Molecular Ecology

                                                               

For more information about Molecular Ecology or education/graduation projects mail to
group leader Hauke Smidt


The research

Molecular microbial ecology is the field of research in which the occurrence and activity of microbes are studied at the DNA/RNA or protein level.
Our current research programme is focused on bacterial diversity, evolution and activity in natural and man-made ecosystems. We have selected two types of ecosystems in which microorganisms (Bacteria, Archaea) play a major role:

• The Gastrointestinal (GI) Tract
• Environment: sludge, river, grassland and subsurface soil
• Marine Sponge Symbiosis

The gastrointestinal (GI) microbes

In a recent survey of 14331 people interviewed in all Member States of the European Union, 32.5% said that "eating healthy" had an important influence on their food choice and an additional 9% chose it as the most important influence in selecting food (I.E.F.S., Dublin 1996). Almost everyone today is more conscious of and better informed about food, nutrition and health than in the past.
The port of entry for food is the gut that consists of a variety of habitats which are colonised by over 1011 microorganisms, predominantly anaerobic, collectively called the microbiota. The microbiota perform essential functions including protection against pathogens, development of the immune system, and positive effects on colonic health and host nutrition.
In fact, although it has been recognised for decades that the gut commensal microbiota is necessary for development and maintenance of normal health, the effects of individual members of the microbiota on our health are still not understood. The diversity of the microbiota has been investigated extensively by anaerobic culture techniques, but the development and application of novel molecular techniques can generate more rapidly insight into the diversity and activities of our microbiota.Knowledge of the structure and function of the normal microbiota, and its response to diet, genetic background and lifetime of the host may reveal mechanisms on how the intestinal microbiota impact on our health. And perhaps we can use this information to remain healthy!

Questions that arise in our research include:

• Which bacterial species are universal cosmopolitan inhabitants of our gut?
• How stable is the gut microbiota in babies, children and adults?
• What happens to our microbiota during intestinal disorders?
• How does the host recognise the bacterial species?
• Do the host intestinal epithelial cells communicate with our microbiota?
• How do bacteria talk to each other in the intestine, as well as to our epithelial cells?
• Does the immune system influences our GI tract microbiota?
• Can diet or probiotic bacteria effect the composition of our microbiota?
• Can prebiotics be used as alternatives for antibiotics in animal feed?

We approach these questions using a variety of molecular techniques. The detection and identification of many of these organisms has largely been hampered by the incomplete knowledge of their culture conditions. Many of the novel molecular methodologies are based on the use of ribosomal RNA (rRNA) and its encoding genes to describe the relationship between the bacteria in such communities and their individual identity. This approach permits the elucidation both qualitatively as well as quantitatively of the abundance of bacterial species and how their presence interacts with diet and health.
For example, using PCR and direct cloning of 16S rDNA sequences from intestinal samples without previous cultivation allows us to detect microbes that we cannot culture. In fact until recently, we didn't know they were present and new members are now being discovered. Fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) allow us to analyse very complex communities without any culture work! With novel genomics and proteomics techniques we can more rapidly discover how bacteria talk to each other and to the intestinal cells.

Read about the projects in the group and you will see that unravelling of the mechanisms behind the activities and interactions in the intestine between both the commensal and probiotic bacteria and their host, has already begun.

Members and ongoing projects in GI-tract research:

    

Mucus degrading bacteria in the gut: Akkermansia municiphila research

Picture from Derrien et al., 2004

Akkermansia muciniphila is a member of the Verrumicrobia phylum and was isolated recently in a quest to identify new mucus-degrading bacteria from human feces (Derrien et al. 2004). This bacterium appears to be a true symbiont of humans, detectable in the majority of tested subjects.  It is abundantly present in the human intestinal tract, making up several % of the bacterial population in the colon. It is one of the driving forces in two of the three recently discovered human gut microbiome enterotypes (Arumugam et al 2011).

Germ-free mice are easily colonized by A. muciniphila, and show no aberrations but display a specific immunological colonic response indicating its capacity of host-signaling . A. municiphila was the most abundantly identified mucolytic mucosa-associated bacterium in healthy controls when compared to patients with IBD and the amount of Akkermansia spp. were found to be inversely related to the severity of appendicitis, obesity and children with autism (for a review see Belzer & de Vos 2012). Hence our research aims to elucidate the functionality of the mucin-degrading A. muciniphila in the intestinal tract.

