Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese

Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years

The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.

Probiotic Potential and Application of Indigenous Non-Starter Lactic Acid Bacteria in Ripened Short-Aged Cheese

There are massive sources of lactic acid bacteria (LAB) in traditional dairy products. Some of these indigenous strains could be novel probiotics with applications in human health and supply the growing needs of the probiotic industry. In this work, were analyzed the probiotic and technological properties of three Lactobacilli strains isolated from traditional Brazilian cheeses. In vitro tests showed that the three strains are safe and have probiotic features. They presented antimicrobial activity against pathogenic bacteria, auto-aggregation values around 60%, high biofilm formation properties, and a survivor of more than 65% to simulated acid conditions and more than 100% to bile salts. The three strains were used as adjunct cultures separately in a pilot-scale production of Prato cheese. After 45 days of ripening, the lactobacilli counts in the cheeses were close to 8 Log CFU/g, and was observed a reduction in the lactococci counts (around -3 Log CFU/g) in a strain-dependent manner. Cheese primary and secondary proteolysis were unaffected by the probiotic candidates during the ripening, and the strains showed no lipolytic effect, as no changes in the fatty acid profile of cheeses were observed. Thus, our findings suggest that the three strains evaluated have probiotic properties and have potential as adjunct non-starter lactic acid bacteria (NSLAB) to improve the quality and functionality of short-aged cheeses.

Comparative study of the bacterial community of organic and conventional cow's milk

Agricultural practises such as conventional and organic farming can potentially affect the microbial communities in milk. In the present study, the bacterial diversity of milk was investigated using high-throughput sequencing on ten organic and ten conventional farms in the Azores, a region where milk production is largely based on year-round grazing systems. The microbiota of milk from both production systems was dominated by Bacillota, Pseudomonadota, Actinomycetota and Bacteroidota. The organic milk showed greater heterogeneity between farms, as reflected in the dispersion of diversity indices and the large variation in the relative abundances of the dominant genera. In contrast, conventionally produced milk showed a high degree of similarity within each season. In the conventional production system, the season also had a strong influence on the bacterial community, but this effect was not observed in the organic milk. The LEfSe analysis identified the genus Iamia as significantly (p < 0.05) more abundant in organic milk, but depending on the season, several other genera were identified that distinguished organic milk from conventionally produced milk. Of these, Bacillus, Iamia and Nocardioides were associated with the soil microbiota in organic farming.

Microbial Evolution in Artisanal Pecorino-like Cheeses Produced from Two Farms Managing Two Different Breeds of Sheep (Comisana and Lacaune)

"Pecorino" is a typical semi-hard cheese obtained with raw or heat-treated sheep milk using procedures to valorize the raw material's chemical and microbiological properties. In the present study, using a high-throughput method of 16S rRNA gene sequencing, we assessed the evolution of the microbiome composition from milk to Pecorino-like cheese in artisanal processes using milk from Comisana and Lacaune sheep breeds. The comparative analysis of the bacterial community composition revealed significant differences in the presence and abundance of specific taxa in the milk microbiomes of the Comisana and Lacaune breeds. Next-Generation Sequencing (NGS) analysis also revealed differences in the curd microbiomes related to dairy farming practices, which have a relevant effect on the final structure of the Pecorino cheese microbiome.

Dynamic microbial and metabolic changes during Apulian Caciocavallo cheese-making and ripening produced according to a standardized protocol

The cheese microbiota plays a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheese coming from 4 different dairies in the same area and produced following standardized procedures have been examined, as well as the different bulk milks and natural whey starter cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis, have been carried out post-salting and throughout ripening time (2 mo) to investigate the major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on the microbiota biodiversity related to the production dairy plant as the result of the use of different NWS or intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by the Lactobacillus and, in 2 dairies (Art and SdC), Streptococcus genera associated with the NWS. The analysis allowed us to show that, although the diversity of identified genera did not change significantly between the rind, under-rind and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The qPCR mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWSs. The primary starter detected in NWS and cheese reassured the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and VFFA during ripening, while cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) have a lower total concentration of acetoin compared with Art and SdC. However, the sub-dominant strains and NSLAB present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although considering a delimited production area.

