A Multi-Omics Approach to Evaluate the Quality of Milk Whey Used in Ricotta Cheese Production

Food Safety Assessment and Nutraceutical Outcomes of Dairy By-Products: Ovine Milk Whey as Wound Repair Enhancer on Injured Human Primary Gingival Fibroblasts

The valorization of milk whey appears to be a promising strategy for managing by-products from dairy food industries, which incur demanding economic costs for treatment and/or disposal. Thanks to its numerous bioactive components, whey is expected to be increasingly incorporated into foods in the future. We investigated the safety of ovine milk whey through in vitro experiments on human primary gingival fibroblast (HGF-1) proliferation and wound healing. Fibroblasts play a crucial role in the repair processes from the late inflammatory phase until the final stages. Cells treated with varying concentrations of ovine whey (0.01%, 0.1%, 1%, and 10%) were able to close wounds more rapidly than vehicle-treated cells. Time- and dose-dependent responses were observed in cell populations exposed to ovine whey. Specifically, wounds treated with 0.1% and 10% milk whey showed better migratory capabilities compared to those treated with 0.01% and 1% milk whey after 24 and 48 h. In addition, ovine milk whey stimulates extracellular matrix deposition, as evidenced by the increasing levels of CD44 antigen density evaluated through FACS analysis, as well as COL1A1 expression measured both via RT-qPCR and immunofluorescence. This phenomenon was particularly evident at concentrations of 0.01% and 10%. Ensuring quality and safety has become a major concern for health authorities in the food industry. Our findings suggest that ovine milk whey is safe and possesses regenerative properties. It facilitates tissue re-establishment following exposure to environmental stress, particularly accelerating gingival wound closure.

Effect of a Co-Feed Liquid Whey-Integrated Diet on Crossbred Pigs' Fecal Microbiota

This study assessed the potential effect of a co-feed liquid whey-integrated diet on the fecal microbiota of 14 crossbred pigs. The experimental design was as follows: seven pigs were in the control group, fed with a control feed, and seven were in the experimental group, fed with the same control feed supplemented daily with liquid whey. The collection of fecal samples was conducted on each animal before the dietary treatment (T0) and one (T1), and two (T2) months after the beginning of the co-feed integration. In addition, blood samples were collected from each pig at the same time points in order to evaluate the physiological parameters. Taxonomic analysis showed a bacterial community dominated by Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria phyla that populated the crossbred pig feces. The diversity metrics suggested that the co-feed supplementation affected some alpha diversity indexes of the fecal microbiota. In addition, the differential abundance analysis at the genus level revealed significant differences for various genera, suggesting that the liquid whey supplementation potentially influenced a part of the bacterial community over time. Spearman's correlations revealed that the differential abundant genera identified are positively or negatively correlated with the physiological parameters.

Sustainable Approaches in Whey Cheese Production: A Review

Whey cheeses have been produced from the very early steps of cheesemaking practices as a sustainable way to utilize whey, which is the main by-product of cheesemaking. Traditional whey cheeses, manufactured with similar processes, are Ricotta, Ricotta salata or Ricottone, and Ricotta fresca in Italy; Anthotyros, Myzithra, Manouri, Xynomyzithra, and Urda in Greece; Urda in Serbia and Romania as well as in other countries such as Israel; Lor in Turkey; Anari in Cyprus; Skuta in Croatia and Serbia; Gjetost and Brunost in Norway; Mesost and Messmör in Sweden; Mysuostur in Iceland; Myseost in Denmark; Requeijão in Portugal; and Requesón in Spain and Mexico. The production of whey cheese is based on the denaturation of whey proteins by heating to 88–92 °C. The specific processing conditions and aspects of the microbiology of whey cheeses are discussed. The special characteristics of whey cheeses, which are high pH and high moisture content, make them susceptible to microbial growth. Due to the limited shelf life of these products, extended research has been carried out to extend the shelf life of whey cheese. The sustainable preservation approaches, such as modified atmosphere packaging, addition of herbs and/or plant extracts, and bio-preservation methods are reviewed. Moreover, novel whey cheeses focused on functional properties have developed during the last 10 years.

Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet

The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3-V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.

Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms

Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers' expectations of healthy products.

