Taxonomic composition of microbial consortium grown anaerobically on lactate
Metagenomic analysis of the microbial communities was performed on the basis of the hypervariable V3-V4 region of the 16S rRNA gene. The specific sequences of universal 341F and 785R primers for the simultaneous detection of Bacteria and Archaea have been used for amplification of the V3-V4 region libraries. PCR was carried out with Q5 Hot Start High-Fidelity Master Mix (NEB). Sequencing was performed on the MiSeq sequencer with the 2 x 250 nt paired-end technology (PE), using the v2 Illumina kit. Automatic analysis of the data identifying the composition of the microbial communities was carried out in 16S Metagenomics software available on a BaseSpace server (Illumina). The analysis consisted of three steps: (i) automatic demultiplexing of the samples, (ii) generation the fastq files containing the raw reads, and (iii) classification of the reads into taxonomic category. The 16S Metagenomics Protocol provides classification of the reads to the species level, based on the reference sequences Greengenes v13_5 database, modified by Illumina.