Fingerprint of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes

Latilactobacillus curvatus: A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits

Latilactobacillus curvatus is a candidate probiotic that has been included in the list of recommended biological agents for certification by the European Food Safety Authority. According to the published genomic information, L. curvatus has several genes that encode metabolic pathways of carbohydrate utilization. In addition, there are some differences in cell surface complex related genes of L. curvatus from different sources. L. curvatus also has several genes that encode bacteriocin production, which can produce Curvacin A and Sakacin P. Due to its ability to produce bacteriocin, it is often used as a bioprotective agent in fermented meat products, to inhibit the growth of a variety of pathogenic and spoilage bacteria. L. curvatus exerts some probiotic effects, such as mediating the production of IL-10 by dendritic cells through NF-κB and extracellular regulated protein kinases (ERK) signals to relieve colitis in mice. This review is the first summary of the genomic and biological characteristics of L. curvatus. Our knowledge on its role in the food industry and human health is also discussed, with the aim of providing a theoretical basis for the development of applications of L. curvatus.

Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates

Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.

Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage

In this study, we present the draft genome sequences of nine strains from various psychrotrophic species identified in meat products and being recognized as important emerging food spoilers. Many of these species have only one or few strains being sequenced, and this work will contribute to the improvement of the overall genomic knowledge about them.

Genotypic and phenotypic characterization of the food spoilage bacterium Brochothrix thermosphacta

Microbial food spoilage is responsible for significant economic losses. Brochothrix thermosphacta is one of the major bacteria involved in the spoilage of meat and seafood. Its growth and metabolic activities during food storage result in the production of metabolites associated with off-odors. In this study, we evaluated the genotypic and phenotypic diversity of this species. A collection of 161 B. thermosphacta strains isolated from different foods, spoiled or not, and from a slaughterhouse environment was constituted from various laboratory collections and completed with new isolates. A PCR test based on the rpoB gene was developed for a fast screening of B. thermosphacta isolates. Strains were typed by MALDI-TOF MS, rep-PCR, and PFGE. Each typing method separated strains into distinct groups, revealing significant intra-species diversity. These classifications did not correlate with the ecological origin of strains. The ability to produce acetoin and diacetyl, two molecules associated with B. thermosphacta spoilage, was evaluated in meat and shrimp juices. The production level was variable between strains and the spoilage ability on meat or shrimp juice did not correlate with the substrate origin of strains. Although the B. thermosphacta species encompasses ubiquitous strains, spoiling ability is both strain- and environment-dependent.

Lactobacillus sakei: A Starter for Sausage Fermentation, a Protective Culture for Meat Products

Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.

Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere

In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This strain was isolated from beef carpaccio packaged in a modified atmosphere. The draft genome will contribute to understanding the role of L. curvatus strains in food products (fermentation, biopreservation, or spoilage) through comparative genomics with other strains.

Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage

In this study, we present a draft genome sequence of Serratia proteamaculans MFPA44A14-05. This strain was isolated from a spoiled organic modified-atmosphere-packed beef carpaccio. The draft genome sequence will contribute to the understanding of the role of the S. proteamaculans species in meat and seafood spoilage.

Kefir Grains Change Fatty Acid Profile of Milk during Fermentation and Storage

Several studies have reported that lactic acid bacteria may increase the production of free fatty acids by lipolysis of milk fat, though no studies have been found in the literature showing the effect of kefir grains on the composition of fatty acids in milk. In this study the influence of kefir grains from different origins [Rio de Janeiro (AR), Viçosa (AV) e Lavras (AD)], different time of storage, and different fat content on the fatty acid content of cow milk after fermentation was investigated. Fatty acid composition was determined by gas chromatography. Values were considered significantly different when p<0.05. The highest palmitic acid content, which is antimutagenic compost, was seen in AV grain (36.6g/100g fatty acids), which may have contributed to increasing the antimutagenic potential in fermented milk. Higher monounsaturated fatty acid (25.8g/100g fatty acids) and lower saturated fatty acid (72.7g/100g fatty acids) contents were observed in AV, when compared to other grains, due to higher Δ9-desaturase activity (0.31) that improves the nutritional quality of lipids. Higher oleic acid (25.0g/100g fatty acids) and monounsaturated fatty acid (28.2g/100g fatty acids) and lower saturated fatty acid (67.2g/100g fatty acids) contents were found in stored kefir relatively to fermented kefir leading to possible increase of antimutagenic and anticarcinogenic potential and improvement of nutritional quality of lipids in storage milk. Only high-lipidic matrix displayed increase polyunsaturated fatty acids after fermentation. These findings open up new areas of study related to optimizing desaturase activity during fermentation in order to obtaining a fermented product with higher nutritional lipid quality.

Packaging gas selects lactic acid bacterial communities on raw pork

AIMS

To study the effect of different CO2-rich packaging atmospheres on the composition of lactic acid bacterial communities proliferating on raw pork.

METHODS AND RESULTS

Raw pork loin was inoculated with a mixture of 14 lactic acid bacteria (LAB) strains previously associated with meat and packaged with four gas atmospheres: (i) 100% CO2 (ii) 80% N2 20% CO2 (iii) 80% N2, 20% CO2, 0·4% CO and (iv) 80% O2, 20% CO2. The colony counts of LAB, pH and composition of packaging gas were monitored every other day during the storage of 14 days at +6°C. The compositions of lactic acid bacterial communities on pork were evaluated after 7 days of storage with culture-independent, terminal restriction fragment length polymorphism analysis of 16S rRNA gene fragments. After 14 days of storage, the compositions of lactic acid bacterial communities were evaluated using identification of plate-grown LAB isolates by numerical ribopattern analysis. The results showed that (i) high concentration of CO2 in packaging atmosphere favoured Lactobacillus sp. (ii) high concentration of O2 favoured Leuconostoc spp. (iii) atmosphere with 80% N2, 20% CO2 favoured Lactococcus sp.

CONCLUSIONS

The composition of modified packaging atmosphere is a major factor selecting lactic acid bacterial communities proliferating on raw meat.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides an explanation for the compositions of lactic bacterial communities on modified atmosphere packaged raw meat observed in other studies. The results should be considered when attempting to manipulate LAB communities in raw meat, e.g. by protective cultures.

Listeria spp. em carpaccio de carne bovina e perfil de resistência aos agentes antimicrobianos

O presente estudo foi conduzido com o objetivo de veri-ficar a ocorrência de Listeria spp. em 50 amostras de carpaccio de carne bovina comercializados em bares e restaurantes do município de Niterói, Rio de Janeiro, e avaliar o perfil de resistência dos isola-dos aos agentes antimicrobianos utilizados no tratamento de infec-ções. Constataram-se que 20% das amostras obtidas de restaurantes e 35% de bares estavam contaminadas com Listeria spp. Dentre as espécies, L. welshimeri foi isolada com maior frequência (81,82%), seguida de L. grayi, (13,66%) e L. monocytogenes(4,55%), sendo o ágar Oxford o meio de plaqueamento mais eficiente para isolamento. Foi verificada a ocorrência de resistência dos isolados frente a todos os agentes antimicrobianos testados, exceto à tetraciclina, diante da qual 95,5% dos isolados apresentaram sensibilidade. A multirresistência foi verificada em 68,75% das estirpes analisadas. Desta forma, concluiu-se que o consumo de carpaccio de carne bovina representa risco potencial, constituindo um grave problema de saúde coletiva, especialmente devido à confrmação de estirpes patogênicas e resistentes aos principais agentes antimicrobianos utilizados no tratamento de listeriose.

Population genetics of Lactobacillus sakei reveals three lineages with distinct evolutionary histories

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.