Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese

Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum

The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.

Linoleic acid enrichment of cheese by okara flour and Geotrichum candidum overexpressing Δ12 fatty acid desaturase

BACKGROUND

Mold-ripened cheeses have low levels of unsaturated fatty acids (UFAs). Geotrichum candidum is an adjunct culture for the development of Geotrichum-ripened cheese but has a low ability to produce high levels of UFAs. Δ12 fatty acid desaturase (FADS12) is a pivotal enzyme that converts oleic acid (OA) to linoleic acid (LA) and plays a vital role in UFA biosynthesis. By investigating FADS12 catalytic activity from various species with OA substrates, we found that FADS12 from Mucor circinelloides (McFADS12) had the highest catalytic activity for OA.

RESULTS

In the current study, a plasmid harboring McFADS12 was constructed and overexpressed in G. candidum. Our results showed that LA production increased to 31.1 ± 1.4% in engineered G. candidum - three times higher than that in wild-type G. candidum. To enhance LA production, an exogenous substrate (OA) was supplemented, and the yield of LA was increased to 154 ± 6 mg L^-1 in engineered G. candidum. Engineered G. candidum was used as an adjunct culture for Geotrichum-ripened cheese production. The LA level reached 74.3 ± 5.4 g kg^-1 cheese, whereas the level of saturated fatty acids (SFAs) decreased by 9.9 ± 0.5%. In addition, the soybean byproduct (okara) was introduced into the engineered G. candidum growth and the level of LA increased to 126 ± 4 g kg^-1 cheese and the percentage of UFAs:SFAs increased from 0.8:1 to 1.3:1.

CONCLUSION

This study offers a suitable technology for converting SFAs to UFAs in Geotrichum-ripened cheeses and provides a novel trend for converting soybean waste into a value-added product. © 2022 Society of Chemical Industry.

Uncovering the Biotechnological Importance of Geotrichum candidum

Fungi make a fundamental contribution to several biotechnological processes, including brewing, winemaking, and the production of enzymes, organic acids, alcohols, antibiotics, and pharmaceuticals. The present review explores the biotechnological importance of the filamentous yeast-like fungus Geotrichum candidum, a ubiquitous species known for its use as a starter in the dairy industry. To uncover G. candidum's biotechnological role, we performed a search for related work through the scientific indexing internet services, Web of Science and Google Scholar. The following query was used: Geotrichum candidum, producing about 6500 scientific papers from 2017 to 2022. From these, approximately 150 that were associated with industrial applications of G. candidum were selected. Our analysis revealed that apart from its role as a starter in the dairy and brewing industries, this species has been administered as a probiotic nutritional supplement in fish, indicating improvements in developmental and immunological parameters. Strains of this species produce a plethora of biotechnologically important enzymes, including cellulases, β-glucanases, xylanases, lipases, proteases, and α-amylases. Moreover, strains that produce antimicrobial compounds and that are capable of bioremediation were identified. The findings of the present review demonstrate the importance of G. candidum for agrifood- and bio-industries and provide further insights into its potential future biotechnological roles.

Higher-order interactions shape microbial interactions as microbial community complexity increases

Non-pairwise interactions, or higher-order interactions (HOIs), in microbial communities have been described as significant drivers of emergent features in microbiomes. Yet, the re-organization of microbial interactions between pairwise cultures and larger communities remains largely unexplored from a molecular perspective but is central to our understanding and further manipulation of microbial communities. Here, we used a bottom-up approach to investigate microbial interaction mechanisms from pairwise cultures up to 4-species communities from a simple microbiome (Hafnia alvei, Geotrichum candidum, Pencillium camemberti and Escherichia coli). Specifically, we characterized the interaction landscape for each species combination involving E. coli by identifying E. coli's interaction-associated mutants using an RB-TnSeq-based interaction assay. We observed a deep reorganization of the interaction-associated mutants, with very few 2-species interactions conserved all the way up to a 4-species community and the emergence of multiple HOIs. We further used a quantitative genetics strategy to decipher how 2-species interactions were quantitatively conserved in higher community compositions. Epistasis-based analysis revealed that, of the interactions that are conserved at all levels of complexity, 82% follow an additive pattern. Altogether, we demonstrate the complex architecture of microbial interactions even within a simple microbiome, and provide a mechanistic and molecular explanation of HOIs.

Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage

Adjuevan is an Ivorian traditional fermented fish used as a condiment. However, the fermentation process and storage conditions may lead to the production of biogenic amines (BA) which can induce severe human toxicological effects. Thus, this study aimed to reveal the bacterial community diversity and the BA contents during the storage. Samples of adjuevan from the fish species Chloroscombrus chrysurus, Galeoides decadactylus, and Thunnus thynnus were collected from local producers, stored at ambient temperature (28-30 °C) and in a refrigerator (4 °C) over a period of 8 weeks. At 2-week intervals, BA were determined by HPLC and the bacterial communities analyzed using high-throughput sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. Results showed that histamine, cadaverine, putrescine, and tyramine were the major compounds. In adjuevan from T. thynnus, the level of histamine was over the maximum level of 200 mg/kg determined by Codex Alimentarius. For the other amines, no safety concerns are related. In total, 21 bacterial genera with a relative abundance ≥ 1% and belonging to 14 families and 5 phyla were detected. The Bacillaceae family was the most found at ambient temperature while Staphylococcaceae and Enterococcaceae were the most abundant in a refrigerator. The analysis of correlation showed that the increase of Lentibacillus leads to a decrease of the major BA at ambient temperature. On the contrary, the increase of Staphylococcus, Lactobacillus, Psychrobacter, Peptostreptococcus, and Fusobacterium leads to an increase of these biogenic compounds. Thus, Lentibacillus acted as BA-oxidizing bacteria while the others were found as BA-producing bacteria during adjuevan storage.

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.

Quantitative PCR reveals the frequency and distribution of 3 indigenous yeast species across a range of specialty cheeses

Indigenous microorganisms are important components of the complex ecosystem of many dairy foods including cheeses, and they are potential contributors to the development of a specific cheese's sensory properties. Among these indigenous microorganisms are the yeasts Cyberlindnera jadinii, Pichia kudriavzevii, and Kazachstania servazzii, which were previously detected using traditional microbiological methods in both raw milk and some artisanal specialty cheeses produced in the province of Québec, Canada. However, their levels across different cheese varieties are unknown. A highly specific and sensitive real-time quantitative PCR assay was developed to quantitate these yeast species in a variety of specialty cheeses (bloomy-rind, washed-rind, and natural-rind cheeses from raw, thermized, and pasteurized milks). The specificity of the quantitative PCR assay was validated, and it showed no cross-amplification with 11 other fungal microorganisms usually found in bloomy-rind and washed-rind cheeses. Cyberlindnera jadinii and P. kudriavzevii were found in the majority of the cheeses analyzed (25 of 29 and 24 of 29 cheeses, respectively) in concentrations up to 10⁴ to 10⁸ gene copies/g in the cheese cores, which are considered oxygen-poor environments, and 10¹ to 10⁴ gene copies/cm² in the rind. However, their high abundance was not observed in the same samples. Whereas C. jadinii was present and dominant in all core and rind samples, P. kudriavzevii was mostly present in cheese cores. In contrast, K. servazzii was present in the rinds of only 2 cheeses, in concentrations ranging from 10¹ to 10³ gene copies/cm², and in 1 cheese core at 10⁵ gene copies/g. Thus, in the ecosystems of specialty cheeses, indigenous yeasts are highly frequent but variable, with certain species selectively present in specific varieties. These results shed light on some indigenous yeasts that establish during the ripening of specialty cheeses.

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.

Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity

A detailed understanding of the microbiome of cheese and dairy products is key to the optimization of flavour, appearance, overall quality and safety. Microorganisms (including bacteria, yeasts, moulds and viruses, especially bacteriophages) from the environment can enter the dairy supply chain at multiple stages with several implications. The ability to track these microorganisms and to understand their function and interaction can be greatly enhanced by the use of high-throughput sequencing. Depending on the specific production technology, dairy products can harbor several strains and antibiotic-resistance genes that can potentially interact with the gut microbiome, once the product is ingested. Milk-associated or cheese-associated microbial communities with their interaction, function and diversity are a key factor for the dairy industry. Multi-omics approaches have been seldom utilized in literature and they need to be further considered. Studying the role, origin, diversity and function of the microbial species involved in the complex system of dairy production can help improve processes in several fields of application. Integrating an extensive sampling procedure with an extensive culture based methodology is necessary. To this end, local producers, and in general stakeholders, should be guided to discover and maintain their microbial diversity. A better management of microbial resources through precision fermentation processes will in turn reduce overall food losses and increase the possibility to use the microbiome in order to increase the local producers' income.

