A Systems-Wide Analysis of Proteolytic and Lipolytic Pathways Uncovers The Flavor-Forming Potential of The Gram-Positive Bacterium Macrococcus caseolyticus subsp. caseolyticus

Lipid Hydrolysis, Oxidation, and Fatty Acid Formation Pathway Mapping of Synergistically Fermented Sausage and Characterization of Lipid Mediating Genes

Starter cultures play a significant role in lipid hydrolysis, prevention of lipid oxidation, and synthesis of fatty acid in fermented sausage, enhancing product quality. In this study, five synergistic bacterial strains were used, including Pediococcus pentosaceus (B-3), Latilactobacillus sakei DLS-24 (D-24), Latilactobacillus acidophilus DLS-29 (D-29), Lactiplantibacillus pentosus (B-1), and Lactiplantibacillus plantarum (B-2). Sausage B1B3D24 gave the highest free fatty acid with 39.45 g/100 g at 45-Day. Based on 2-thiobarbituric acid reactive substance, B2B3 contains 112.68 MDA/kg. Lipoxygenase activity displays the lowest in B1B3D24 with 0.095 μmol/min·mg followed by B2B3 with 0.145 μmol/min·mg. B1B3D24 contains 11.35 g/kg of monounsaturated fatty acid with the highest content in eicosenoic acid (C20:1) and palmitoleic acid (C16:1). The fatty acid synthesis pathway in B1B3D24 contains an active positive interaction with PUFA to increase the isotopomers of ω-3 and ω-6 fatty acids. In addition, lipid mediating genes in B1B3D24 show the highest counts in fatty-acid synthase, carbonyl reductase 4, 3-oxoacyl-[acyl-carrier-protein] synthase III, hydroxysteroid 17-beta dehydrogenase 8, and acetyl-CoA carboxylase.

Revealing the characteristic aroma and boundary compositions of five pig breeds based on HS-SPME/GC-O-MS, aroma recombination and omission experiments

To clarify the characteristic aroma compounds and flavor discrepancies of five Chinese typical pig species, headspace-solid phase microextraction gas chromatography-olfactometry-mass spectrometry (HS-SPME/GC-O-MS), electronic nose (E-nose), aroma recombination and omission experiments were used to analyze the characteristic aroma and boundary of five boiled pork. A total of 38 volatile compounds were identified, of which 14 were identified as important odorants with odor-activity values (OAVs) greater than 1. Aroma recombination and omission experiments revealed 8 key characteristic aroma compounds, which significantly contributed to the overall aroma. Sensory evaluation of the recombination model with the 8 aroma compounds scored 3.0 to 4.0 out of 5 points. 12 potential markers were identified to distinguish by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), including (E)-2-octenal, 3-ethyl-2-methyl-1,3-hexadiene, (E)-2-heptenal, 2-pentylfuran, cyclooctanol, 1-heptanol, sec-butylamine, D-limonene, N-vinylformamide, 2,3-octanedione, 2-ethylfuran and 3-pentanamine. Alongside benzaldehyde and pentanal, the combinations and fluctuations of these 14 aroma markers were proposed to constitute the aroma boundaries of different pork breeds. The aroma-active substances were able to effectively differentiate different breeds.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

Effects of Ultra-High Pressure Synergistic Enzymatic Hydrolysis on Flavor of Stropharia rugoso-annulata

In this study, using gas chromatography-mass spectrometry (HS-SPME-GC-MS), electronic nose (E-nose), high performance liquid chromatography (HPLC), and electronic tongue (E-tongue) to analyze the effect of ultra-high pressure (UHP) synergistic enzymatic hydrolysis on the flavor compounds of enzymatic hydrolysates of S. rugoso-annulata. The results demonstrated that 38 volatile flavor substances were identified in the enzymatic hydrolysates of S. rugoso-annulata treated at atmospheric pressure and 100, 200, 300, 400, and 500 MPa, mainly 6 esters, 4 aldehydes, 10 alcohols, 5 acids, and 13 other volatile flavor substances, and the most kinds of flavor substances reached 32 kinds when the pressure was 400 MPa. E-nose can effectively distinguish the overall changes of enzymatic hydrolysates of S. rugoso-annulata treated with atmospheric pressure and different pressures. There was 1.09 times more umami amino acids in the enzymatic hydrolysates at 400 MPa than in the atmospheric pressure enzymatic hydrolysates and 1.11 times more sweet amino acids at 500 MPa than in the atmospheric pressure enzymatic hydrolysates. The results of the E-tongue indicate that the UHP treatment increased umami and sweetness and reduced bitterness, which was also confirmed by the results of amino acid and 5'-nucleotide analysis. In conclusion, the UHP synergistic enzymatic hydrolysis can effectively improve the overall flavor of the enzymatic hydrolysates of S. rugoso-annulata; this study also lays the theoretical foundation for the deep processing and comprehensive utilization of S. rugoso-annulata.