Brazilian indigenous nonstarter lactic acid bacteria enhance the diversification of volatile compounds in short-aged cheese

There is growing interest in using autochthonous lactic acid bacteria (LAB) that provide unique sensory characteristics to dairy products without affecting their safety and quality. This work studied the capacity of three Brazilian indigenous nonstarter LABs (NSLAB) to produce biogenic amines (BAs) and evaluated their effect on the volatile organic compounds (VOCs), microbial LAB communities, and physicochemical profile of short-aged cheese. Initially, the strain's potential for biosynthesis of BAs was assessed by PCR and in vitro assays. Then, a pilot-scale cheese was produced, including the NSLAB, and the microbial and VOC profiles were analyzed after 25 and 45 days of ripening. As a results, the strains did not present genes related to relevant BAs and did not produce them in vitro. During cheese ripening, the Lactococci counts were reduced, probably in the production of alcohols and acid compounds by the NSLAB. Each strain produces a unique VOC profile that changes over the ripening time without the main VOCs related to rancid or old cheese. Particularly, the use of the strain Lacticaseibacillus. paracasei ItalPN16 resulted in production of ester compounds with fruity notes. Thus, indigenous NSLAB could be a valuable tool for the enhancement and diversification of flavor in short-aged cheese.

Microbial succession and its correlation with the dynamics of flavor compounds involved in the fermentation of Longxi bacon

Introduction

Longxi bacon is a traditional fermented meat from Gansu province, China. The ripening process of the bacon is crucial for quality and flavor. The aim of this study was to gain deeper knowledges on the bacterial and fungal community diversity and the changes of chemical components including fatty acids and volatile compounds at different time points during the ripening of the bacon and to understand the relationship between microbial profiles and the chemical components related the bacon flavor.

Methods

Bacon samples were collected from days 0, 15, 30, 60 and 90. The bacterial and fungal compositions were analyzed with next generation sequencing targeting the 16S rDNA loci for bacteria and ITS loci for fungi. The fatty acids and the volatile components were analyzed by headspace solid phase micro extraction followed by gas chromatography/mass spectrometry (HS-SPME-GC/MS).

Results

We found that the abundance of bacteria in bacon was higher than that of fungi, and Psychrobacter, Brochothrix, Phoma and Trichoderma was the dominant bacon's population. The largest contributors of volatiles were aldehydes, ketones and esters, and the main fatty acids were palmitic, oleic and linoleic acids. Pearson correlation analysis between microbial succession and key flavor substances showed that the production of Longxi bacon flavor is the result of a combination of bacteria and fungi. Ten bacteria genera and six fungi genera were determined as functional core microbiota for the flavor production based their dominance and functionality in microbial community. In addition, bacteria and fungi are involved in the oxidation and hydrolysis of fatty acids during the ripening of bacon, which also contributes to the formation of bacon flavor.

Discussion

This study provides a comprehensive analysis of the key microbiota involved in shaping bacon's distinctive flavor. Here, the results presented should provide insight into the influence of the microenvironment on the microbial community in bacon and lay a foundation for further investigations into the food ecology of bacon.

Amino Acids Drive the Deterministic Assembly Process of Fungal Community and Affect the Flavor Metabolites in Baijiu Fermentation