Growth and Biocontrol of Listeria monocytogenes in Greek Anthotyros Whey Cheese without or with a Crude Enterocin A-B-P Extract: Interactive Effects of the Native Spoilage Microbiota during Vacuum-Packed Storage at 4 °C

Effective biopreservation measures are needed to control the growth of postprocess Listeria monocytogenes contamination in fresh whey cheeses stored under refrigeration. This study assessed growth and biocontrol of inoculated (3 log₁₀ CFU/g) L. monocytogenes in vacuum-packed, fresh (1-day-old) or ‘aged’ (15-day-old) Anthotyros whey cheeses, without or with 5% of a crude enterocin A-B-P extract (CEntE), during storage at 4 °C. Regardless of CEntE addition, the pathogen increased by an average of 2.0 log₁₀ CFU/g in fresh cheeses on day 15. Gram-negative spoilage bacteria also increased by an average of 2.5 log₁₀ CFU/g. However, from day 15 to the sell-by date (days 35–40), L. monocytogenes growth ceased, and progressively, the populations of the pathogen declined in most cheeses. This was due to an unmonitored, batch-dependent natural acidification by spoilage lactic acid bacteria, predominantly Leuconostoc mesenteroides, which reduced the cheese pH to 5.5, and finally to ≤5.0. The pH reductions and associated declines in pathogen viability were greater in the CEntE-treated samples within each batch. L. monocytogenes failed to grow in cheeses previously ‘aged’ in retail for 15 days. Overall, high population levels (>7.5 log₁₀ CFU/g) of psychrotrophic Enterobacteriaceae, particularly Hafnia alvei, were associated with an extended growth and increased survival of L. monocytogenes during storage.

Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics

BACKGROUND

Protein powder identification presents a challenge in quality control. There is current deliberation of the specificity of methods for the identification of milk proteins, and the consensus identification method of whey protein from the United States Pharmacopeia Food Chemical Codex relies on a combined analysis of the testing of ash, fat, lactose, loss on drying, and protein. These methods are non-specific. Milk and whey proteins both contain background DNA content. Both milk and whey proteins retain source DNA (cow), but also have bacterial DNA from natural flora, the dairy plant, and in whey protein, the cheesemaking process. The DNA in these materials is retained post-processing, even after the pasteurization process.

OBJECTIVE

By utilizing 16S metagenomics, the bacterial DNA in protein powders can be sequenced and cross-referenced to a curated library to ultimately create a microbiome profile of these raw materials. This microbiome can be measured for alpha and beta diversity, specifically how many and which species of bacteria are present.

METHOD

Using 16S metagenomics, we measure alpha and beta diversity of the microbiome profile of each protein powder and use principle coordinate analysis to produce differential groupings, providing a novel identification method for raw materials.

RESULTS

In this study, we demonstrate that the microbiome of cow proteins can be used for raw material identification, as the microbiome of milk and whey proteins differ significantly. We also demonstrate that the microbiome of whey protein concentrate can differ from supplier to supplier.

CONCLUSIONS

Microbiome profiling by 16S metagenomics can be an important forensic tool for quality control.

HIGHLIGHTS

Principle Coordinate Analysis can be used as a statistical tool for protein differentiation using the protein microbiome.

Stem Cell Impairment at the Host-Microbiota Interface in Colorectal Cancer

Colorectal cancer (CRC) initiation is believed to result from the conversion of normal intestinal stem cells (ISCs) into cancer stem cells (CSCs), also known as tumor-initiating cells (TICs). Hence, CRC evolves through the multiple acquisition of well-established genetic and epigenetic alterations with an adenoma-carcinoma sequence progression. Unlike other stem cells elsewhere in the body, ISCs cohabit with the intestinal microbiota, which consists of a diverse community of microorganisms, including bacteria, fungi, and viruses. The gut microbiota communicates closely with ISCs and mounting evidence suggests that there is significant crosstalk between host and microbiota at the ISC niche level. Metagenomic analyses have demonstrated that the host-microbiota mutually beneficial symbiosis existing under physiologic conditions is lost during a state of pathological microbial imbalance due to the alteration of microbiota composition (dysbiosis) and/or the genetic susceptibility of the host. The complex interaction between CRC and microbiota is at the forefront of the current CRC research, and there is growing attention on a possible role of the gut microbiome in the pathogenesis of CRC through ISC niche impairment. Here we primarily review the most recent findings on the molecular mechanism underlying the complex interplay between gut microbiota and ISCs, revealing a possible key role of microbiota in the aberrant reprogramming of CSCs in the initiation of CRC. We also discuss recent advances in OMICS approaches and single-cell analyses to explore the relationship between gut microbiota and ISC/CSC niche biology leading to a desirable implementation of the current precision medicine approaches.

