Biology subjects

Coeuret, G.

Publications and source records attributed to Coeuret, G..

5 recordsLinked to original sources

bioRxiv2023

Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios

The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages).We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.

microbiology↗

bioRxiv2020

Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions

The international market of fresh-cut products has witnessed dramatic growth in recent years, stimulated by consumers demand for healthy, nutritious and convenient foods. One of the main challenging issues for the quality and safety of these products is the potential microbial spoilage that can significantly reduce their shelf-life. The complete identification of fresh-cut product microbiota together with the evaluation of environmental factors impact on microbial composition is of primary importance. We therefore assessed the fungal communities associated with the spoilage of ready-to-eat (RTE) pineapple using a metagenetic amplicon sequencing approach, based on the ITS2 region. Our results revealed a significant variability on fungal species composition between the different batches of RTE pineapple. The initial microbiota composition was the main influencing factor and determined the progress of spoilage. Temperature and storage time were the secondary factors influencing spoilage and their impact was depending on the initial prevalent fungal species, which showed different responses to the various modifications. Our results strongly suggest that further large-scale sampling of RTE pineapple production should be conducted in order to assess the full biodiversity range of fungal community involved in the spoilage process and for unravelling the impact of important environmental factors shaping the initial microbiota.

microbiology↗

bioRxiv2020

Positive effect of combining high pressure and biopreservation treatments on lowering the bacterial growth during storage of diced cooked ham with reduced nitrite salt

We investigated the combined effects of biopreservation and high pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of dice cooked ham from local supermarkets, were characterised and stored frozen. Second, sterile diced cooked ham, prepared with reduced level of nitrite was inoculated with two different microbiota collected from the aforementioned commercial samples together with a nisin producing Lactococcus lactis protective strain able to recover from a 500 MPa high pressure treatment. Dices were then treated at 500 MPa for 5 minutes and bacterial dynamics was monitored during storage at 8{degrees}C. Depending on samples, ham microbiota were dominated by different Proteobacteria (Pseudomonas, Serratia, Psychrobacter, or Vibrio) or by Firmicutes (Latilactobacillus and Leuconostoc). Applied alone, none of the treatments stabilized durably the growth of hams microbiota. Nevertheless, the combination of biopreservation and high pressure treatment was efficient to reduce the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that use of biopreservation and high pressure treatment as an alternative to nitrite reduction for ensuring cooked ham microbial safety merits attention but still requires improvement.

microbiology↗

bioRxiv2019

Heme uptake in Lactobacillus sakei evidenced by a new ECF-like transport system.

Lactobacillus sakei is a non-pathogenic lactic acid bacterium and a natural inhabitant of meat ecosystems. Although red meat is a heme-rich environment, L. sakei does not need iron or heme for growth, while possessing a heme-dependent catalase. Iron incorporation into L. sakei from myoglobin and hemoglobin was formerly shown by microscopy and the L. sakei genome reveals a complete equipment for iron and heme transport. Here, we report the characterization of a five-gene cluster (lsa1836-1840) encoding a putative metal iron ABC transporter. Interestingly, this cluster, together with a heme dependent catalase gene, is also conserved in other species from the meat ecosystem. Our bioinformatic analyses revealed that the locus might refer to a complete machinery of an Energy Coupling Factor (ECF) transport system. We quantified in vitro the intracellular heme in wild-type (WT) and in our {Delta}lsa1836-1840 deletion mutant using an intracellular heme sensor and ICP-Mass spectrometry for quantifying incorporated 57Fe heme. We showed that in the WT L. sakei, heme accumulation occurs fast and massively in the presence of hemin, while the deletion mutant was impaired in heme uptake; this ability was restored by in trans complementation. Our results establish the main role of the L. sakei Lsa1836-1840 ECF-like system in heme uptake. This research outcome shed new light on other possible functions of ECF-like systems. ImportanceLactobacillus sakei is a non-pathogenic bacterial species exhibiting high fitness in heme rich environments such as meat products, although it does not need iron nor heme for growth. Heme capture and utilization capacities are often associated with pathogenic species and are considered as virulence-associated factors in the infected hosts. For these reasons, iron acquisition systems have been deeply studied in such species, while for non-pathogenic bacteria the information is scarce. Genomic data revealed that several putative iron transporters are present in the genome of the lactic acid bacterium L. sakei. In this study, we demonstrate that one of them, is an ECF-like ABC transporter with a functional role in heme transport. Such evidence has not yet been brought for an ECF, therefore our study reveals a new class of heme transport system.

microbiology↗

bioRxiv2019

LARGE MICROBIOTA SURVEY REVEALS HOW THE MICROBIAL ECOLOGY OF COOKED HAM IS SHAPED BY DIFFERENT PROCESSING STEPS

The production of cooked ham involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O2 packaging permeability. We obtained about 200 samples from the same facility and we characterized i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to D-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O2-permeable packaging. Within a given slicing line, we observed campaign-based variations, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with L-lactic acid production and C. maltaromaticum with formic and acetic acid productions.

microbiology↗