Nutrient fluctuation is ubiquitous in fermentation ecosystems. However, the microbial community assembly mechanism and metabolic characteristics in response to nutrient variation are still unclear. Here, we used Baijiu fermentation as a case example to study the responses of microbial community assembly and metabolic characteristics to the variation of amino acids using high-throughput sequencing and metatranscriptomics analyses. We chose two fermentation groups (group A with low amino acid and group B with high amino acid contents). The two groups showed similar succession patterns in the bacterial community, whereas they showed different succession in the fungal community wherein Pichia was dominant in group A and Zygosaccharomyces was dominant in group B. The β-nearest taxon index (βNTI) revealed that bacterial community was randomly formed, whereas fungal community assembly was a deterministic process. Variance partitioning analysis and redundancy analysis revealed that amino acids showed the largest contribution to the fungal community (37.64%, P = 0.005) and were more tightly associated with it in group B. Further study revealed that serine was positively related to Zygosaccharomyces and promoted its growth and ethanol production. Metatranscriptomic analysis revealed that the differential metabolic pathways between the two groups mainly included carbohydrate metabolism and amino acid metabolism, which explained the differences of ethanol production and volatile metabolites (such as isoamylol, isobutanol, and 2-methyl-1-butanol). Then these metabolic pathways were constructed and related gene expression and active microorganisms were listed. Our study provides a systematical understanding of the roles of amino acids in both ecological maintenance and flavor metabolism in fermentation ecosystems. IMPORTANCE In spontaneous fermented foods production, nutrient fluctuation is a critical factor affecting microbial community assembly and metabolic function. Revealing the microbial community assembly mechanism and how it regulates its metabolic characteristics in response to nutrient variation is helpful to the management of the fermentation process. This study provides a systematical understanding of the effect of amino acids on the microbial community assembly and flavor metabolisms using Baijiu fermentation as a case example. The data of this study highlight the importance of the nutrient management in fermentation ecosystems.

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: "which and how many LAB are present in cow raw milk used for cheese production?," this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the "history" of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.

Distinctive Traits of Four Apulian Traditional Agri-Food Product (TAP) Cheeses Manufactured at the Same Dairy Plant

This study aimed to highlight the distinctive features of four Traditional Agri-food Products (TAP), namely, Caprino, Pecorino, Vaccino, and Cacioricotta cheeses produced at the same dairy plant to reveal any possible relationships between their microbiological and biochemical characteristics. Two distinct natural whey starter (NWS) cultures were used during Caprino and Vaccino cheesemaking, whereas no starter was used for the other cheeses. Cacioricotta retained the highest concentrations of salt and residual carbohydrates. Lactic acid bacteria dominated the microbiota of the cheeses. Furthermore, staphylococci represented an additional dominant microbial population in Cacioricotta. Although culture-dependent analysis showed that the use of NWS cultures only slightly affected the microbial community of cheeses, 16S metagenetic analysis showed that Lactobacillus helveticus dominated both the NWS cultures and the corresponding Caprino and Vaccino cheeses. This analysis indicated that Staphylococcus equorum and Streptococcus thermophilus dominated Cacioricotta and Pecorino cheeses, respectively. The highest peptidase activities were found in either Caprino or Vaccino. Enzymes involved in the catabolism of free amino acids and esterase showed the highest activity in Pecorino cheese. Each cheese showed a distinct profile of volatile organic compounds, with Pecorino being the richest cheese in carboxylic acids, ketones, and esters, related to lipolysis. The results of this study contribute to valorizing and safeguarding these TAP cheeses, sustaining local farming.

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.

Modelling and predicting population of core fungi through processing parameters in spontaneous starter (Daqu) fermentation

Traditional fermented foods are usually produced by spontaneous fermentation with multiple microorganisms. Environmental factors play important roles in microbial succession. However, it is still unclear how the processing parameters regulate the microbiota during fermentation. Here, we reveal the effects of processing parameters on the core microbiota in spontaneous fermentation of Chinese liquor starter. Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis, Aspergillus and Saccharomyces were identified as core microbiota using amplicon sequencing and metaproteomics analysis. Fermentation moisture gradually decreased from 34.8% to 14.2%, and fermentation temperature varied between 17.0 °C and 35.3 °C during the fermentation. Mantel test showed that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.05) significantly affected the core microbiota. Moreover, structural equation modelling analysis indicated that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.001) were respectively influenced by the processing parameters, room humidity and room temperature. The succession of Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis and Aspergillus were significantly affected by room humidity (P < 0.05), and the succession of Saccharomyces was significantly affected by room temperature (P < 0.001). Further, models were constructed to predict the population of core microbiota by room humidity and room temperature, using Gaussian process regression and linear regression (P < 0.05). This work would be beneficial for regulating microorganisms via controlling processing parameters in spontaneous food fermentations.

Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity

RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

The effects of dynamic bacterial succession on the flavor metabolites during Baijiu fermentation

The succession of microbial community significantly affect the flavor formation of traditional fermented foods and beverages. Chinese liquor (Baijiu) fermentation is a typical spontaneous solid-state fermentation process driven by natural microbiota. The type of process used to make liquor-craft or industrial-alters the operational environment and the aromatic qualities of the product contributed by various microbial consortia. But differences in microbial community assembly and temporal succession are often overlooked. In this study, we investigated bacterial community dynamics, substrate consumption, and metabolite production during both craft and industrial liquor-making processes (CLP and ILP, respectively). We found that the compositions of bacterial communities were different, even though no significant difference (p > 0.05) was observed in bacterial species between CLP and ILP at the beginning of fermentation. During ILP, glucose was used more rapidly by microflora, leading in turn to a higher ethanol production rate during the early stage of fermentation. The higher rate of ethanol production in ILP shortened the lifetime of bacteria such as Weissella, Pediococcus, Leuconostoc, and Bacillus during the early stage of fermentation. Lactobacillus sp. became dominant earlier in ILP than in CLP. Finally, the change in bacterial community dynamics led to changes in aroma compounds. Using CLP and ILP as a model system, our results illustrate the dynamic nature of Baijiu fermentations and microbial succession patterns therein. This can be applied to optimize the fermentation processes and flavors attributes of this and other fermented foods.

Human bile microbiota: A retrospective study focusing on age and gender

AIMS

The emerging biliary colonization of microorganisms in patients with biliary diseases may be devastating. Recent evidence suggests that age and gender may influence changes in the microbial composition of gut microbiota. To study the relationship between these parameters on bile microbiota, we retrospectively reviewed positive bile cultures following an endoscopic retrograde cholangiopancreatography (ERCP) in a QA-certified academic surgical unit of a single institution.

METHODS

449 positive bile cultures from 172 Italian patients with diseases of the biliopancreatic system hospitalized from 2006 through 2017 were investigated for aerobic, anaerobic, and fungal organisms. The patients were stratified into four age intervals (22-66, 67-74, 75-81, and 82-93 years) and followed up for five years.

RESULTS

Gram-positive bacteria (GPB) was negatively associated with age only in multivariate analysis (R_partial = -0.114, p = 0.017), with younger patients prone to harbor GPB and older patients likely to have Gram-negative bacteria (GNB). There was a definite link with the male gender using both univariate and multivariate analysis (p < 0.001). Enterococcus spp. was the most common strain identified in patients with GPB except for patients aged 67-74 years for male (95.2%) and female (80.9%) patients. Escherichia coli and Klebsiella spp. were most frequent than others in every group analyzed. Analogous results were found for bacteria Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas spp. and Stenotrophomonas spp. apart of the 2nd quartile.

CONCLUSIONS

Our study strengthens the bond of age and gender with bile microbiota composition and suggests that further investigations may be required in targeting the aging microbiome. Other studies should also focus on Mediterranean epidemiological characteristics and antibiotic resistance surveillance system strategies.

Bacterial Succession through the Artisanal Process and Seasonal Effects Defining Bacterial Communities of Raw-Milk Adobera Cheese Revealed by High Throughput DNA Sequencing

The bacterial community of the artisanal Adobera cheese from Los Altos de Jalisco was described through high-throughput sequencing of 16S rRNA gene libraries. Samples were collected in two different seasons (dry and rainy) during four key steps of the manufacturing process (raw milk, fresh curd, matured curd, and cheese). Bacterial diversity was higher in early steps in comparison with the final elaboration stages. Firmicutes and Proteobacteria were the most abundant phyla, strongly represented by the Streptococcaceae, Enterobacteriaceae and Lactobacillaceae families, and core bacteria genera such as Streptococcus spp., Lactococcus spp., and Lactobacillus spp. Undesirable bacteria, including Pseudomonas spp. and Acinetobacter spp., were also detected in raw milk but almost undetectable at the end of the cheese manufacturing process, and seemed to be displaced by lactic-acid bacteria-related genera. Seasonal effects were observed on the community structure but did not define the core microbiota composition. Predictive metabolism was related to membrane transport, and amino-acid, lipid, and carbohydrate metabolism pathways. Our results contribute to deduce the role of bacteria involved in Adobera cheese manufacturing in terms of the metabolism involved, cheese microbial safety, and how undesirable bacterial populations could be regulated by process standardization as a potential tool to improve safety.