The emergence of novel macrolide resistance island in Macrococcus caseolyticus and Staphylococcus aureus of food origin

Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRI_msr) were found in multidrug-resistant S. aureus. In this study, novel SaRI_msr, SaRI_msr-III emerged from S. aureus. Another novel SaRI_msr-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRI_msr strains. All SaRI_msr-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRI_msr types, SaRI_msr-I (15.1 kb), SaRI_msr-II (16-17 kb), and SaRI_msr-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRI_msr-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRI_msr-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRI_msr-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRI_msr-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRI_msr-(I-III) and SaRI_msr-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRI_msr-III, SaRI_msr-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRI_msr-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRI_msr-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.

In vitro and in silico assessment of probiotic and functional properties of Bacillus subtilis DE111®

Bacillus subtilis DE111^® is a safe, well-tolerated commercially available spore-forming probiotic that has been clinically shown to support a healthy gut microbiome, and to promote digestive and immune health in both adults and children. Recently it was shown that this spore-forming probiotic was capable of germinating in the gastrointestinal tract as early as 3 h after ingestion. However, a better understanding of the mechanisms involved in the efficacy of DE111^® is required. Therefore, the present investigation was undertaken to elucidate the functional properties of DE111^® through employing a combination of in vitro functional assays and genome analysis. DE111^® genome mining revealed the presence of several genes encoding acid and stress tolerance mechanisms in addition to adhesion proteins required to survive and colonize harsh gastrointestinal environment including multi subunit ATPases, arginine deiminase (ADI) pathway genes (argBDR), stress (GroES/GroEL and DnaK/DnaJ) and extracellular polymeric substances (EPS) biosynthesis genes (pgsBCA). DE111^® harbors several genes encoding enzymes involved in the metabolism of dietary molecules (protease, lipases, and carbohyrolases), antioxidant activity and genes associated with the synthesis of several B-vitamins (thiamine, riboflavin, pyridoxin, biotin, and folate), vitamin K2 (menaquinone) and seven amino acids including five essential amino acids (threonine, tryptophan, methionine, leucine, and lysine). Furthermore, a combined in silico analysis of bacteriocin producing genes with in vitro analysis highlighted a broad antagonistic activity of DE111^® toward numerous urinary tract, intestinal, and skin pathogens. Enzymatic activities included proteases, peptidases, esterase's, and carbohydrate metabolism coupled with metabolomic analysis of DE111^® fermented ultra-high temperature milk, revealed a high release of amino acids and beneficial short chain fatty acids (SCFAs). Together, this study demonstrates the genetic and phenotypic ability of DE111^® for surviving harsh gastric transit and conferring health benefits to the host, in particular its efficacy in the metabolism of dietary molecules, and its potential to generate beneficial SCFAs, casein-derived bioactive peptides, as well as its high antioxidant and antimicrobial potential. Thus, supporting the use of DE111^® as a nutrient supplement and its pottential use in the preparation of functional foods.

