16S Metagenomics Analysis of Microbial Communities

The analysis was applied using the 16S Metagenomics app (version 1.1.0) from the Illumina BaseSpace platform and sequences with Phred < Q20 were removed. Operational taxonomic units (OTUs) were created, using Ribosomal Database Project Classifier (Wang et al., 2007 (link)) against the Illumina-curated version of GreenGenes reference taxonomy database (DeSantis et al., 2006 (link)), as described previously (Yuan et al., 2018 (link)). The classified OTUs were defined at ≥97% of sequence homology and converted to percentages (relative abundances), to determine the representation of each microbe among treatments. Alpha diversity indexes were calculated using the EstimateS version 9.1.0¹, by different metrics (Chao, Shannon, Simpson) after performing a rarefaction analysis. Rarefied OTU to 54,488 sequences (lowest number of reads obtained) were used to obtain these indices. Finally, all sequences were deposited to the National Centre for Biotechnology Information (NCBI) in Sequence Read Archive (SRA) under the BioProject PRJNA600153.

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Anagnostopoulos D.A., Kamilari E, & Tsaltas D. (2020). Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation. Frontiers in Microbiology, 11, 1128.

Publication 2020

16S Metagenomics app

Ribosomal

Corresponding Organization : Cyprus University of Technology

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independent variables

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dependent variables

Representation of each microbe among treatments (relative abundances), Alpha diversity indexes (Chao, Shannon, Simpson)

control variables

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