Mannitol and erythritol reduce the ethanol yield during Chinese Baijiu production

Chinese Baijiu is prepared using multiple microbial strains and complex metabolites by simultaneous saccharification and fermentation (SSF). Yeasts are challenged by various endogenous and exogenous factors, detrimentally affecting the ethanol yield. It is imperative to identify and control inhibitory factors. In the present study, microbial taxa and metabolites during Baijiu fermentation were evaluated to identify inhibitors of ethanol production. We found that filamentous fungi and Bacillus, contributing to saccharification, were negatively related to the ethanol content (Spearman's |ρ| > 0.5, P < 0.05). To explore how they affect ethanol production, ten filamentous fungi and three Bacillus strains were isolated. In addition to glucose and maltose, polyols were simultaneously generated by filamentous fungi and Bacillus via the hydrolysis of starch, among which mannitol and erythritol had the highest contents of up to 41.56 ± 2.01 g/kg and 16.16 ± 1.13 g/kg, respectively. The presence of mannitol and erythritol inhibited ethanol production by the functional yeasts Saccharomyces cerevisiae and Pichia kudriavzevii. The presence of 10.0 g/L mannitol significantly (P < 0.01) decreased the ethanol yield of S. cerevisiae by 12.67% (from 39.34 ± 0.02% to 32.71 ± 0.49%). These results revealed that polyols may inhibit the production of Baijiu and other fermented foods, suggesting that the origin and influence of polyols should be a focus of future research.

Microbial high throughput phenomics: The potential of an irreplaceable omics

The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.

Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation

Table olives are one of the most well-known traditionally fermented products, and their global consumption is exponentially increasing. In direct brining, table olives are produced spontaneously, without any debittering pre-treatment. Up to date, fermentation process remains empirical and inconstant, as it is affected by the physicochemical attributes of the fruit, tree and fruit management of pro and post-harvest. In the present study, whole and cracked Picual table olives were fermented at industrial scale for 120 days, using three distinct methods (natural fermentation, inoculation with lactic acid bacteria (LAB) at a 7 or a 10% NaCl concentration). Microbial, physicochemical and sensorial alterations monitored during the whole process, and several differences were observed between treatments. Results indicated that in all treatments, the dominant microflora were LAB. Yeasts also detected in noteworthy populations, especially in non-inoculated samples. However, LAB population was significantly higher in inoculated compared to non-inoculated samples. Microbial profiles identified by metagenomic approach showed meaningful differences between spontaneous and inoculated treatments. As a result, the profound dominance of starter culture had a severe effect on olives fermentation, resulting in lower pH and higher acidification, which was mainly caused by the higher levels of lactic acid produced. Furthermore, the elimination of Enterobacteriaceae was shortened, even at lower salt concentration. Although no effect observed concerning the quantitated organoleptic parameters such as color and texture, significantly higher levels in terms of antioxidant capacity were recorded in inoculated samples. At the same time, the degradation time of oleuropein was shortened, leading to the production of higher levels of hydroxytyrosol. Based on this evidence, the establishment of starter culture driven Picual olives fermentation is strongly recommended. It is crucial to mention that the inoculated treatment with reducing sodium content was highly appreciated by the sensory panel, enhancing the hypothesis that the production of Picual table olives at reduced NaCl levels is achievable.

Structural and metabolic performance of p-cresol producing microbiota in different carbon sources

