DNA extraction and whole-genome shotgun sequencing
Microbial DNA extraction from the fecal samples was performed using the
Power Fecal DNA Isolation Kit (Mobio, USA), according to manufacturer’s
protocol. WGS library was constructed according to standard True Seq WGS
protocol provided by Illumina, Inc. (San Diego, USA). Library quality
for fragment size distribution was checked on Bioanalyzer 2100 using
high sensitivity DNA kit (Agilent technologies, USA). Library
quantification was performed using a Qubit Fluorometer (Invitrogen, USA)
and a Stratagene Mx3000P Real-time PCR Cycler (Agilent, USA) prior to
cluster generation in a c-Bot automated sequencing system (Illumina,
Inc.).