The different pipelines that may be used in 16S rRNA gene profiling of bacterial 
communities are known to have a significant impact on alpha and beta diversity 
measures and this may prevent direct comparison of results obtained in studies 
using different bioinformatic approaches to analyse raw sequences. To evaluate 
the feasibility of meta-studies on food bacterial communities, we compared four 
analysis procedures, varying in OTU picking and taxonomy assignment strategies. 
A closed reference OTU picking resulted in the most divergent results in terms 
of both alpha and beta diversity, compared to open reference methods. 
Nevertheless, when OTUs were collapsed at the genus level, a high correlation 
was obtained among the estimated abundances of taxa for most studies. 
Aggregation of samples by their nature and occurrence of food spoilage or 
fermentation resulted in a very similar classification using two beta diversity 
analysis methods. We conclude that comparisons of data obtained from different 
studies are feasible at the genus level, when the same OTU picking strategy is 
used. Finally, we provide a new version of FoodMicrobionet (Parente et al., 
2016), including data from 26 recent studies on food bacterial communities, 
together with R scripts allowing both the extraction of data in formats which 
can be used in several analysis tools (including the R package phyloseq and the 
Cytoscape app CoNet) and the statistical and graphical analysis using common 
alpha- and beta-diversity analysis methods.