DNA Extraction and metagenomic sequencing
To compare our results with the study performed by (Bendia, Signori, et
al., 2018), we used the same dataset and DNA extractions as a template
for the metagenomics. Due to low DNA mass even after several
concentration efforts, extracted DNA was subjected to multiple
displacement amplification (MDA) using the illustra GenomiPhi V2 DNA
amplification kit (GE Healthcare, Piscataway, NJ, USA), following the
manufacturer’s instructions. Three amplification reactions per sample
were pooled to obtain sufficient DNA for sequencing. DNA was then
purified using AMPure XP beads kit (Beckman Coulter) following the
manufacturer’s instructions. Library constructions and shotgun
metagenomic sequencing were conducted at “Laboratório Central de
Tecnologias de Alto Desempenho em Ciências da Vida” (LaCTAD),
Universidade Estadual de Campinas State (UNICAMP), on the Illumina Hiseq
2000 platform using 2x100 bp paired-end system.