Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

Type Article
Date 2015-05
Language English
Author(s) Chaillou Stephane1, 2, Chaulot-Talmon Aurelie1, 2, Caekebeke Helene3, Cardinal MireilleORCID4, Christieans Souad5, Denis Catherine6, Desmonts Marie Helene7, Dousset Xavier8, 9, Feurer Carole10, Hamon Erwann7, Joffraud Jean-Jacques4, La Carbona Stephanie6, Leroi Francoise4, Leroy Sabine11, Lorre Sylvie12, Mace Sabrina8, 9, Pilet Marie-France8, 9, Prevost Herve8, 9, Rivollier Marina5, Roux Dephine3, Talon Regine11, Zagorec Monique8, 9, Champomier-Verges Marie-Christine1, 2
Affiliation(s) 1 : INRA, Lact Acid Bacteria & Meat Microbial Ecosyst Lab, UMR1319 Micalis, F-78350 Paris, France.
2 : AgroParis Tech, UMR Micalis, Paris, France.
3 : Plate Forme Innovat Nouvelles Vagues, Boulogne Sur Mer, France.
4 : IFREMER, Nantes, France.
5 : ADIV, Clermont Ferrand, France.
6 : ACTALIA, Villers Bocage, France.
7 : Aerial, Strasbourg, France.
8 : INRA, Secalim UMR1014, F-44026 Nantes, France.
9 : LUNAM Univ, Nantes, France.
10 : IFIP, Paris, France.
11 : INRA, Microbiol UR454, F-63122 St Genes Champanelle, France.
12 : Bioceane, Nantes, France.
Source Isme Journal (1751-7362) (Nature Publishing Group), 2015-05 , Vol. 9 , N. 5 , P. 1105-1118
DOI 10.1038/ismej.2014.202
WOS© Times Cited 119
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.
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Chaillou Stephane, Chaulot-Talmon Aurelie, Caekebeke Helene, Cardinal Mireille, Christieans Souad, Denis Catherine, Desmonts Marie Helene, Dousset Xavier, Feurer Carole, Hamon Erwann, Joffraud Jean-Jacques, La Carbona Stephanie, Leroi Francoise, Leroy Sabine, Lorre Sylvie, Mace Sabrina, Pilet Marie-France, Prevost Herve, Rivollier Marina, Roux Dephine, Talon Regine, Zagorec Monique, Champomier-Verges Marie-Christine (2015). Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. Isme Journal, 9(5), 1105-1118. Publisher's official version : https://doi.org/10.1038/ismej.2014.202 , Open Access version : https://archimer.ifremer.fr/doc/00268/37960/