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Protocol publication

[…] -threads 16 -blast6out $i.ublast; done, To visualize the output from the CAZy annotation as a Venn diagram, generate protein ID lists for each enzyme class using a bash loop. Type "for i in *.ublast; do"., To transfer column 1 from the output file and to a new file, type "cat $i | cut -f 1 >$i.list"., Terminate the loop and type "; done"., Open the .list files in a text editor. Go to the website , select the number of sets as 5 and paste the content of each list file in a separate box. Download the resulting diagram as a .SVG file. for i in *.ublast; do cat $i | cut -f 1 >$i.list; done, Prior to bioinformatic processing, raw sequence reads were trimmed and adapters were removed using Trimmomatic software 28. After the trimming and filtering step, the number of reads was reduced to 50% of the sequence reads (Table 1). The average base phred score was >30 after quality control (Figure 2)., Pairs of DNA sequences which had overlapping regions were merged using FLASH software 29 to generate single longer reads, non-overlapping reads were kept in a separate file. 45.47% reads (105,343) combined successfully. Following the overlapping of reads using FLASH of reads, the resulting extended fragments underwent bacterial taxonomic classification using Kraken software 7 and were subsequently visualized with Krona software (Figure 3)., The majority of the bacterial species present in the silage metagenome are found within 4 prokaryotic phyla: Firmicutes (34%), Actinobacteria (28%), Proteobacteria (27%) and Bacteroidetes (7%). The distribution of classes present within these phyla can be seen in Figure 4. The most abundant species in the metagenome were Lactobacillus spp. (24%; Firmicutes), Corynebacterium spp. (8%; Actinobacteria), Propionibacterium spp. (3%; Actinobacteria) and Prevotella spp. (3%; Bacteroidetes). Species important to animal health and implicated in disease were also observed; Clostridium spp. (1%) Bacillus spp. (0.6%), Listeria spp. (0.2%) were predicted to be present in the s […]

Pipeline specifications

Software tools Trimmomatic, Kraken, Krona