title: Molecular comparative assessment of the microbial ecosystem in rumen and faeces of goats fed alfalfa hay alone or combined with oats.
abstract: The objective of this work was to compare the biomass and community structure of bacteria, protozoa and archaea communities in samples of rumen and faeces of goats and to what extent the diet (alfalfa hay with or without supplemented oats) offered to them exert an influence. Four cannulated adult goats fistulated in the rumen were used in a cross over design experiment in two experimental periods of 26 days, consisting in 14 days of adaptation, 7 days of sampling rumen contents and 5 days of digestibility measurement. Bacterial, protozoa and archaeal biomass and the communities' structure was assessed by real time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The numbers of archaea and bacteria in both rumen and faeces were higher and lower, respectively, in animals fed AH diet (P < 0.005). Contrary, protozoal numbers were not affected by the diet but were lower (P < 0.001) in faeces than in rumen. The analysis of the community structure revealed a consistently different population in structure in rumen and faeces for the three studied microbial groups and that supplementing alfalfa hay with oats led to a decrease in the similarity between sites in the rumen and faeces: similarity indexes for bacteria (57 and 27%), archaea (26 and 9%) and protozoa (62 and 22%) in animals fed AH and AHO diets, respectively.
authors: Animal Nutrition Institute, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain; Department of Animal Science, Faculty of Agriculture, University of Tabriz, Iran.
authors: Hamid
authors: H
authors: Mohammadzadeh
authors: Animal Nutrition Institute, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
authors: David R
authors: DR
authors: Yáñez-Ruiz
authors: Animal Nutrition Institute, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
authors: Gonzalo
authors: G
authors: Martínez-Fernandez
authors: Animal Nutrition Institute, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain. Electronic address: leticia.abecia@eez.csic.es.
authors: Leticia
authors: L
authors: Abecia
mesh_terms: D000693:Anaerobiosis; D000821:Animal Feed; D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D018554:Avena / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D002404:Catheterization; D016798:Ciliophora / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D005243:Feces / Q000382:microbiology; D005285:Fermentation; D006041:Goats / Q000382:microbiology; D000455:Medicago sativa / Q000378:metabolism*; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D012417:Rumen / Q000382:microbiology; D013559:Symbiosis / Q000502:physiology
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D016054:DNA, Protozoan
keywords: DGGE; Faecal microbiota; Methanogenic archaea; Structure of rumen microbiota; qPCR