Sensory active substances causing off-odour in liquid whey during storage

Liquid whey is a nutritious product with high water activity and neutral pH. Therefore, it is very susceptible to microbiological spoilage that results in undesirable off-odors. Additionally, minimally processed foods are the recent trend so setting an appropriate shelf life is essential. The commonly used microbiological methods are lengthy and time-demanding, so a quick and early identification of microbial degradation would be a significant benefit. Here we tested a solid-phase microextraction, gas chromatography with mass spectrometry coupled with olfactometry analysis (SPME-GC-MS/O) on samples of sweet unpasteurized liquid whey stored at 6 °C, 12 °C and 25 °C for a week. We compared the common methods – plate methods, measurement of pH, and dry matter determination with our proposed SPME-GC-MS/O. We have identified seven sensory active compounds while octanoic acid and a compound not reliably identified by the MS detector (with main m/z observed 133 (100), 151 (65), and 135 (26)) being the most prominent. Microbiological methods proved irreplaceable for proper setting of storage conditions (with the growth of coliforms being significant (p <0.001) at 25 °C). However, SPME-GC-MS/O was able to identify volatile substances responsible for off-odors and can be used as a powerful tool to detect the cause of undesirable chemical and microbial changes in whey beverages.

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.

Enhanced Aromatic Profile and Functionality of Cheese Whey Beverages by Incorporation of Probiotic Cells Immobilized on Pistacia terebinthus Resin

: In the present study, cheese whey was utilized for the development of a novel functional beverage, using Lactobacillus casei ATCC 393 probiotic cells immobilized on Pistacia terebinthus resin (pissa Paphos). Evaluation of shelf life of the produced beverages showed that spoilage microorganisms were not observed in beverages containing P. terebinthus resin. Terpenes' rich content might have contributed to the antimicrobial activity of the produced beverages; however, no significant effect on the viability of the immobilized probiotic cells was obtained. Whey beverages containing the immobilized biocatalyst retained a high viability (>1 × 106 CFU/g) of probiotic cells during a storage period of 30 days at 4 °C. The superiority of whey beverages containing the immobilized biocatalyst was also highlighted by GC-MS analysis, while the enhanced aromatic profile, which was mostly attributed to the higher concentration of terpenes, was also detected during the sensory evaluation performed. Conclusively, this study indicated the high commercialization potential of these novel functional whey beverages, within the frame of a sustainable dairy waste valorization approach. To the best of our knowledge, this is the first food-oriented approach within the guidelines of the circular economy reported in the literature, using the autochthonous Pistacia terebinthus resin for the production of functional whey beverages.

Adalimumab Therapy Improves Intestinal Dysbiosis in Crohn's Disease

The response to treatment with biologic drugs, in patients with Crohn’s disease, could be associated with changes in gut microbiota composition. The aim of our study was to analyse the modification of microbiota during adalimumab therapy in patients with Crohn’s disease. We performed a prospective study in patients with Crohn’s disease analysing gut microbiota before start of adalimumab therapy (T0) and after six months of therapy (T1). Among the 20 included patients, the phylum Proteobacteria fell from 15.7 ± 3.5% at T0 to 10.3 ± 3.4% at T1 (p = 0.038). Furthermore, the trend in relation to therapeutic success was analysed. Regarding bacterial phyla, Proteobacteria decreased in patients in whom therapeutic success was obtained, passing from a value of 15.8% (± 4.6%) to 6.8 ± 3.1% (p = 0.049), while in non-responder patients, percentages did not change (T0 = 15.6 ± 5.7%, T1 = 16.8 ± 7.6%, p = 0.890). Regarding the Lachnospiraceae family, in patients with normalization of C reactive protein six 6 months of adalimumab therapy, it increased from 16.6 ± 3.1% at T0 to 23.9 ± 2.6% at T1 (p = 0.049). In conclusion, in patients who respond to Adalimumab therapy by decreasing inflammation, there is a trend of intestinal eubiosis being restored.

