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.

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis

“…By comparing our results with a similar study on meat or fish products (Chaillou et al, 2015), it appears that environmental contamination through water seems to affect microbial spoilage population in food more than animal contamination.…”

Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity

“…For each sample, barcoded pyrosequencing of the 16S rRNA V1 to V3 region was performed using 27F and 534R universal primers, as described by Chaillou et al (20). Ten nanograms of DNA was used as the PCR template, and PCR bias was minimized with the following cycling conditions: a temperature gradient (60°C to 0.5°C/cycle) and 25 cycles, as described by Barott et al (28).…”

“…Depending on the degree of salt reduction, bacterial populations may remain quite stable, sometimes even with a decreased incidence of bacteria that cause meat spoilage (17). Furthermore, food microbiologists have recently highlighted the weaknesses of plating methods in assessing the overall diversity of potential meat spoilers (1,2,(19)(20)(21), in that the most abundant (often psychrotrophic) species are among the hardest to cultivate using conventional media. If the effect of salt reduction on the meat microbiota is to be thoroughly assessed, it is necessary to analyze the whole bacterial community, as the meat microbiota is often divided into a core dominant population and a productspecific subdominant population (20).…”

“…Furthermore, food microbiologists have recently highlighted the weaknesses of plating methods in assessing the overall diversity of potential meat spoilers (1,2,(19)(20)(21), in that the most abundant (often psychrotrophic) species are among the hardest to cultivate using conventional media. If the effect of salt reduction on the meat microbiota is to be thoroughly assessed, it is necessary to analyze the whole bacterial community, as the meat microbiota is often divided into a core dominant population and a productspecific subdominant population (20). Variations in these complex microbial assemblages can result in different forms and degrees of spoilage (22)(23)(24).…”

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

“…NGS analysis is aiming to tackle these obstacles, but as a relatively new approach so far has yielded descriptive results on the bacteria and yeast genera abundances that have been encountered during the various fermentation stages. Until now, studies from the food industry have already evinced this type of analysis as a promising strategy for the detection of previously undescribed spoiler bacteria [75,76], underlying its suitability for controlling alcoholic fermentation. Nevertherless, NGS analysis has as an intrinsic difficulty the overwhelming amount of metagenomic analysis tools, machine-learning algorithms, databases and parameters that the researcher has to choose from.…”