Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn’s disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, “Gentlemen, the microbes will have the last word for human health.” In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

The immune system is vital for safeguarding the human body against infections and inflammatory diseases. The role of diet and meal patterns in modulating immune function is complex, and highlighting this topic is crucial for identifying potential ways to improve immune health. In Europe, the Mediterranean diet and Western diet are the most common dietary patterns, and gaining an understanding of how they affect immune function is essential for public health. There are numerous inflammatory diseases that are observed in younger and older people. Some of the common diseases include polymyalgia rheumatica (PMR), spinal muscular atrophy (SMA), vasculitis, sarcopenia, cirrhosis, cancer, and fibromyalgia, but the main focus in this review article is on irritable bowel disease (IBD). In general, dietary choices can have an immense impact on the microbial flora of the gut in people with inflammatory diseases. The intake of Mediterranean-style foods promotes the growth of healthy bacteria that enhances the function of the immune system. On the other hand, it is mostly seen that the intake of Western-style foods leads to the growth of harmful gut bacteria that contributes to inflammation and disease development by weakening the immune system. Additionally, inflammation in the gut can impact brain function, leading to mood disorders, such as anxiety and depression. Rare inflammatory diseases, such as psoriasis and sarcoidosis, are of main interest in this article. All the above-mentioned common and rare inflammatory diseases have a certain relationship with the microbiota of the gut. The gut microbiome plays a significant role in IBD; fiber and prebiotic interventions may represent promising adjunct therapies for pediatric IBD by targeting the gut microbiome. By advancing a good overall arrangement of microorganisms in the stomach through dietary mediations, working on the side effects and alleviating of diseases might be conceivable. The gut microbiota can be affected differently by various dietary fatty acid types. There is also an involvement of genetics in the progression of IBD, such as transcriptional factors, and one gene of interest is the LCT gene, which encodes for lactase, an enzyme responsible for digesting lactose in the gut.

The increase in antimicrobial resistance and tolerance over the years has become a serious public health problem, leading to the inevitable development of alternative antimicrobial agents as substitutes for industrial pharmaceutical antibiotics targeting humans and animals under the concept of one health. Essential oils (EOs) extracted from aromatic and pharmaceutical plants incorporate several bioactive compounds (phytochemicals) that positively affect human and animal health. Herein, this work aimed to examine a standardized chemical composition and screen the antimicrobial and anti-biofilm activity of Thymus sibthorpii, Origanum vulgare, Salvia fruticosa, and Crithmum maritimum EOs against three different Staphylococcus aureus strains by gold-standard disc diffusion, broth microdilution, and microtiter plate biofilm assays. Therefore, the evaluation of the above-mentioned EOs were considered as substitutes for antibiotics to combat the ever-mounting antimicrobial resistance problem. The observed bacterial growth inhibition varied significantly depending on the type and concentration of the antimicrobials. Thymus sibthorpii was determined as the strongest antimicrobial, with 0.091 mg/mL minimum inhibitory concentration (MIC) and a 14–33 mm diameter inhibition zone at 5% (v/v) concentration. All tested EOs indicated almost 95% inhibition of biofilm formation at their half MIC, while gentamicin sulfate did not show sufficient anti-biofilm activity. None of the methicillin-resistant strains showed resistance to the EOs compared to methicillin-sensitive strains. Thymus sibthorpii and Origanum vulgare could be potential alternatives as antimicrobial agents to overcome the problem of microbial resistance. The tested EOs might be incorporated into antimicrobial products as safe and potent antimicrobial and anti-biofilm agents.

Origanum vulgare subsp. hirtum, Thymus vulgaris, and Salvia fructicosa are aromatic plants commonly found in Mediterranean countries and are traditionally used in Greece as a remedy for humans, since they are well known as potent antibacterial, antioxidant, and anti-inflammatory agents. Essential oils (EOs) derived from plants cultivated in the mountainous region of Epirus, Greece, were investigated for their inhibitory activity against key microorganisms with relevance to avian health, while also assessing their antioxidant and anti-inflammatory activity. The total phenolic content (TPC) of the EOs was estimated according to the Folin–Ciocalteu method, while the antioxidant capacity was tested through the EOs’ ability to scavenge free radicals by means of the DPPH, ABTS, and FRAP assays. Antibacterial and anti-inflammatory effects were examined by the agar disc diffusion method and the lipoxygenase (LOX) inhibition test, respectively. Furthermore, the EOs’ ability to inhibit the invasion of sporozoites of Eimeria tenella (Wisconsin strain) along with any toxic effects were assayed in Madin–Darby bovine kidney (MDBK) cells. The antioxidant activity of the EOs was observed in descending order: oregano > thyme > sage. The antimicrobial effects of thyme and oregano were equivalent and higher than that of sage, while the anti-inflammatory effect of thyme was higher compared to both sage and oregano. The intracellular invasion of sporozoites was evaluated by the detection of E. tenella DNA by qPCR from cell monolayers harvested at 2 and 24 h post-infection. Parasite invasion was inhibited by the addition of oregano essential oil at the concentration of 100 μg/mL by 83% or 93% after 2 or 24 h, respectively, and was higher compared to the addition of thyme and sage, which had similar effects, but at a less intensive level. The cytotoxic assessment of all three essential oils revealed that they had no effect on MDBK cells compared to dimethyl sulfoxide (DMSO), used as the control substance. The supplementation of oregano, thyme, and sage essential oils had a potent antioxidant, anti-inflammatory, antimicrobial, and anticoccidial in vitro effect that is comparable to synthetic substances or approved drugs, justifying the need for further evaluation by in vivo studies in broilers reared in the absence of antimicrobial and anticoccidial drugs or synthetic antioxidant and/or anti-inflammatory compounds.

Biomaterial-based therapies have been receiving attention for treating microbial infections mainly to overcome the increasing number of drug-resistant bacterial strains and off-target impacts of therapeutic agents by conventional strategies. A fibrous, non-soluble protein, collagen, is one of the most studied biopolymers for the development of antimicrobial biomaterials owing to its superior physicochemical, biomechanical, and biological properties. In this study, we reviewed the different approaches used to develop collagen-based antimicrobial devices, such as non-pharmacological, antibiotic, metal oxide, antimicrobial peptide, herbal extract-based, and combination approaches, with a particular focus on preclinical studies that have been published in the last decade.

Feta is a Greek protected designation of origin (PDO) brined curd white cheese made from small ruminants’ milk. In the present research, Greek Feta cheese bacterial diversity was evaluated via matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Analysis of 23 cheese samples, produced in different regions of the country, was performed in two ripening times (three or six months post-production). The identified microbiota were primarily constituted of lactic acid bacteria. A total of 13 different genera were obtained. The dominant species in both ripening times were Lactobacillus plantarum (100.0% and 87.0%, at three or six months post-production, respectively), Lactobacillus brevis (56.5% and 73.9%), Lactobacillus paracasei (56.5% and 39.1%), Lactobacillus rhamnosus (13.0% and 17.4%), Lactobacillus paraplantarum (4.3% and 26.1%), Lactobacillus curvatus (8.7% and 8.7%). Other species included Enterococcus faecalis (47.8% and 43.5%), Enterococcus faecium (34.8% and 17.4%), Enterococcus durans (13.0% and 17.4%), Enterococcus malodoratus (4.3% and 4.3%), and Streptococcus salivarius subsp. thermophilus (21.7% and 30.4%). The increased ripening time was found to be correlated to decreased total solids (r = 0.616; p = 0.002), protein (r = 0.683; p < 0.001), and PH (r = 0.780; p < 0.001). The results of this study contribute to a better understanding of the core microbiota of Feta cheese.