This paper describes current research and future perspectives of treatment of C. difficile infections that is based on gut microbiome restoration.
COBISS.SI-ID: 512496184
Clostridium difficile infection (CDI) is associated with disturbance of intestinal microbiota. This paper gives the overview of studies of C. difficile and microbiota in patients with CDI. Microbiota of CDI patients usually shows decreased diversity, increase of facultative anaerobes, and decreased levels of bifidobacteria, Bacteroidetes, Lachnospiraceae, and butyrate-producing bacteria. Studies including symptomatic, asymptomatic, recurrent, and fecal therapy-treated patients could result in the recognition of microbial markers for CDI risk or could provide the combination of beneficial microbes for a C. difficile-specific probiotic.
COBISS.SI-ID: 512431160
This review in the highest ranking journal in Microbiology field summarizes clinical features of C. difficile infections, new trends in epidemiology and new data on virulence factors and pathogenesis. C. difficile is typically associated with disturbed gut microbiota and study of interactions between C. difficile and microbiota are one of the important part of current research programme.
COBISS.SI-ID: 652319
In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samplesfrom healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Bifidobacterium longum was the single most important species associated with C. difficile negative samples. This was one of the first studies that used machine learning approaches and first that identified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.
COBISS.SI-ID: 16731158
Bacterial, fungal and archaeal microbiota was analysed by DHPLC in 143 chicken faecal samples from a single poultry farm. Acidaminococcus intestini, described here for the first time as a part of poultry faecal microbiota, was significantly more likely present in C. difficile negative samples, while presence/absence of some other microorganisms (Enterococcus cecorum, Lactobacillus galinarum, Moniliella sp. and Trichosporon asahii) was close to significance. Differences in microbiota diversity depend on animal age, but not on the presence of C. difficile. With machine learning (WEKA J48) we have defined specific combinations of microbial groups predictive for C. difficile colonisation. Microbial groups associated with C. difficile colonisation in poultry are different than those reported for humans and include bacteria as well as fungi.
COBISS.SI-ID: 16908054
The chapter describes continuous production of bacteria and bacteriophages. The methodology could be used for cultivation of bacterial cultures, microbial communities, and propagation of bacteriophages.
COBISS.SI-ID: 4505720
This paper describes genome sequencing and analysis of two phages and documents the expertise of project partners for phage genome analysis.
COBISS.SI-ID: 3866760
This paper documents the expertise of project partners (Rupnik, Mahnic) in the molecular analysis of complex microbial communities which is applied also in the research included in this program.
COBISS.SI-ID: 21936392
This book chapter describes a new modification of PCR ribotyping established in our laboratory. The new method is culture independent and therefore much faster than classical PCR ribotyping. PCR ribotyping is important method used also in several studies included in this research programme. Direct PCR ribotyping also enables continuous follow up of C. difficile strains in in vitro model of interaction with gut microbiota.
COBISS.SI-ID: 512626744
In this review we describe the recent developments and some changes in the nomenclature of toxinotyping, a method established in our laboratory.
COBISS.SI-ID: 512578872