title: Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.
abstract: The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.
authors.affiliation: 1] INRA, UMR1319 Micalis, Lactic Acid Bacteria & Meat Microbial Ecosystems Laboratory, Paris, France [2] AgroParisTech, UMR Micalis, Paris, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Chaillou
authors.affiliation: 1] INRA, UMR1319 Micalis, Lactic Acid Bacteria & Meat Microbial Ecosystems Laboratory, Paris, France [2] AgroParisTech, UMR Micalis, Paris, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chaulot-Talmon
authors.affiliation: Plate-Forme d'Innovations Nouvelles Vagues, Boulogne-sur-mer, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Caekebeke
authors.affiliation: Ifremer, Nantes, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Cardinal
authors.affiliation: ADIV, Clermont-Ferrand, France.
authors.forename: Souad
authors.initials: S
authors.lastname: Christieans
authors.affiliation: ACTALIA, Villers Bocage, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Denis
authors.affiliation: Aérial, Strasbourg, France.
authors.forename: Marie Hélène
authors.initials: MH
authors.lastname: Desmonts
authors.affiliation: 1] INRA, UMR1014 Secalim, Nantes, France [2] LUNAM Université, Oniris, Nantes, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Dousset
authors.affiliation: IFIP, Paris, France.
authors.forename: Carole
authors.initials: C
authors.lastname: Feurer
authors.affiliation: Aérial, Strasbourg, France.
authors.forename: Erwann
authors.initials: E
authors.lastname: Hamon
authors.affiliation: Ifremer, Nantes, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Joffraud
authors.affiliation: ACTALIA, Villers Bocage, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: La Carbona
authors.affiliation: Ifremer, Nantes, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Leroi
authors.affiliation: INRA, UR454 Microbiologie, Saint-Genès-Champanelle, France.
authors.forename: Sabine
authors.initials: S
authors.lastname: Leroy
authors.affiliation: Biocéane, Nantes, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Lorre
authors.affiliation: 1] INRA, UMR1014 Secalim, Nantes, France [2] LUNAM Université, Oniris, Nantes, France.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Macé
authors.affiliation: 1] INRA, UMR1014 Secalim, Nantes, France [2] LUNAM Université, Oniris, Nantes, France.
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Pilet
authors.affiliation: 1] INRA, UMR1014 Secalim, Nantes, France [2] LUNAM Université, Oniris, Nantes, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Prévost
authors.affiliation: ADIV, Clermont-Ferrand, France.
authors.forename: Marina
authors.initials: M
authors.lastname: Rivollier
authors.affiliation: Plate-Forme d'Innovations Nouvelles Vagues, Boulogne-sur-mer, France.
authors.forename: Dephine
authors.initials: D
authors.lastname: Roux
authors.affiliation: INRA, UR454 Microbiologie, Saint-Genès-Champanelle, France.
authors.forename: Régine
authors.initials: R
authors.lastname: Talon
authors.affiliation: 1] INRA, UMR1014 Secalim, Nantes, France [2] LUNAM Université, Oniris, Nantes, France.
authors.forename: Monique
authors.initials: M
authors.lastname: Zagorec
authors.affiliation: 1] INRA, UMR1319 Micalis, Lactic Acid Bacteria & Meat Microbial Ecosystems Laboratory, Paris, France [2] AgroParisTech, UMR Micalis, Paris, France.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Champomier-Vergès
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D005060:Europe; D005506:Food Contamination; D005516:Food Microbiology; D008460:Meat / Q000382:microbiology*; D064307:Microbiota; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017747:Seafood / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S