To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period

Microbiological Quality of Plant-based Meat-alternative Products Collected at Retail Level in Switzerland

As the interest in plant-based alternative food products has increased significantly in the last years, it is also important to investigate these products regarding microbiological aspects. The aim of this study was to assess the microbiological quality and the occurrence of selected foodborne pathogens in plant-based meat alternative products (PBMA) collected at retail level in Switzerland. A total of 100 PBMA (84 vegan and 16 vegetarian products) was analyzed qualitatively for the presence of Salmonella, Listeria monocytogenes and quantitatively for Staphylococcus aureus, Bacillus cereus group members, Enterobacteriaceae, and the total viable count. Furthermore, pH measurements were carried out and the aw-value was determined. Isolates were further analyzed with Whole Genome Sequencing. The total viable count before the expiration date was between <2 log and 7 log CFU/g (median: 5.97 log CFU/g). In six (6%) samples, Enterobacteriaceae with 2 log to 3 log CFU/g were detected. No Salmonella and no Listeria monocytogenes were detected. However, seven products (7%) were contaminated with other Listeria spp. (six L. innocua and one L. seeligeri). Further findings were two (2%) Staphylococcus aureus ST8 with the presence of selx and tsst-1 genes, and five (5%) Bacillus cereus group members (three B. paranthracis, one B. cereus sensu stricto, and one B. cytotoxicus) which all were diarrhea-associated strains. This study provides data that are relevant for HACCP concepts of companies that produce plant-based meat alternative products and helps to define microbiological parameters that should be included when testing such products.

The microbial contaminants of plant-based meat analogues from the retail market

The aim of the study was to analyse the key microbial contaminants of plant-based meat analogues (PBMA) from retail. A total of 43 samples of PBMAs (12 frozen/31 chilled) in the "ready-to-cook" category, such as hamburgers, meatballs or breaded imitation steaks were purchased in retail stores in the Czech Republic in summer (n = 21) and autumn 2022 (n = 22). The detected indicator bacteria (total viable count, lactic acid bacteria, Enterobacteriaceae, yeasts, moulds) had relatively low values in the analysed PBMA samples and only rarely reached levels of 7 log CFU/g. E. coli, STEC and coagulase-positive staphylococci were not detected by isolation from plates in any of analysed samples. Mannitol positive Bacillus spp. were isolated from almost half of the analysed samples of the PBMA. B. cereus sensu lato was isolated from 3 samples by isolation from plates, and after enrichment in 35 samples (81 %). Clostridium perfringens could not be detected by isolation from plates, nevertheless after multiplication, it was detected in 21 % of samples. Analyses of PBMA samples revealed considerable variability in microbial quality. The presence of spore-forming bacteria with the potential to cause foodborne diseases is alarming. However, to evaluate the risks, further research focused on the possibilities of growth under different conditions of culinary treatment and preservation is needed.

Beef carcass microbiota after slaughtering and primary cooling: A metataxonomic assessment to infer contamination drivers

The impact of primary cooling on beef microbiota was investigated on six beef carcasses consecutively processed with the parallel use of metataxonomic and culture-dependent analysis. Samples were collected immediately after slaughtering (AS) and after the 24th-hour post-cooling (PC) from three different surfaces, namely neck, flank and thigh. The main objective was to examine whether the microbiota composition of beef carcasses changes as function of the surface sampled, primary cooling (from AS to PC) and animal's origin (breeder). The outcomes underline that primary cooling did not affect qualitatively the composition of the potentially active microbiota or the carcass superficial counts. Although slight changes in chemical-physical parameters like volatile organic compounds (VOCs) were observed after cooling, the carcasses microbiota and its inferred metabolic pathways varied among animals as a function of their origin. Co-occurrence and co-exclusion analyses underlined competition for the colonisation of the carcass surface between Brochothrix-Psychrobacter and Carnobacterium-Serratia-Pseudomonas. Once integrated in a comprehensive monitoring of the supply chain, the metataxonomic characterisation of the beef carcasses microbiota might represent a valid integrative approach to define the cuts' perishability and their appropriateness to specific packaging and storage methods. These new bits of knowledge could be the base to define good strategies for the prevention of meat spoilage.

Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina

We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.

Non-animal-based options for animal-based foods- towards a systematic terminology

The market has seen a rapid increase in animal-free products intended to replace animal-based foods due to concerns for human health and environmental sustainability. However, there is a lack of consistent terminology for these products, with various terms being used interchangeably, creating ambiguity. To address this issue, we propose a systematic nomenclature that defines the most commonly used terms, namely alternative, substitute, replacement, and analog, along with examples of each. In this nomenclature, a substitute primarily serves a culinary purpose, while a replacement is concerned with nutritional properties. An analog strives to satisfy both culinary and nutritional attributes to closely mimic animal-based foods in terms of sensory, nutritional, and functional characteristics. The term "alternative" serves as an umbrella term encompassing all possibilities. This work aims to promote a clearer understanding of such products and their intended use and facilitate a unified use of terminology across disciplines. This will also enable informed decision-making for consumers and greater transparency in the food industry. The health and environmental implications of these products are not discussed in this perspective.

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.