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Projects / Programmes source: ARRS

Molecular approach to gut microbial ecology

Research activity

Code Science Field Subfield
4.02.01  Biotechnical sciences  Animal production  Genetics and selection 

Code Science Field
B230  Biomedical sciences  Microbiology, bacteriology, virology, mycology 
T490  Technological sciences  Biotechnology 
Keywords
microbiology, molecular biology, phylogenetics, systematics, microbial ecology, DNA, RNA, 16S, seqence analysis, probes, gut, Prevotella, CFB, Bifidobacteium, Lactobacillus
Evaluation (rules)
source: COBISS
Researchers (5)
no. Code Name and surname Research area Role Period No. of publications
1.  08320  PhD Gorazd Avguštin  Animal production  Principal Researcher  2000 - 2001  351 
2.  11765  PhD Lijana Fanedl  Animal production  Researcher  1999 - 2001  98 
3.  08404  PhD Romana Marinšek Logar  Animal production  Researcher  1998 - 2001  501 
4.  03098  PhD Franc-Viktor Nekrep  Animal production  Researcher  2000 - 2001  196 
5.  17864  PhD Maša Zorec  Animal production  Researcher  1998 - 2001  68 
Abstract
Ecological studies of microbial communities in their natural habitats became possible through the recent development of rapid nucleic acid sequencing and computational analysis of the sequence data. Search for and design of specific oligonucleotide DNA probes allows rapid, specific and sensitive observations of microbial groups, species or even genera in their natural habitats. Techniques like PCR or in situ hybridisation combined with digital image analysis supported epifluorescent microscopy or flow cytometry developed and introduced into microbiology in recent years made detailed microbial ecological studies possible. Such studies should when successful provide new knowledge of phylogenetic relationships and positions of already known and new organisms and of their role in the ecosystem studied. In last years detailed investigation of the gut microbial communities was on going in our group, concentrating predominately on bacteria from the Cytophaga Flexibacter Bacteroides phylum from the rumen and members of the genera Bifidobacterium and Lactobacillum from rat gut. In order to investigate isolated bacterial strains and total microbial community, a variety of molecular biology methods was used i.e. RAPD, RFLP and sequence analysis of ribosomal genes. Phylogenetic distances were determined and large genetic heterogeneity established. Oligonucleotide sequence signatures were identified and used for construction of PCR primers and oligonucleotide probes. Both were used for specific identification of investigated microorganisms in vivo and in vitro using a variety of detection techniques. The further research on the above mentioned topics is going to concentrate on the genetic analysis of the number, structure and genetic heterogeneity of the ribosomal genes and operons in some of the important bacterial species from rumen i.e. members of the genus Prevotella. Quantitative PCR and/or flow cytometry techniques are going to be developed in order to investigate the influence of the different 16S gene number and sequence heterogeneities on apparent bacterial phylogenetic diversity in rumen and rat gut. In situ hybridisation, using already developed oligonucleotide probes and combined with epifluorescent microscopy, is going to be further developed in order to alow the space distribution studies of the targeted bacteria in their ecosystems. Flow cytometry is going to be introduced into the field in order to monitor the fate of the targeted bacteria under dietary stress (i.e. lectin additions to the feed). We intend to continue the research on the phylogenetic diversity of microbial populations inhabiting the above mentioned habitats and will try to develop new oligonucleotide probes for specific detection of investigated microorganisms. A combination of the described methods should finally give important answers to the questions concerning the basic knowledge of microbial colonisation of the gut, which is the background for the understanding of, and targeted intervention into, microbial processes, the key processes of the nutrition and health in man and animal.
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