Laboratory of Anaerobic Microbiology

Microbiology, Biochemistry, Genomics and Molecular Ecology of microbial hydrolysis of cellulose, hemicelulose and chitin in the animal and human digestive tract. Genomics of anaerobic bacteria and fungi.

Butyrate producing bacteria                     

Our interest on the butyrate-producing bacteria originated with transformation of ”Butyrivibrio fibrisolvens”  isolates with a shuttle vector, carrying dehalogenase gene. Expressed dehalogenase in the rumen was then able to detoxify plant fluoroacetate, a widespread toxin in Australian and South African plants. The transformation was successful with a very low number of isolates, indicating a high variability in isolates of motile, butyrate-producing anaerobic rods from the rumen. The high variability was also observed in fermentation products, extracellular polysaccharides, cell wall monosaccharides, hydrolytic activities, restriction barriers, C+G content and DNA sequences. Phylogenetic trees of 16S rDNA revealed at least 8 new or closely related bacterial species to Butyrivibrio fibrisolvens. To clarify the relations among the isolates, we have described two new species: Butyrivibrio hungatei, Pseudobutyrivibrio xylanivorans and were involved in description of Butyrivibrio proteoclasticus. Their counts were confirmed by selective counting methods, by cPCR, and RT PCR, both we have developed for Butyrivibria and Pseudobutyrivibria. Now, we are involved in the genome description of important butyrate-producing bacteria.

Bifidobacteria

Genetic studies of bifidobacteria were focused on the colonization of newborn children, presence of bifidobacteria in patients with Celiac Disease and several types of the Inflammation Bowel Disease. Recently we have described new bifidobacteria in the gut of insects. There are Bifidobacterium bombi, B. bohemicum and B. actinicoloniformis and a new
genus Bombiscardovia (Bombiscardovia coagulans). 

Anaerobic fungi

Monocentric and polycentric fungi in the rumen produce very efficient hydrolytic enzymes and in case of ß-1,4-endoglucanase, the fungal specific activity is the highest ever observed. Our attention is focused on the occurrence and properties of Anaeromyces isolates in the digestive tract of herbivorous animals. Species of this genus are very efficient fiber degraders and there is not deep knowledge about their properties, taxonomic position and interactions with other microbes in the rumen. The cell wall of anaerobic fungi is based on chitin molecules. Therefore it is clear that other chitinolytic microbes are able to limit the growth of anaerobic fungi.

Chitinolytic microorganisms

We have described a chitinolytic bacterial population in the digestive tract of herbivorous animals. In the chitinolytic population are prevailing Clostridium species. Pure strains are able to slow down or eliminate growth of rumen fungi in vitro. The sensitivity of anaerobic fungi to bacterial chitinases differs significantly from genus to genus. Similar chitinolytic bacteria were isolated from digesta of human colon. The presence of these bacteria there could reflect the eating habits of our ancestors.