Metataxonomic Profiling of Native and Starter Microbiota During Ripening of Gouda Cheese Made With Listeria monocytogenes-Contaminated Unpasteurized Milk

Fermented Foods, Health and the Gut Microbiome

Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.

Metagenomics Approaches for Improving Food Safety: A Review

ABSTRACT

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.

HIGHLIGHTS

The Use of Unique, Environmental Lactic Acid Bacteria Strains in the Traditional Production of Organic Cheeses from Unpasteurized Cow's Milk

The aim of this study was to use local LAB cultures for the production of organic acid-rennet cheeses from unpasteurized cow’s milk. Under industrial conditions, three types of cheese were produced, i.e., traditionally with acid whey (AW), with starter culture L. brevis B1, or with starter culture L. plantarum Os2. Strains were previously isolated from traditional Polish cheeses. Chemical composition, physico-chemical, microbiological, and sensory studies during 2 months of storage were carried out. As a result of this research, it was found that the basic composition was typical for semi-hard, partially skimmed cheeses. Mainly saturated fatty acids were detected. The cheeses were rich in omega-3, -6, and -9 fatty acids and conjugated linoleic acid (CLA), and were characterized by good lipid quality indices (LQI). All of the cheeses were characterized by a high number of lactic acid bacteria, with Enterobacteriaceae, yeast, molds, and staphylococci contaminants, which is typical microbiota for unpasteurized milk products. Water activity, pH, and total acidity were typical. A lower oxidation-reduction potential (ORP) of cheeses with the addition of strains and stability of the products during storage were observed. The B1 and Os2 cheeses were lighter, less yellow, had a more intense milk and creamy aroma, were softer, moister, and more elastic than AW cheese. The research results indicate the possibility of using environmental LAB strains in the production of high-quality acid-rennet cheeses, but special attention should be paid to the production process due to the microbiological quality of the cheeses.