Analytical concept for microbial communities

Gut bacteria are of crucial importance both for human and animal health. However, in order to manipulate and intervene with gut systems we need basic knowledge in:

  • coevolution between bacteria and the animal host
  • ecological processes in the interaction between bacteria and host
  • population dynamic processes among bacteria

The main research objective of the Rudi Lab is to develop and implement a complete analytical concept for microbial community analyses. The concept includes all steps from sample preparation data analysis and interpretation.

Our mission is to understand basic concept with respect to coevolution of the animal host and intestinal bacteria, and to use this information to improve human and animal health. Our activities focused on analyses of in vivo and in vitro gut models, and the applied consequence for humans and economically important food- producing animals.

1 Gut systems

We chose the gut systems for comparative studies from simple abiotic systems to complex gut systems involving both innate and adaptive immune systems. The rationale for the choice of gut systems is to obtain a global understanding of the mechanisms governing the interactions between gut bacteria and the animal host.

1.1 Anaerobe fermentation

We use anaerobe fermentors to investigate basic population dynamic processes. The benefit is that anarobe fermentors are very easily controllable, and it is possible to dissect the effect of single factors.

1.2 Earthworm

Cleopatra was one of the first to recognize the importance of eartworms. Charles Darwin had a very strong interest in eartworms because earthworms are involved in global soil transformations.

We want to use earthworm as a model for gut bacteria in order to understand fundamental questions with respect to spatial distribution and individual variation in the microflora. Earthworms are also easy to manipulate experientially enabling experiments not possible with other organisms.

1.3 Chicken

We have a wide experience in analyzing the chicken gut. Our focus here has been on pathogen colonization, in particularly Campylobacter jejuni which is the most common food-borne pathogen in the developed world.

1.4 Horse

Horses has a gut that resembles the human gut with the small intestine followed by the caecum.We have access to caecum fistulated raising horses. This gives us an unique opportunity to investigate microbial population dynamic processes, and to relate these to the performance of the horses.

1.5 Human

We are conducting large-scale screening of the human microflora with respect to the risk of allergy development in children. These screenings are conducted using both real-time PCR and DNA microarrays.

We have also reanalyzed the extensive clone library generated by the Relman group www.sciencemag.org/cgi/content/abstract/308/5728/1635 Our analyses show a detailed map of the human microflora.

A density distribution map of common bacteria in the human microflora. The color code shows the natural logarithm of the densities.

2 Molecular methods

The main focus for the development of molecular methods is the description of complex microbial communities. We are working with three main aspect; quantification of predefined groups of bacteria, quantification of previously uncharacterized bacteria, an the determination metabolic and physiological state of the bacteria.

2.1 Single nucleotide extension (SNE) probes

The principle of SNE probes is to conduct single basepair DNA sequencing. There is a wide diversity of approaches for detecting SNE probe signals, ranging from caplillary gel electrophoresis to mass spectroscopy.

Our focus has been on the development of both real-time quantitative, and DNA array approaches for SNE probe detection.

3 Bioinformatics

Our focus is to develop bioinformatic tools to describe evolutionary relations, describe dynamic interactions in microbial communities, model interactions in microbial communities, and for data generation and interpretation.

Our vision with software development is to develop user friendly and intuitive tools.

3.1 Evolution

I am focusing on the development tools to describe evolutionary relations that enable analyses and interpretation of large sets of data. Soon, there will be more than 1000 bacterial genomes sequenced, and for the 16S rRNA gene which is the most widely used phylogenetic marker there will be more than 1 million sequences within a couple of years.

It is clear that using traditional alignment-based phylogenetic reconstructions and description of evolutionary relations can not be used to analyze such sets of data.We have therefore developed alternative alignment-independent strategies for phylogenetic reconstruction. Our approach describe phylogenetic relations in an absolute coordinate space, enabling the analyses of very large sets of data. We have developed a software which can be downloaded free of charge.

Figure showing a global description of evolutionary relatedness prokaryotes based on nearly 4000 fullength 16S rRNA gene sequences. See reference: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16825631 

4 Evolution

We focus on the effect of the environment on long therm evolution of rRNA. Our hypothesis is that the environment is important for shaping the nucleotide composition of rRNA. This could be important for understanding the dynamics in microbial communities.

5 Ecology

The current focus in microbial ecology is on biodiversity description. Our focus, on the other hand, is on description of dynamics in microbial communities. This field is virtually unexplored in microbiology. Since the field of ecology is much better developed for higher organisms than bacteria, we have adapted tools this filed to microbiology.

Due to the short generation time - microorganisms may also offer an advantage to general ecology as a model systems.

6 Commercialization

I am actively engaged in commercialization, and all results with commercials interest will be commercialized. I have 4 granted patens and 4 patents pending, and I was one of the cofounders of the biotechnology company Genpoint which now have been sold to the company Nordiag

My current focus is the commercialization of gut microflora analyses. I want to develop a standardized system including databases and analytical tools. Standardized analytical systems will be will be important for both food and pharmaceutical companies in document medical and health claim effects. I will also develop global databases and strain collections of well documented strains. In 2008 I was involved in the establishment of a new company dedicated to gut microbiota analyses.