title: Biodiversity and fermentative activity of caecal microbial communities in wild and farm rabbits from Spain.
abstract: In order to study the microbial caecal ecosystem of wild and domestic rabbits through the fermentation characteristics and concentration and diversity of bacterial and archaeal communities, caecal samples from sixteen wild rabbits (WR) were contrasted with two groups (n = 4) of farm rabbits receiving low (LSF) or high (HSF) soluble fibre diets from 28 (weaning) to 51 days of age. DNA was extracted for quantifying bacteria and Archaea by qPCR and for biodiversity analysis of microbial communities by DGGE. Samples from WR had lower caecal pH and ammonia and higher volatile fatty acids concentration than farm animals. Lower acetate and higher butyrate proportions were detected in WR. Bacterial and archaeal DGGE profiles were clearly different between wild and farm rabbits, and diet-affected population of farm rabbits. Similarity index of bacteria was lower than 0.40 among WR, and 0.52 among farm rabbits. In conclusion, caecal fermentation characteristics differ between wild and farm rabbits, which harbour clearly different bacterial and archaeal communities. In farm rabbits, diversity is influenced by the dietary level of soluble fibre.
authors.affiliation: Instituto Universitario de Investigación en Ciencias Ambientales, Dept. Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Spain.
authors.forename: L
authors.initials: L
authors.lastname: Abecia
authors.forename: N
authors.initials: N
authors.lastname: Rodríguez-Romero
authors.forename: D R
authors.initials: DR
authors.lastname: Yañez-Ruiz
authors.forename: M
authors.initials: M
authors.lastname: Fondevila
mesh_terms: D000641:Ammonia / Q000737:chemistry; D000818:Animals; D000835:Animals, Wild; D001105:Archaea / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D044822:Biodiversity; D002432:Cecum / Q000382:microbiology*; D019641:DNA, Archaeal / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D058645:Denaturing Gradient Gel Electrophoresis; D005232:Fatty Acids, Volatile / Q000737:chemistry; D005260:Female; D005285:Fermentation; D005766:Gastrointestinal Contents / Q000737:chemistry / Q000382:microbiology; D006863:Hydrogen-Ion Concentration; D008297:Male; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011817:Rabbits / Q000382:microbiology*; D060888:Real-Time Polymerase Chain Reaction; D013030:Spain
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D005232:Fatty Acids, Volatile; D012336:RNA, Ribosomal, 16S; D000641:Ammonia