p-Cresol (PC) is a potential off-flavor and carcinogenic compound that affects food flavor and safety. However, controlling the production of PC when making fermented food is hindered by a lack of knowledge of the microbial diversity and the growth requirements of the microbiota that produce PC. To address this, the present study used three media with selected carbon sources (glucose, ethanol and lactic acid) to explore the microbial origin of PC and to determine the preferred carbon source for the PC-producing microbiota in the pit mud of the strong-aroma type Baijiu. The results showed that the different carbon sources affected the microbial structure, especially of the PC-producing microbiota. Glucose led to the highest production of PC and lactic acid to the lowest. The production of PC was significantly correlated (p < 0.05, |ρ| > 0.6) with Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella Soehngenia, Clostridium and Sedimentibacter in the glucose medium; with Proteiniborus, Ruminococcus and Sporanaerobacter in the ethanol medium; and with Lutispora and Tepidimicrobium in the lactic acid medium. Multiphasic metabolite target analysis further indicated that the PC-producing microbiota could also metabolize flavor compounds. Lactic acid could inhibit the production of PC and ensure that the microbiota produced the appropriate flavor compounds during culture. Collectively, Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella_Soehngenia, Clostridium, Sedimentibacter, Proteiniborus, Ruminococcus and Lutispora were identified as potential PC producers in three media with glucose preferred as the carbon source. These findings provide a perspective on the microbiota and carbon source preference for ultimately improving the quality of distilled alcoholic beverage.

Modeling and Regulation of Higher Alcohol Production through the Combined Effects of the C/N Ratio and Microbial Interaction

Too large of a higher alcohol content has negative effects on the liquor taste and health. Revealing the key microbes and their key driving forces is essential to regulate the higher alcohol content in spontaneous liquor fermentation. Herein, we used high-throughput sequencing associated with a multivariate statistical algorithm to reveal the contributing microbes for higher alcohol production in Chinese light-aroma-type liquor and identified that Saccharomyces and Pichia were the main contributors. In addition, the C/N ratio and microbial interaction were found to significantly affect the production of higher alcohols. Herein, we used response surface methodology to establish a predictive model for higher alcohol production with the regulating factors, and the content of total higher alcohols decreased significantly from 328.80 ± 24.83 to 114.88 ± 5.02 mg/L with the optimized levels of the regulators. This work would facilitate the control of flavor production via regulating microbial communities in food fermentation.

Finding a common core microbiota in two Brazilian dairies through culture and DNA metabarcoding studies

Dairy foods are complex ecosystems composed of microorganisms from different origins that can affect flavor and safety of final products. The objective of this paper is to assess the in-house microbiota of two Brazilian dairies and to discuss the possible implications of the taxa determined for food protection. In total, 27 samples from dairies were cultured in selective (Baird Parker, de Man, Rogosa and Sharpe) and non-selective (Brain Heart Infusion) media, and the isolates were identified by Sanger sequencing. Moreover, metagenomic DNA was directly extracted from samples and the structure of the bacterial community was determined by massive DNA sequencing followed by bioinformatics analyses. The results showed the majority of isolates belonged to the group of lactic acid bacteria, but Enterobacteriaceae, Staphylococcacceae, Bacillaceae, Pseudomonadaceae and Moraxellaceae were also detected. From the reads obtained in metataxonomics analyses, a heatmap was constructed and the top 20 OTUs (operational taxonomic units) were determined. Besides, 12 most prevalent bacterial taxa were assigned to the core microbiota of the dairies evaluated, which included Thiomonas thermosulfata, Alkalibacillus salilacus, Pseudomonas clemancea, Erythrobacter aquimans, Tetragenococcus doogicus, Macrococcus brunensis, Pseudomonas ludensis, Streptococcus dentinousetti, Serratia entomophila, Vagococcus teuberi, Lactococcus fujiensis and Tolumonas auensis. In conclusion, the results reveal the presence of bacteria that may be related to spoilage and also foodborne diseases, in microbial niches that also present rare taxa, highlighting the importance to consider culture-independent results to evaluate and improve food safety.

Raw Material Regulates Flavor Formation via Driving Microbiota in Chinese Liquor Fermentation

Raw material is important for flavors in fermented foods. Here, the effect of hulless barley on the microbiota in Chinese liquor was studied using two main cultivars (heilaoya and dulihuang). Six genera (Lactobacillus, Saccharomyces, Komagataella, Aspergillus, Pichia, and Weissella) were identified as flavor producers. Komagataella, mainly correlated with esters, dominated in heilaoya, and Pichia, mainly correlated with carbonyls, dominated in dulihuang. The Mantel test indicated reducing sugar drove the succession of microbiota (heilaoya: P = 0.001; dulihuang: P = 0.006). Especially, glucose (P = 0.0226) and fructose (P = 0.0168) presented the most significant correlations with Pichia and Komagataella, respectively. The simulative fermentation confirmed Komagataella phaffii QK2 grew better in heilaoya with more fructose, whereas Pichia fermentans PF grew better in dulihuang with more glucose. This work highlighted the effect of raw material on microbiota, which would be beneficial for regulating the quality of fermented foods.

