Application of 16S rRNA gene-targetted fluorescence in situ hybridization and restriction fragment length polymorphism to study porcine microbiota along the gastrointestinal tract in response to different sources of dietary fibre

A total of 32 pigs of 15 +/- 0.38 kg body weight were fed for 6 weeks one of four diets differing in their source of dietary fibre. FISH was used to quantify the main bacterial groups in the pig gut using the following probes: Eub338, Bac303, Rfla729, Rbro730, Erec482, Fprau645, Prop853, Str493 and Lab158. FISH counts revealed important differences at four sites along the pig gastrointestinal tract, but we were unable to show differences related to diets. Stomach and jejunal samples gave total bacterial counts of 0.1-5.3 x 10(8) g(-1) of contents. In the stomach, streptococci and lactobacilli were predominant, and the clostridial cluster IX group was abundant (14-41% of total bacterial count). Clostridial cluster IX bacteria were present elsewhere in the gastrointestinal tract at 1-8%. The other groups were generally more abundant in the proximal colon and rectum: Bacteroides/Prevotella (5-10%), clostridial cluster XIVa (10-19%), and cluster IV relatives of Faecalibacterium prausnitzii (1-4%) and ruminococcus (4-10%). Restriction fragment length polymorphism profiles showed changes related to diet, with pigs fed wheat bran having the lowest richness of all diets (P=0.008).