2.3. Microbiota determination

MZ María Zapata-García
AM Alba Moratiel-Pellitero
DI Dolores Isla
EG Eva Gálvez
MG Marta Gascón-Ruiz
AS Andrea Sesma
RB Raquel Barbero
JG Javier Galeano
RC Rosa del Campo
MO Maitane Ocáriz
EQ Elisa Quílez
MC Mara Cruellas
AR Ariel Remírez-Labrada
JP Julián Pardo
LM Luis Martínez-Lostao
MD María Pilar Domingo
PE Patricia Esteban
IT Irene Torres-Ramón
AY Alfonso Yubero
JP José Ramón Paño
RL Rodrigo Lastra
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Samples were slowly defrosted at −20 °C for 24 h and 4 °C for another 24 h, to avoid bacterial death and DNA fragmentation. Total DNA was obtained by the QiaAmp kit (QIAGEN) from the saliva pellet after centrifugation. The bacterial composition was determined by polymerase chain reaction (PCR) amplification of the 16S rDNA V3–V4 region, and PCR products were pooled equally and submitted to massive sequencing (2x300 bp) on a MiSeq (Illumina, San Diego, CA, USA) platform at traslational genomics core support unit (UCAT) -Ramon y Cajal Health Research Institute (Madrid, Spain). The sequence's quality control was performed with DADA2, with a rarity of 12,000 sequences per sample. Amplicon sequencing variants were obtained by taxonomic assignment with the Silva_132 classifier. Alpha and beta diversity studies were performed, employing the q2-diversity add-on of QIIME2, after normalizing the samples by rarefaction (subsampling without replacement). In addition, a linear effect size discriminant analysis (LEfSe) was performed to assess which taxa explained the differences between groups. Sequence data were deposited in Genbank (BioProjectPRJNA1054537).

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