title: Archaeal microbiota population in piglet feces shifts in response to weaning: Methanobrevibacter smithii is replaced with Methanobrevibacter boviskoreani.
abstract: Methanogens commonly inhabit swine intestine. We analyzed the gut archaeal population by extracting DNA from the feces of nine piglets. We performed PCR to target the V6-V8 region of the 16S rRNA gene. Subsequent denaturing gradient gel electrophoresis (DGGE) revealed the presence of Methanobrevibacter boviskoreani, which has not previously been identified in pigs. We confirmed these data with a PCR-DGGE analysis of the mcrA gene, and subsequent sequencing. At 63 days old, the only band in fecal samples corresponded to M. boviskoreani. The DGGE analysis also showed that Methanobrevibacter smithii, which was abundant at 28 days, was dramatically reduced at 42 days, and it completely disappeared at 63 days. To confirm these data, we quantified M. smithii and the total archaeal population by quantitative PCR (qPCR); moreover, we designed a new set of species-specific primers based on the 16S rRNA gene of M. boviskoreani. The qPCR results confirmed the reduction in M. smithii over time and a simultaneous increase in M. boviskoreani. At 63 days, the total numbers of archaea and M. boviskoreani genomes were comparable, which suggested that M. boviskoreani represented the dominant archaea. This work showed that the archaeal population shifted during weaning, and M. boviskoreani replaced M. smithii.
authors.affiliation: Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Federici
authors.affiliation: Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Miragoli
authors.affiliation: Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy.
authors.forename: Vincenza
authors.initials: V
authors.lastname: Pisacane
authors.affiliation: Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Rebecchi
authors.affiliation: Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29122 Piacenza, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Morelli
authors.affiliation: Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy marialuisa.callegari@unicatt.it.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Callegari
mesh_terms: D000818:Animals; D004262:DNA Restriction Enzymes / Q000235:genetics; D019641:DNA, Archaeal; D058645:Denaturing Gradient Gel Electrophoresis; D005243:Feces / Q000382:microbiology*; D041581:Methanobrevibacter / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D064307:Microbiota; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013552:Swine / Q000382:microbiology* / Q000502:physiology; D014886:Weaning
chemical_list: D019641:DNA, Archaeal; D012336:RNA, Ribosomal, 16S; D004262:DNA Restriction Enzymes; C060629:endodeoxyribonuclease McrA
keywords: 16S rRNA gene; PCR-DGGE; mcrA gene; methanogenic archaea; qPCR