title: Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet.
abstract: High-grain feeding used in the animal production is known to affect the host rumen bacterial community, but our understanding of consequent changes in goats is limited. This study was therefore aimed to evaluate bacterial population dynamics during 20 days adaptation of 4 ruminally cannulated goats to the high-grain diet (grain: hay - ratio of 40:60). The dietary transition of goats from the forage to the high-grain-diet resulted in the significant decrease of rumen fluid pH, which was however still higher than value established for acute or subacute ruminal acidosis was not diagnosed in studied animals. DGGE analysis demonstrated distinct ruminal microbial populations in hay-fed and grain-fed animals, but the substantial animal-to-animal variation were detected. Quantitative PCR showed for grain-fed animals significantly higher number of bacteria belonging to Clostridium leptum group at 10 days after the incorporation of corn into the diet and significantly lower concentration of bacteria belonging to Actinobacteria phylum at the day 20 after dietary change. Taxonomic distribution analysed by NGS at day 20 revealed the similar prevalence of the phyla Firmicutes and Bacteroidetes in all goats, significantly higher presence of the unclassified genus of groups of Bacteroidales and Ruminococcaceae in grain-fed animals and significantly higher presence the genus Prevotella and Butyrivibrio in the forage-fed animals. The three different culture-independent methods used in this study show that high proportion of concentrate in goat diet does not induce any serious disturbance of their rumen ecosystem and indicate the good adaptive response of caprine ruminal bacteria to incorporation of corn into the diet.
authors.affiliation: Facultad de Ciencias Veterinarias y Ambientales, Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, CP 5519, Mendoza, Argentina; Instituto de Histología y Embriología de Mendoza, Universidad Nacional de Cuyo, Casilla de Correo 56, CP 5500, Mendoza, Argentina. Electronic address: diegogrilli@yahoo.com.ar.
authors.forename: Diego Javier
authors.initials: DJ
authors.lastname: Grilli
authors.affiliation: Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska 1083, CP 142 20, Prague, Czech Republic.
authors.forename: Kateřina
authors.initials: K
authors.lastname: Fliegerová
authors.affiliation: Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska 1083, CP 142 20, Prague, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Kopečný
authors.affiliation: Instituto Argentino de Investigaciones de las Zonas Áridas, Centro Científico y Tecnológico, M5502BPB, Mendoza, Argentina.
authors.forename: Sebastián Paez
authors.initials: SP
authors.lastname: Lama
authors.affiliation: Instituto Argentino de Investigaciones de las Zonas Áridas, Centro Científico y Tecnológico, M5502BPB, Mendoza, Argentina.
authors.forename: Vanina
authors.initials: V
authors.lastname: Egea
authors.affiliation: Facultad de Ciencias Veterinarias y Ambientales, Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, CP 5519, Mendoza, Argentina.
authors.forename: Noelia
authors.initials: N
authors.lastname: Sohaefer
authors.affiliation: Facultad de Ciencias Veterinarias y Ambientales, Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, CP 5519, Mendoza, Argentina.
authors.forename: Celia
authors.initials: C
authors.lastname: Pereyra
authors.affiliation: Facultad de Ciencias Veterinarias y Ambientales, Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, CP 5519, Mendoza, Argentina.
authors.forename: María Soledad
authors.initials: MS
authors.lastname: Ruiz
authors.affiliation: Instituto de Histología y Embriología de Mendoza, Universidad Nacional de Cuyo, Casilla de Correo 56, CP 5500, Mendoza, Argentina.
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Sosa
authors.affiliation: Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, CP 5500, Mendoza, Argentina.
authors.forename: Graciela Nora
authors.initials: GN
authors.lastname: Arenas
authors.affiliation: Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Videnska 1083, CP 142 20, Prague, Czech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Mrázek
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D000821:Animal Feed / Q000032:analysis; D000824:Animal Nutritional Physiological Phenomena; D000818:Animals; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000378:metabolism; D045856:Butyrivibrio / Q000145:classification / Q000235:genetics / Q000378:metabolism; D003013:Clostridium / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005285:Fermentation; D000068536:Bacillota / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005747:Gastric Fistula; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D006041:Goats; D006863:Hydrogen-Ion Concentration; D010802:Phylogeny; D006109:Poaceae / Q000737:chemistry / Q000378:metabolism*; D018720:Prevotella / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012417:Rumen / Q000382:microbiology*; D045857:Ruminococcus / Q000145:classification / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000737:chemistry / Q000378:metabolism*
keywords: Bacteria; Creole goats; NGS; PCR-DGGE; Rumen; qPCR