Microbial shifts in Minas artisanal cheeses from the Serra do Salitre region of Minas Gerais, Brazil throughout ripening time

The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.

Microbial diversity and chemical analysis of Shuidouchi, traditional Chinese fermented soybean

Shuidouchi is a traditional Chinese fermented soybean product and its quality is largely affected by the microbes involved in the fermentation. In this study, eleven Shuidouchi samples were collected from southwest China and the microbial diversity and its correlations with chemical characteristics were investigated. Bacterial community was detected using 16S rRNA sequencing, along with bacterial and fungal viable plate counts. Biogenic amines and other chemical characteristics were determined by HPLC and corresponding chemical reaction methods. Among eleven Shuidouchi samples, 21 phyla and 356 genera were identified. Firmicutes, Bacteroidetes and Proteobacteria were the predominant phyla while Bacillus, Bacteroides and Lactobacillus were the main genera. The average cell number of bacteria, lactic acid bacteria and fungi were 1.6 × 106, 5.9 × 104 and 7.6 × 103 CFU/g, respectively. HPLC results showed that the mean concentration of tryptamine, β-phenylethylamine, putrescine, cadaverine, histamine, tyramine, spermidine and spermine were 23.11, 3.66, 12.21, 7.12, 8.13, 22.98, 24.72, and 39.00 mg/kg, respectively. The average content of other characteristics including amino acid nitrogen, titratable acidity, and reducing sugar were 2.08, 3.44, and 25.78 g/kg, respectively. Shuidouchi samples were slightly acidic or neutral. Fibrinolytic enzyme activity was detected only in one sample. Among top 52 identified genera, 9 genera showed positive correlations with the chemical characteristics of Shuidouchi while 15 genera were negatively associated. Our results indicated that Shuidouchi contained rich microbial resources and were edible safety based on the tested indexes. The associations identified between microbes and chemical characteristics could be further utilized in the food fermentation industry.

Use of autochthonous mesophilic lactic acid bacteria as starter cultures for making Pecorino Crotonese cheese: Effect on compositional, microbiological and biochemical attributes

The use of selected autochthonous mesophilic lactic acid bacteria as starter cultures was investigated according to the traditional protocol for making Pecorino Crotonose (PC). Leuconostoc mesenteroides subsp. mesenteroides 2A, Lactobacillus casei 23C and Lactobacillus plantarum 18C (Autochthonous Starter, AS1) and Leuc. mesenteroides subsp. mesenteroides 2A, and L. casei 25D and 16A (AS2) were isolated and identified from aged ewes' milk PC cheeses, selected based on several enzymatic activities, and used as starter cultures. As shown by the in vitro kinetic of acidification, selected starter cultures had suitable capabilities to acidify. The manufacture of PC cheeses was carried out at an industrial plant scale. A control cheese (CC) was also made, using commercial starters consisting of mesophilic and thermophilic species. Ripening lasted 105 days at 10 °C. A poly-phasic approach was used to compare cheeses during manufacture and ripening, mainly based on pyrosequencing of the 16S rRNA targeting DNA, proteolysis and volatile component analyses. Compared to CC, both autochthonous starter cultures slightly affected the gross chemical composition of PC cheese. The cell density of thermophilic starters of CC progressively decreased throughout ripening. Plate count and RAPD-PCR showed that the cell number of autochthonous lactobacilli cultures of PC cheeses, made with AS1 and AS2, was almost constant throughout ripening and abundantly higher than that observed in CC. As shown by culture-independent analysis, the OTUs found during ripening varied depending on the manufacture with or without autochthonous starter cultures. The major chemical differences among cheeses were the concentration of free amino acids and the synthesis of some key volatile components (e.g., 2-methyl-1-propanol, 2-methyl-1-butanol, isobutyric, isovaleric, and isocaproic acids). Compared to CC, the use of AS1 positively affected the overall cheese quality.

Evaluating the microbial ecology and metabolite profile in Kazak artisanal cheeses from Xinjiang, China

Kazak artisanal cheese is one of the famous fermented food in Uighur Autonomy Region of Xinjiang, China. However, the microbial ecology in Kazak artisanal cheeses across different regions is unclear. In this study, we determined the microbial community composition through amplicon sequencing and measured the flavor profile of 10 cheese samples from different regions of Xinjiang. The associations between microbial communities, flavors and environmental factors were examined by redundancy analysis and Monte Carlo permutation test. Cheeses from different regions had different microbial communities, which was mainly reflected in the relative abundance of Lactobacillus, Streptococcus, Issatchenkia, Debaryomyces and Kluyveromyces. In addition, Pichia and Torulaspora were also the key microbial groups, according to the high relative abundance and large co-occurrence incidence in the correlation network. Using the microbe-metabolites correlation analysis, the major flavor-producing taxa were identified as Kluyveromyces, Anoxybacillus, Torulaspora, Lactobacillus, Streptococcus and Dipodascus. Environmental factors accounted for the majority of the microbial community variations, 88.54% for bacteria and 75.71% for fungi. Compared to physico-chemical factors (temperature, moisture, and pH), geographical factors (longitude, latitude and elevation) had a stronger effect on microbial communities in cheese samples from different regions of Xinjiang.

Potential characterization of yeasts isolated from Kazak artisanal cheese to produce flavoring compounds

Cheese is a typical handcrafted fermented food in Kazak minority from the Uighur Autonomy Region in China and Central Asia. Among the microbial community that is responsible for Kazak cheese fermentation, yeasts play important role in flavor formation during ripening. To develop ripening cultures, we isolated 123 yeasts from 25 cheese products in Kazak, and identified 87 isolates by the D1/D2 domain of the large subunit rRNA gene sequence. Pichia kudriavzevii was the dominant yeast in Kazak cheese, followed by Kluyveromyces marxianus and Kluyveromyces lactis. Of these, the ability to exhibit enzyme of dominant isolates and contribution to the typical flavor of cheeses was assessed. Enzyme producing yeast strains were inoculated in Hazak cheese‐like medium and volatile compounds were identified by head space solid phase micro extraction coupled to gas chromatography and mass spectroscopy. Pichia kudriavzevii N‐X displayed the strongest extracellular proteolytic and activity on skim milk agar and produced a range of aroma compounds (ethanol, ethyl acetate, 3‐methylbutanol, and acetic acid) for Kazak cheese flavor, could be explored as ripening cultures in commercial production of Kazak cheeses.

Metagenomics insights into food fermentations

This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

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

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples.

Spatial Distribution of the Metabolically Active Microbiota within Italian PDO Ewes' Milk Cheeses

Italian PDO (Protected Designation of Origin) Fiore Sardo (FS), Pecorino Siciliano (PS) and Pecorino Toscano (PT) ewes' milk cheeses were chosen as hard cheese model systems to investigate the spatial distribution of the metabolically active microbiota and the related effects on proteolysis and synthesis of volatile components (VOC). Cheese slices were divided in nine sub-blocks, each one separately subjected to analysis and compared to whole cheese slice (control). Gradients for moisture, and concentrations of salt, fat and protein distinguished sub-blocks, while the cell density of the main microbial groups did not differ. Secondary proteolysis differed between sub-blocks of each cheese, especially when the number and area of hydrophilic and hydrophobic peptide peaks were assessed. The concentration of free amino acids (FAA) agreed with these data. As determined through Purge and Trap (PT) coupled with Gas Chromatography-Mass Spectrometry (PT-GC/MS), and regardless of the cheese variety, the profile with the lowest level of VOC was restricted to the region identified by the letter E defined as core. As shown through pyrosequencing of the 16S rRNA targeting RNA, the spatial distribution of the metabolically active microbiota agreed with the VOC distribution. Differences were highlighted between core and the rest of the cheese. Top and bottom under rind sub-blocks of all three cheeses harbored the widest biodiversity. The cheese sub-block analysis revealed the presence of a microbiota statistically correlated with secondary proteolysis events and/or synthesis of VOC.