We perform genome-based studies of the physiology and metabolism of A. muciniphila that is involved in mucin degradation. We employ genetic and immunological screens to measure the effects of A. muciniphila derived products on the host immune system. Furthermore we measure the persistence, abundance and, activity of Akkermansia spp. in the human gut in relation to diet, genetic background and, disease. Finally, we are isolating and characterizing new Akkermansia isolates in order to understand their evolution and host adaptation.

Scientific Management Team & Contact:

Prof. Willem M. de Vos, PhD.; willem.devos@wur.nl and willem.devos@helsinki.fi

Clara Belzer, PhD.; clara.belzer@wur.nl

References:

M Arumugam^, J Raes, E Pelletier, D Le Paslier, T Yamada, DR Mende, GR Fernandes, J Tap, T Bruls, JM Batto, M Bertalan, N Borruel, F Casellas, L Fernandez, L Gautier, T Hansen, M Hattori, T Hayashi, M Kleerebezem, K Kurokawa, M Leclerc, F Levenez, C Manichanh, HB Nielsen, T Nielsen, N Pons, J Poulain, J Qin, T Sicheritz-Ponten, S Tims, D Torrents, E Ugarte, EG. Zoetendal, J Wang, F Guarner, O Pedersen, WM de Vos, S Brunak, J Doré, MetaHIT Consortium, J Weissenbach, SD Ehrlich, and P Bork (2011) Enterotypes of the human gut microbiome. Nature 473: 174-80.

M. Derrien, E.E. Vaughan, C.M. Plugge & W.M. de Vos (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.
Int. J. Syst. Evol. Microbiol. 54: 1469-76

C Belzer & WM de Vos (2012). Microbes Inside - From Diversity to Function: The Case of Akkermansia. ISME J in press.

Members and ongoing projects in Akkermansia research:                  

 Environmental research

The anaerobic sludge reactor

In close collaboration with the research going on within the Microbial Physiology Group, we aim to further our understanding of both structural as well as functional diversity and stability in microbial communities active in anaerobic sludge reactors. One part of our work on anaerobic sludge aims to characterise the dominant microbes (Bacteria and Archaea) by 16S rRNA analyses with the ultimate purpose to develop a DNA array for rapid monitoring. Another project deals with syntrophic propionate-oxidizing bacteria isolated from granular sludge. It is expected that hydrogenases/formate dehydrogenases are involved in interspecies hydrogen/ formate transfer during syntrophic propionate oxidation. The task of this project is to sequence hydrogenase/formate dehydrogenase genes of Syntrophobacter fumaroxidans with the aim to compare their expression in pure culture, syntrophic cocultures and granular sludge. in collaboration with researchers from the University of Braga, Portugal, microbiota involved in long chain fatty acid degradation are investigated.

Grassland soils

Our current research focuses on the study of abundance and genomic diversity of important groups of soil microbiota, including Bacillus spp. and Verrucomicrobia. Bacillus spp., closely related to B. benzoevorans, have until recently been overlooked by cultivation-based approaches, and their high abundance in Dutch grassland soils has triggered our interest in their phylogenetic microdiversity as well as soil functional relevance in a variety of soil ecosystems.
In collaboration with Peter H. Janssen (University of Melbourne), we are interested in the the relation of genomic and functional diversity of Verrucomicrobia, which have been isolated from ecosystems as diverse as the human intestine and aquatic and terrestrial environments. 
 
Contaminated subsurface soils and rivers

The current work on soil is focussed on the detection of genes involved in the halorespiration of chlorinated compounds in contaminated soils. The study is part of a bioremediation project in which we follow the development and spread of halorespiring bacteria by retrieving the mRNA of dehalogenases.

Members and ongoing projects in environmental research:

 Marine Sponge Symbiosis

Marine sponges harbour an extraordinary diversity of microorganisms inside their tissue. Many of these microorganisms are associated with the production of secondary metabolites that have potential pharmaceutical applications. Our research is focused at:

·         Characterising microorganisms that are associated with sponges

·         Cultivation of symbionts for the production of bioactive compounds

·         Genomic analysis of symbionts to understand the nature of symbiosis

Members and ongoing projects in sponge microbiology: