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Istituto di scienza dell'alimentazione

Torna all'elenco Contributi in rivista anno 2018

Contributo in rivista

Tipo: Articolo in rivista

Titolo: A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota

Anno di pubblicazione: 2018

Formato: Elettronico

Autori: De Filippis F.; Parente E.; Zotta T.; Ercolini D.

Affiliazioni autori: Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", Portici, 80055, , Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Napoli, , Italy; Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, 85100, , Italy; Istituto di Scienze dell'Alimentazione - CNR, Avellino, 84100, , , Italy; Istituto di Scienze dell'Alimentazione - CNR, Avellino, 84100, , , Italy

Autori CNR:


Lingua: inglese

Abstract: 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.

Lingua abstract: inglese

Pagine da: 9

Pagine a: 17


International journal of food microbiology Elsevier
Paese di pubblicazione: Paesi Bassi
Lingua: inglese
ISSN: 0168-1605

Numero volume: 265

DOI: 10.1016/j.ijfoodmicro.2017.10.028

Referee: Sì: Internazionale

Stato della pubblicazione: Published version

Indicizzato da: Scopus [2-s2.0-85032670542]

Parole chiave:

  • 16S rRNA gene sequencing
  • De novo OTU clustering
  • OTU picking strategies
  • Alpha diversity
  • Beta diversity

URL: http://www.scopus.com/record/display.url?eid=2-s2.0-85032670542&origin=inward

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