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Gioddu, also known as “Miciuratu”, “Mezzoraddu” or “Latte ischidu” (literally meaning acidulous milk), is the sole variety of traditional Italian fermented milk. The aim of the present study was to elucidate the microbiota and the mycobiota occurring in artisan Gioddu sampled from three Sardinian producers by combining the results of viable counting on selective culture media and high-throughput sequencing. Physico-chemical parameters were also measured. The overall low pH values (3.80–4.22) recorded in the analyzed Gioddu samples attested the strong acidifying activity carried out by lactic acid bacteria during fermentation. Viable counts revealed the presence of presumptive lactococci, presumptive lactobacilli and non-Saccharomyces yeasts. A complex (kefir-like) microbiota of bacteria and yeasts was unveiled through sequencing. In more detail, Lactobacillus delbrueckii was found to dominate in Gioddu together with Streptococcus thermophilus, thus suggesting the establishment of a yogurt-like protocooperation. Unexpectedly, in all the three analyzed batches from two out of the three producers Lactobacillus kefiri was also detected, thus representing an absolute novelty, which suggests the presence of bioactive compounds (e.g. exopolysaccharides) similar to those characterizing milk kefir beverage. Mycobiota population, studied for the very first time in Gioddu, revealed a more complex composition, with Kluyveromyces marxianus, Galactomyces candidum and Geotrichum galactomyces constituting the core species. Further research is needed to disclose the eventual occurence in Gioddu of probiotic cultures and bioactive compounds (e.g. exopolysaccharides, angiotensin-converting enzyme inhibitory peptides and antimicrobial compounds) with potential health-benefits for the consumers.

The microbial contamination that occurs during the slaughtering process and during handling of the meat results in a shortening of the shelf-life of meat. In this study, which has had the aim of extending the shelf life of beefsteaks, pilot-scale treatments were carried out with aqueous ozone (AO) and electrolyzed water (EW) before vacuum packaging (VP). The development of the potentially active microbiota and the associated volatilome were followed over 15days of storage under refrigerated conditions (4°C), in order to define the potential long-term effects of the treatments and storage condition on microbiota. The targeted RNA-based amplicon sequencing identified Pseudomonas fragi as the most frequent species before and after the treatments with AO and EW, as well as in the untreated control. The tested treatments did not reduce the overall presence of this species, but they affected the intra-species distribution of its oligotypes, albeit slightly. With the progression of the refrigerated storage and the reduction of the oxygen availability, Lactobacillus sakei, Leuconostoc gasicomitatum and Lactococcus piscium became the dominant, potentially active, beef microbiota, as confirmed by microbiological data. When the OTU abundances and volatilome were coupled, a significant association was observed between the organic acids, esters and aldehydes and these lactic acid bacteria species. In spite of the limited effectiveness of the treatments over the short and long term, this study has provided a detailed view of beef spoilage using RNA as the sequencing target, strengthening and confirming the current knowledge based on DNA-amplicon sequencing.

In Italy, fermented sausages (called “salami”) are consumed in large quantities. Salami samples from a local meat factory in the area of Torino were analyzed at 0, 3, 7, 30 and 45 days of ripening. Swab samples from the production environment were also collected at the beginning of the experiment. The diversity of metabolically active microbiota occurring during the natural fermentation of salami was evaluated by using RT-PCR-DGGE coupled with RNA-based pyrosequencing of the 16S rRNA gene. A culture-dependent approach was also applied to identify and characterize isolated Staphylococcaceae and LAB populations. Staphylococcus succinus , Staphylococcus xylosus and Lactobacillus sakei were the species most frequently isolated during the maturation time. Rep-PCR analysis showed that S . succinus and S . xylosus isolated from swabs and salami samples clustered together, suggesting possible contamination during the production process. RT-PCR-DGGE and rRNA-based pyrosequencing showed that the metabolically active populations were dominated by S . succinus , Lb . sakei and Leuconostoc carnosum . In this specific case study, only a few species belonging to Staphylococcaceae, Lactobacillaceae and Leuconostocaceae may be metabolically active and contribute to determine the final characteristics of the products.

Next-generation sequencing has been used to strengthen knowledge about taxonomic diversity and ecology of fungi within food ecosystems. However, primer amplification and identification bias could edge our understanding into the fungal ecology. The aim of this study is to compare the performance of two primer pairs over two nuclear ribosomal RNA (rRNA) regions of the fungal kingdom, namely the ITS2 and 26S regions. Fermented cocoa beans were employed as biological material and the fungal ecology during fermentation was studied using amplicon-based sequencing tools, making use of a manually curated 26S database constructed in this study, and validated with SILVA's database. To explore potential biases introduced by PCR amplification of fungal communities, a mock community of known composition was prepared and tested. The relative abundances observed for ITS2 suggest that species with longer amplification fragments are underestimated and concurrently species that render shorter amplification fragments are overestimated. However, this correlation between amplicon length and estimation is not valid for all the species analysed. Variability in the amplification lengths contributed to the preferential amplification phenomenon. DNA extracted from twenty fermented cocoa bean samples were used to assess the performance of the two target regions. Overall, the metataxonomic data set recovered similar taxonomic composition and provided consistent results in OTU richness among biological samples. However, 26S region provided higher alpha diversity index and greater fungal rRNA taxonomic depth and robustness results compared with ITS2. Based on the results of this study we suggest the use of the 26S region for targeting fungi. Furthermore, this study showed the efficacy of the manually curated reference database optimized for annotation of mycobiota by using the 26S as a gene target.

Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry.

An antimicrobial polyethylene (PE) film was obtained by coating a nisin-based antimicrobial solution. PE sheets were coated on both sides and were used for the packaging of beefsteaks to be stored in air or modified atmosphere packaging (MAP, 60% O₂-40% CO₂). Microbial populations, species diversity, headspace volatile organic compounds, colour and sensory properties were monitored after 0, 1, 7 and 12 days of storage at 4 °C. The viable counts showed that there was an effect of MAP and antimicrobial film on the development of all the spoilage associated microbial populations. Carnobacterium spp., Brochothrix thermosphacta, Pseudomonas fragi and Rhanella aquatilis were found in most of the samples. C. maltaromaticum was identified in MRS bulk cells from samples stored in air as well as MAP. Quantitative data of headspace-SPME-GC/MS analysis showed that during storage the production of volatile organic compounds (VOCs) was affected by the use of the treated film and the MAP storage. Compounds such as phenylethylalcohol, nonanal, decanal and ethylbutanoate were produced only from 7 to 12 day of storage and only in the samples stored in air. In agreement with the microbiological and VOCs data, the meat stored in active packaging scored the best rankings in the sensory evaluation. Principal component analysis of microbial, sensory and instrumental data showed that beefsteaks stored with the combination of MAP and active packaging for 12 days at 4 °C differed from the other samples that were more associated to high microbial loads, VOCs concentration and meat off odour perception. In conclusion, the antimicrobial sheets in combination with MAP storage at 4 °C were effective for the storage of beefsteaks by retarding the growth of spoilage bacteria, determining lower concentration of VOCs and keeping acceptable levels of colour and other sensory parameters for more than 10 days.