Unraveling the Effects of Biochemical Drivers on the Bacterial Communities and Volatile Profiles in Refrigerated Sturgeon Filets at 4°C

Spoilage bacteria seriously influence the flavor and quality of fish meat. In this study, we investigated the quality characteristics, bacterial community, and volatile profiles of refrigerated (4°C) sturgeon filets during 10-day storage. On day 10, the refrigerated samples showed the lowest bacterial diversity and the largest difference in microbiota and biochemistry. The dominant genera in the fresh samples were Macrococcus, Acinetobacter, Moraxella, Brucella, and Pseudomonas, while the dominant bacteria changed into Acinetobacter, Carnobacterium, Macrococcus, Pseudomonas, and Psychrobacter at the end of storage. Our results suggest that these dominant taxa contribute to the spoilage of the refrigerated sturgeon filets. Meanwhile, during the storage, total viable counts, total volatile basic nitrogen, thiobarbituric acid-reactive substances, and trichloroacetic acid-soluble peptide significantly increased (P < 0.05), while the sensory score decreased steadily. Additionally, the ATP-related compounds and the K-value showed similarly increasing trends. The shelf-life of the refrigerated sturgeon filets was less than 8 days. The gas chromatography–ion mobility spectrometry results suggest that hexanal, ethyl acetate, ethanol, butanal, 1-propanol, isopentyl alcohol, 2-pentanone, 2-heptanone, ethyl propanoate, and propyl sulfide are potential chemical spoilage markers. The predicted metabolic pathways indicated an abundant carbohydrate metabolism and amino metabolism in the refrigerated sturgeon filets. This study provides insight into the determinants of sturgeon shelf-life and the spoilage process involved in refrigerated fish.

Analysis of the relationship between microorganisms and flavour development in dry-cured grass carp by high-throughput sequencing, volatile flavour analysis and metabolomics

Complex microbial community plays an important role for flavor formation in traditional dry-cured grass carp. To investigate the correlation between microorganisms and flavour development, the bacterial diversity and flavour quality of dry-cured fish at different stages of fermentation were analysed using high-throughput sequencing, volatile flavour analysis and metabolomics. Cobetia, Staphylococcus and Ralstonia were the dominant genera in dry-cured fish, with relative abundances of 37.78%, 34.46% and 3.2%, respectively. The flavour of dry-cured fish samples varied as the abundance of aldehydes, alcohols, small peptides, FAAs and carboxylic acids showed a great increase during fermentation. Moreover, there were significant correlations (P < 0.05) between specific microorganisms and volatile indicators, as well as flavour metabolites. Staphylococcus, as the dominant bacterial genus, is involved in the mechanism of flavour formation in dry-cured fish during fermentation. This information is useful for elucidating the mechanism of flavour formation in dry-cured fish.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Developments in effective use of volatile organic compound analysis to assess flavour formation during cheese ripening

In the burgeoning demand for optimization of cheese production, ascertaining cheese flavour formation during the cheese making process has been the focal point of determining cheese quality. In this research reflection, we have highlighted how valuable volatile organic compound (VOC) analysis has been in assessing contingent cheese flavour compounds arising from non-starter lactic acid bacteria (NSLAB) along with starter lactic acid bacteria (SLAB), and whether VOC analysis associated with other high-throughput data might help provide a better understanding the cheese flavour formation during cheese process. It is widely known that there is a keen interest to merge all omics data to find specific biomarkers and/or to assess aroma formation of cheese. Towards that end, results of VOC analysis have provided valuable insights into the cheese flavour profile. In this review, we are pinpointing the effective use of flavour compound analysis to perceive flavour-forming ability of microbial strains that are convenient for dairy production, intertwining microbiome and metabolome to unveil potential biomarkers that occur during cheese ripening. In doing so, we summarised the functionality and integration of aromatic compound analysis in cheese making and gave reflections on reconsidering what the role of flavour-based analysis might have in the future.

Technological Applications of Macrococcus caseolyticus and its Impact on Food Safety

Macrococcus spp. are Gram-positive cocci that belong to the Staphylococcaceae family; they are closely related to staphylococci, but, unlike staphylococci, they are not considered as human pathogens. Macrococcus spp. are recognized as relevant veterinary pathogens, and their presence has been reported in food products of animal origin. Macrococcus caseolyticus, the most studied species of the Macrococcus genus, is associated with the development of aroma and flavor in fermented foods and is, thus, used as starter cultures in fermentations. However, certain important issues regarding food safety must be taken into account when employing these microorganisms in fermentations. Recent studies have reported the presence of genes associated with resistance to methicillin and other antibiotics in M. caseolyticus. This can be harmful to human health as these genes can be transferred to other bacteria present in the food, mainly staphylococcal species. This work, therefore, aims to highlight the importance of a more critical view on the presence of macrococci in foods and the possible indirect risks to human health.