Volatile Flavor Compounds Profile and Fermentation Characteristics of Milk Fermented by Lactobacillus delbrueckii subsp. bulgaricus

Lactobacillus delbrueckii subsp. bulgaricus is one of the predominant lactic acid bacterial species used as starter cultures in industrial fermented dairy manufacturing, as it strongly affects the quality of the products. Volatile flavor compound profiles and fermentation characteristics are considered to be the most important indicators for starter culture screening. In the present study, volatile compounds in milk fermented by 17 test strains of L. delbrueckii subsp. bulgaricus and a commercial strain used as a control were identified using solid-phase microextraction (SPME) methods coupled with gas chromatography mass spectrometry (GC-MS). In total, 86 volatile flavor compounds were identified in the fermented milk upon completion of fermentation, including 17 carboxylic acids, 14 aldehydes, 13 ketones, 29 alcohols, 8 esters, and 5 aromatic hydrocarbon compounds. Various volatile flavor compounds (acetaldehyde, 3-methyl-butanal, (E)-2-pentenal, hexanal, (E)-2-octenal, nonanal, 2,3-butanedione, acetoin, 2-heptanone, 2-non-anone, formic acid ethenyl ester) were identified due to their higher odor activity values (>1). In addition, of the 17 test strains of L. delbrueckii subsp. bulgaricus, IMAU20312 (B14) and IMAU62081 (B16) strains exhibited good fermentation characteristics in milk compared with the control strain. The combination of the volatile flavor compound profile and fermentation characteristics in this work could be useful when selecting lactic acid bacteria that may serve as important resources in the development of novel fermented milk products.

Volatile aroma composition of distillates produced from fermented sweet and acid whey

Lactose within whey can be fermented and distilled to produce a potable distilled spirit. The aim of this study was to determine if acid and sweet whey types can be fermented and distilled using similar processes and to investigate differences in volatile aroma compounds for the 2 distillates. Fermentation and distillation of the 2 whey types progressed in a similar manner, using Kluyveromyces marxianus for the initial fermentation and a glass still fitted with a Vigreux column for the subsequent distillation. Ethanol content of the wash (fermented whey) varied considerably following each fermentation and ranged from 1.2 and 2.0% (wt/wt) with no clear trend between acid and sweet whey samples. Volatile aroma compounds were extracted using headspace solid-phase microextraction and identified via gas chromatography-mass spectrometry. Acid and sweet whey distillates contained unique volatile aromatic compounds, and significant differences in compound peak areas were observed. These differences may have an effect upon the organoleptic qualities of spirits produced from whey; therefore, whey source may be an important factor when fermenting and distilling whey.

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods

The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.

Effect of Microbial Interaction on Urea Metabolism in Chinese Liquor Fermentation

Urea is the primary precursor of the carcinogen ethyl carbamate in fermented foods. Understanding urea metabolism is important for controlling ethyl carbamate production. Using Chinese liquor as a model system, we used metatranscriptome analysis to investigate urea metabolism in spontaneous food fermentation processes. Saccharomyces cerevisiae was dominant in gene transcription for urea biosynthesis and degradation. Lysinibacillus sphaericus was dominant for urea degradation. S. cerevisiae degraded 18% and L. sphaericus degraded 13% of urea in their corresponding single cultures, whereas they degraded 56% of urea in coculture after 12 h. Compared to single cultures, transcription of CAR1, DAL2, and argA, which are related to urea biosynthesis, decreased by 51, 36, and 69% in coculture, respectively. Transcription of DUR1 and ureA, which are related to urea degradation, increased by 227 and 70%, respectively. Thus, coexistence of the two strains promoted degradation of urea via transcriptional regulation of genes related to urea metabolism.

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing

This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values. Acidity values showed a great variability too, probably in relation to the brine use prior to sampling. Despite their high salt content, brine microbial loads ranged from 2.11 to 6.51 log CFU/mL for the total mesophilic count. Microbial community profiling assessed by 16S rRNA gene sequencing showed that these ecosystems were dominated by Firmicutes and Proteobacteria, followed by Actinobacteria and Bacteroidetes. Cheese type and brine salinity seem to be the main parameters accountable for brine microbial diversity. On the contrary, brine pH, acidity and protein concentration, correlated to cheese brine age, did not have any selective effect on the microbiota composition. Nine major genera were present in all analyzed brines, indicating that they might compose the core microbiome of cheese brines. Staphylococcus aureus was occasionally detected in brines using selective culture media. Interestingly, bacterial genera associated with a functional and technological use were frequently detected. Indeed Bifidobacteriaceae, which might be valuable probiotic candidates, and specific microbial genera such as Tetragenococcus, Corynebacterium and non-pathogenic Staphylococcus, which can contribute to sensorial properties of ripened cheeses, were widespread within brines.