microbes including bacteria, fungi and viruses, which are either detrimental (pathogens), or beneficial (symbionts), for the host.

Symbionts play an important, yet poorly understood role in sustaining the health and fitness of their animal hosts. Still, while it is difficult to fully understand the diversity and usefulness of symbionts, fascinating discoveries are increasingly being made. In particular, advances in molecular techniques have enabled a notable surge in researchers’ ability to study these organisms in depth.

Most commonly, insects harbour two kinds of symbionts: endosymbiotic, which are found inside the cells or body of insects, and exosymbiotic, which exist on the outer cuticle or inside the intestines. Endosymbiotic microbes have a significant impact on the interactions between their host insects and pathogens (that is, disease causing agents). This is because to promote their own survival, the microbes often assist their host insects in the defence against pathogens.

Microbiome research at icipe
The Spirovector project intends to advance Africa’s capacity in developing insect endosymbiont-based strategies for the control of vector-borne diseases. Here, Sharon Towett, an MSc student in the project is screening Spiroplasma endosymbionts.

In 2014, icipe started studies to explore the potential of endosymbionts in making insects more resistant to pathogens and to prevent the transmission of diseases. The Centre’s primary focus is the development of insect endosymbiont-based strategies for the control of vector-borne diseases, which exert their greatest impact in developing regions, including Africa. Globally, insect endosymbionts are emerging as a promising alternative in vector-borne diseases management. However, there has been minimal progress in the development of endosymbiont-based strategies to control vector-borne diseases of great importance in Africa. In contrast to the explosion of research on endosymbiont strategies to manage arboviral diseases, there has been much less focus on similar strategies for vector-borne diseases that are caused by eukaryotic parasites. This distinction is significant because most of the important vector-borne diseases in Africa are indeed caused by eukaryotic parasites (e.g. Plasmodium, the malaria parasite; Leishmania, which is responsible for leishmaniasis, and Trypanosoma, which causes African trypanosomiasis).

icipe’s research, which is being conducted through the Spirovector project, supported by the R. Geigy Foundation, the Swiss National Science Foundation (Switzerland), and the Wellcome Trust (UK), has two key objectives: to obtain a better understanding of diverse insect endosymbioses and to explore their potential use to control insect vector-borne diseases. The Centre’s researchers have screened populations of numerous vectors throughout Kenya and they have identified several strains of Spiroplasma, insect-endosymbiotic bacteria that are known for their ability to protect insects against eukaryotic parasites. Notably, Spiroplasma strains have been discovered in Anopheles arabiensis (major vector of Plasmodium), Glossina fuscipes (major vector of Trypanosoma) and Culex quinquefasciatus (major vector of filarial nematodes). Currently, the scientists are investigating the Spiroplasma strains for their potential as a tool for blocking parasite transmission.

With support from the European Union, icipe is also conducting studies to understand the basis of interactions between endosymbionts (specifically Spiroplasma), and Bactrocera and Ceratitis fruit fly species. In Africa, fruit flies are one of the major constraints to realising the huge potential of fruit production for income generation, food and nutritional security. Over the years, icipe in collaboration with partners from Africa, Asia, Europe and USA, has developed integrated pest management (IPM) packages for exotic and native fruit flies, which are aimed at reducing yield losses and the enormous expenditure incurred by farmers to purchase pesticides, and to mitigate the health and environmental risks associated with the use (and misuse) of such chemicals. The IPM packages include fungi-derived biopesticides, baiting and male annihilation techniques, biological control with parasitoids, cultural control through field sanitation, minimal use of pesticide in localised bait stations of spot spray, and proper post-harvest treatment to provide and assure quarantine security.

icipe is now studying the interactions between endosymbionts and a number of the components of the Centre’s fruit fly IPM package, specifically parasitoid wasps, biopesticides and host marking pheromone production. As a result, our researchers have developed novel tools to identify endosymbionts in African fruit flies, leading to the discovery of Spiroplasma species that are entirely new to science in the invasive fruit fly species Bactrocera dorsalis. Our scientists are now investigating how this strain of Spiroplasma affects the biology of the pest.

The Centre’s most recent initiative in microbiome research is a project launched in September 2016, with support from the Swiss National Science Foundation, to assess the connection between honeybee gut microbiota and the overall health of the insect. icipe recognises the rising threats to bees in Africa and globally, in part due to unresolved issues surrounding bee health.  Therefore, the Centre has in recent years made bee health a primary research focus, as part of the process towards securing the bee industry in Africa, while contributing to global sustainability of bees.

Bee gut microbiota abundance and diversity have been shown to be good indicators of hive health and stress. By studying the honeybee gut microbiota, icipe aims to establish microbe-based diagnosis technique to improve bee health management. This study will also provide a better understanding of the distribution of bee diseases and improve risk mapping. Finally it will guide the development of probiotics to increase hive resistance to a broad range of pathogens.

The advances made by icipe so far are an important step in the long term vision of using endosymbiotic microbes to prevent insect vectored pathogens. The progress also demonstrates and reinforces icipe’s centre of excellence status.

Most of the microbiome research is being undertaken within the icipe Martin Lüscher Emerging Infectious Laboratory (ML-EID), which includes biosafety level 2 and 3 facilities for pathogen culture and high-throughput molecular surveillance, as well as insectaries for controlled experimental studies.

In addition, through the Spirovector project, the Centre has obtained a Leica SP5 confocal microscope, donated to the Centre by Cellular Imaging Facility, Lausanne University Hospital, Switzerland, through the mediation of TReND Africa which is now installed in the ML-EID. The equipment, the first operational confocal in the East African region, will enable the Centre’s researchers to acquire optical sections of specimens without background noise and image degradation.

icipe’s microbiome research is also being conducted within the Centre’s African Reference Laboratory for Bee Health, which is equipped with cutting edge instrumentation for molecular procedures and microbiology practices.

Most importantly, the microbiome research is contributing to icipe’s vision of scientific leadership by amalgamating regional and global talent. The research team is currently led by two scientists whose previous research has had global impact on the understanding of insect-endosymbionts: Dr Jeremy Herren (Switzerland), a Sir Henry Wellcome Postdoctoral Research Fellow, and Dr Juan Paredes (Colombia).

Six scholars are currently conducting microbiome research at the Centre. They include two PhD students: Hellen Butungi (Uganda) and Joseph Gichuhi (Kenya); and three MSc students: Lillian Mbaisi (Kenya), Enock Mararo (Kenya) and Sharon Towett (Kenya).

In advancing its microbiome research, icipe is grateful to partner with the Swiss Federal Institute of Technology (EPFL), Lausanne, University of Lausanne, Switzerland, and the universities of Lancaster, Glasgow and Liverpool, in the UK.