A Review on the General Cheese Processing Technology, Flavor Biochemical Pathways and the Influence of Yeasts in Cheese

Cheese has a long history and this naturally fermented dairy product contains a range of distinctive flavors. Microorganisms in variety cheeses are an essential component and play important roles during both cheese production and ripening. However, cheeses from different countries are still handmade, the processing technology is diverse, the microbial community structure is complex and the cheese flavor fluctuates greatly. Therefore, studying the general processing technology and relationship between microbial structure and flavor formation in cheese is the key to solving the unstable quality and standardized production of cheese flavor on basis of maintaining the flavor of cheese. This paper reviews the research progress on the general processing technology and key control points of natural cheese, the biochemical pathways for production of flavor compounds in cheeses, the diversity and the role of yeasts in cheese. Combined with the development of modern detection technology, the evolution of microbial structure, population evolution and flavor correlation in cheese from different countries was analyzed, which is of great significance for the search for core functional yeast microorganisms and the industrialization prospect of traditional fermented cheese.

Comparative Peptidomic and Metatranscriptomic Analyses Reveal Improved Gamma-Amino Butyric Acid Production Machinery in Levilactobacillus brevis Strain NPS-QW 145 Cocultured with Streptococcus thermophilus Strain ASCC1275 during Milk Fermentation

The high-gamma-amino butyric acid (GABA)-producing bacterium Levilactobacillus brevis strain NPS-QW 145, along with Streptococcus thermophilus (one of the two starter bacteria used to make yogurt for its proteolytic activity), enhances GABA production in milk. However, a mechanistic understanding of how Levilactobacillus brevis cooperates with S. thermophilus to stimulate GABA production has been lacking. Comparative peptidomic and metatranscriptomic analyses were carried out to unravel the casein and lactose utilization patterns during milk fermentation with the coculture. We found that particular peptides hydrolyzed by S. thermophilus ASCC1275 were transported and biodegraded with peptidase in Lb. brevis 145 to meet the growth needs of the latter. In addition, amino acid synthesis and metabolism in Lb. brevis 145 were activated to further support its growth. Glucose, as a result of lactose hydrolysis by S. thermophilus 1275, but not available lactose in milk, was metabolized as the main carbon source by Lb. brevis 145 for ATP production. In the stationary phase, under acidic conditions due to the accumulation of lactic acid produced by S. thermophilus 1275, the expression of genes involved in pyridoxal phosphate (coenzyme of glutamic acid decarboxylase) metabolism and glutamic acid decarboxylase (Gad) in Lb. brevis 145 was induced for GABA production.SIGNIFICANCE A huge market for GABA-rich milk as a dietary therapy for the management of hypertension is anticipated. The novelty of this work lies in applying peptide profiles supported by metatranscriptomics to elucidate (i) the pattern of casein hydrolysis by S. thermophilus 1275, (ii) the supply of peptides and glucose by S. thermophilus 1275 to Lb. brevis 145, (iii) the transportation of peptides in Lb. brevis and the degradation of peptides by this organism, which was reported to be nonproteolytic, and (iv) GABA production by Lb. brevis 145 under acidic conditions. Based on the widely reported contribution of lactic acid bacteria (LAB) and GABA to human health, the elucidation of interactions between the two groups of bacterial communities in the production of GABA-rich milk is important for promoting the development of functional dairy food and may provide new insight into the development of industrial GABA production.

Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum

The yeast Geotrichum candidum (teleomorph Galactomyces candidus) is inoculated onto mold- and smear-ripened cheeses and plays several roles during cheese ripening. Its ability to metabolize proteins, lipids, and organic acids enables its growth on the cheese surface and promotes the development of organoleptic properties. Recent multilocus sequence typing (MLST) and phylogenetic analyses of G. candidum isolates revealed substantial genetic diversity, which may explain its strain-dependant technological capabilities. Here, we aimed to shed light on the phenotypic and genetic diversity among eight G. candidum and three Galactomyces spp. strains of environmental and dairy origin. Phenotypic tests such as carbon assimilation profiles, the ability to grow at 35°C and morphological traits on agar plates allowed us to discriminate G. candidum from Galactomyces spp. The genomes of these isolates were sequenced and assembled; whole genome comparison clustered the G. candidum strains into three subgroups and provided a reliable reference for MLST scheme optimization. Using the whole genome sequence as a reference, we optimized an MLST scheme using six loci that were proposed in two previous MLST schemes. This new MLST scheme allowed us to identify 15 sequence types (STs) out of 41 strains and revealed three major complexes named GeoA, GeoB, and GeoC. The population structure of these 41 strains was evaluated with STRUCTURE and a NeighborNet analysis of the combined six loci, which revealed recombination events between and within the complexes. These results hint that the allele variation conferring the different STs arose from recombination events. Recombination occurred for the six housekeeping genes studied, but most likely occurred throughout the genome. These recombination events may have induced an adaptive divergence between the wild strains and the cheesemaking strains, as observed for other cheese ripening fungi. Further comparative genomic studies are needed to confirm this phenomenon in G. candidum. In conclusion, the draft assembly of 11 G. candidum/Galactomyces spp. genomes allowed us to optimize a genotyping MLST scheme and, combined with the assessment of their ability to grow under different conditions, provides a reliable tool to cluster and eventually improves the selection of G. candidum strains.

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses?

Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.

Milk microbiota: Characterization methods and role in cheese production

Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.

Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese

Fermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here, we show that during adaptation to cheese, phenotypic and metabolomic traits of wild Penicillium molds rapidly change to produce domesticated phenotypes with properties similar to those of the industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wild Penicillium strains serially passaged on cheese had reduced pigment, spore, and mycotoxin production. Domesticated strains also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g., geosmin) to fatty and cheesy volatiles (e.g., 2-nonanone, 2-undecanone). RNA sequencing demonstrated a significant decrease in expression of 356 genes in domesticated strains, with an enrichment of many secondary metabolite production pathways in these downregulated genes. By manipulating the presence of neighboring microbial species and overall resource availability, we demonstrate that the limited competition and high nutrient availability of the cheese environment promote rapid trait evolution of Penicillium molds.IMPORTANCE Industrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culture Penicillium camemberti can readily lose traits and quickly shift toward producing desirable aroma compounds. In addition to experimentally demonstrating a putative domestication pathway for P. camemberti, our work suggests that wild Penicillium isolates could be rapidly domesticated to produce new flavors and aesthetics in fermented foods.

Debaryomyces hansenii Metabolism of Sulfur Amino Acids As Precursors of Volatile Sulfur Compounds of Interest in Meat Products

The ability of Debaryomyces hansenii to produce volatile sulfur compounds from sulfur amino acids and the metabolic pathway involved have been studied in seven strains from different food origins. Our results proved that l-methionine is the main precursor for sulfur compound generation. Crucial differences in the sulfur compound profile and amino acid consumption among D. hansenii strains isolated from different food sources were observed. Strains isolated from dry pork sausages displayed the most complex sulfur compound profiles. Sulfur compound production, such as that of methional, could result from chemical reactions or yeast metabolism, while according to this study, thioester methyl thioacetate appeared to be generated by yeast metabolism. No relationship between sulfur compounds production by D. hansenii strains and the expression of genes involved in sulfur amino acid metabolism was found, except for the ATF2 gene in the L1 strain for production of methyl thioacetate. Our results suggest a complex scenario during sulfur compound production by D. hansenii.

Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei

Ripening cultures containing fungi and bacteria are widely used in smear-ripened cheese production processes, but little is known about the biotic interactions of typical ripening microorganisms at the surface of cheese. We developed a lab-scale mini-cheese model to investigate the biotic interactions of a synthetic community that was composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei, three species that are commonly used for smear-ripened cheese production. Transcriptomic analyses of cheese samples produced with different combinations of these three species revealed potential mechanisms of biotic interactions concerning iron acquisition, proteolysis, lipolysis, sulfur metabolism, and D-galactonate catabolism. A strong mutualistic interaction was observed between H. alvei and B. aurantiacum. We propose an explanation of this positive interaction in which B. aurantiacum would benefit from siderophore production by H. alvei, and the latter would be stimulated by the energy compounds liberated from caseins and triglycerides through the action of the proteases and lipases secreted by B. aurantiacum. In the future, it would be interesting to take the iron acquisition systems of cheese-associated strains into account for the purpose of improving the selection of the ripening culture components and their association in mixed cultures.

A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes

Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.

Cheese yeasts

Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt-tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH₃ from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so-called deacidification process enables the establishment of a salt-tolerant, Gram-positive bacterial community that is less acid-tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface-ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose-fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface-ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off-flavour, brown discolouration, and other visible alterations of cheese.

Symposium review: Genomic investigations of flavor formation by dairy microbiota

Flavor is one of the most important attributes of any fermented dairy product. Dairy consumers are known to be willing to experiment with different flavors; thus, many companies producing fermented dairy products have looked at culture manipulation as a tool for flavor diversification. The development of flavor is a complex process, originating from a combination of microbiological, biochemical, and technological aspects. A key driver of flavor is the enzymatic activities of the deliberately inoculated starter cultures, in addition to the environmental or "nonstarter" microbiota. The contribution of microbial metabolism to flavor development in fermented dairy products has been exploited for thousands of years, but the availability of the whole genome sequences of the bacteria and yeasts involved in the fermentation process and the possibilities now offered by next-generation sequencing and downstream "omics" technologies is stimulating a more knowledge-based approach to the selection of desirable cultures for flavor development. By linking genomic traits to phenotypic outputs, it is now possible to mine the metabolic diversity of starter cultures, analyze the metabolic routes to flavor compound formation, identify those strains with flavor-forming potential, and select them for possible commercial application. This approach also allows for the identification of species and strains not previously considered as potential flavor-formers, the blending of strains with complementary metabolic pathways, and the potential improvement of key technological characteristics in existing strains, strains that are at the core of the dairy industry. An in-depth knowledge of the metabolic pathways of individual strains and their interactions in mixed culture fermentations can allow starter blends to be custom-made to suit industry needs. Applying this knowledge to starter culture research programs is enabling research and development scientists to develop superior starters, expand flavor profiles, and potentially develop new products for future market expansion.

Ergot Alkaloid Synthesis Capacity of Penicillium camemberti

Ergot alkaloids are specialized fungal metabolites with potent biological activities. They are encoded by well-characterized gene clusters in the genomes of producing fungi. Penicillium camemberti plays a major role in the ripening of Brie and Camembert cheeses. The P. camemberti genome contains a cluster of five genes shown in other fungi to be required for synthesis of the important ergot alkaloid intermediate chanoclavine-I aldehyde and two additional genes (easH and easQ) that may control modification of chanoclavine-I aldehyde into other ergot alkaloids. We analyzed samples of Brie and Camembert cheeses, as well as cultures of P. camemberti, and did not detect chanoclavine-I aldehyde or its derivatives. To create a functioning facsimile of the P. camembertieas cluster, we expressed P. camemberti easH and easQ in a chanoclavine-I aldehyde-accumulating easA knockout mutant of Neosartorya fumigata The easH-easQ-engineered N. fumigata strain accumulated a pair of compounds of m/z 269.1288 in positive-mode liquid chromatography-mass spectrometry (LC-MS). The analytes fragmented in a manner typical of the stereoisomeric ergot alkaloids rugulovasine A and B, and the related rugulovasine producer Penicillium biforme accumulated the same isomeric pair of analytes. The P. camemberti eas genes were transcribed in culture, but comparison of the P. camemberti eas cluster with the functional cluster from P. biforme indicated 11 polymorphisms. Whereas other P. camembertieas genes functioned when expressed in N. fumigata, P. camembertieasC did not restore ergot alkaloids when expressed in an easC mutant. The data indicate that P. camemberti formerly had the capacity to produce the ergot alkaloids rugulovasine A and B.IMPORTANCE The presence of ergot alkaloid synthesis genes in the genome of Penicillium camemberti is significant, because the fungus is widely consumed in Brie and Camembert cheeses. Our results show that, although the fungus has several functional genes from the ergot alkaloid pathway, it produces only an early pathway intermediate in culture and does not produce ergot alkaloids in cheese. Penicillium biforme, a close relative of P. camemberti, contains a similar but fully functional set of ergot alkaloid synthesis genes and produces ergot alkaloids chanoclavine-I, chanoclavine-I aldehyde, and rugulovasine A and B. Our reconstruction of the P. camemberti pathway in the model fungus Neosartorya fumigata indicated that P. camemberti formerly had the capacity to produce these same ergot alkaloids. Neither P. camemberti nor P. biforme produced ergot alkaloids in cheese, indicating that nutritionally driven gene regulation prevents these fungi from producing ergot alkaloids in a dairy environment.

Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi

In industry, filamentous fungi have a prominent position as producers of economically relevant primary or secondary metabolites. Particularly, the advent of genetic engineering of filamentous fungi has led to a growing number of molecular tools to adopt filamentous fungi for biotechnical applications. Here, we summarize recent developments in fungal biology, where fungal host systems were genetically manipulated for optimal industrial applications. Firstly, available inducible promoter systems depending on carbon sources are mentioned together with various adaptations of the Tet-Off and Tet-On systems for use in different industrial fungal host systems. Subsequently, we summarize representative examples, where diverse expression systems were used for the production of heterologous products, including proteins from mammalian systems. In addition, the progressing usage of genomics and functional genomics data for strain improvement strategies are addressed, for the identification of biosynthesis genes and their related metabolic pathways. Functional genomic data are further used to decipher genomic differences between wild-type and high-production strains, in order to optimize endogenous metabolic pathways that lead to the synthesis of pharmaceutically relevant end products. Lastly, we discuss how molecular data sets can be used to modify products for optimized applications.

Sequencing of the Cheese Microbiome and Its Relevance to Industry

The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

The Evolution of gene regulation research in Lactococcus lactis

Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism. Among many other things, this has provided an unprecedented view of the major gene regulatory pathways involved in nitrogen and carbon metabolism and their overlap, and has led to the blossoming of the field of L. lactis systems biology. All of these advances have made L. lactis the paradigm of the LAB. This review will deal with the exciting path along which the research on the genetics of and gene regulation in L. lactis has trodden.

Shotgun Metagenomics and Volatilome Profile of the Microbiota of Fermented Sausages

Changes in the microbial gene content and abundance can be analyzed to detect shifts in the microbiota composition due to the use of a starter culture in the food fermentation process, with the consequent shift of key metabolic pathways directly connected with product acceptance. Meat fermentation is a complex process involving microbes that metabolize the main components in meat. The breakdown of carbohydrates, proteins, and lipids can lead to the formation of volatile organic compounds (VOCs) that can drastically affect the organoleptic characteristics of the final products. The present meta-analysis, performed with the shotgun DNA metagenomic approach, focuses on studying the microbiota and its gene content in an Italian fermented sausage produced by using a commercial starter culture (a mix of Lactobacillus sakei and Staphylococcus xylosus), with the aim to discover the connections between the microbiota, microbiome, and the release of volatile metabolites during ripening. The inoculated fermentation with the starter culture limited the development of Enterobacteriaceae and reduced the microbial diversity compared to that from spontaneous fermentation. KEGG database genes associated with the reduction of acetaldehyde to ethanol (EC 1.1.1.1), acetyl phosphate to acetate (EC 2.7.2.1), and 2,3-butanediol to acetoin (EC 1.1.1.4) were most abundant in inoculated samples (I) compared to those in spontaneous fermentation samples (S). The volatilome profiles were highly consistent with the abundance of the genes; elevated acetic acid (1,173.85 μg/kg), ethyl acetate (251.58 μg/kg), and acetoin (1,100.19 μg/kg) were observed in the presence of the starters at the end of fermentation. Significant differences were found in the liking of samples based on flavor and odor, suggesting a higher preference by consumers for the spontaneous fermentation samples. Inoculated samples exhibited the lowest scores for the liking data, which were clearly associated with the highest concentration of acetic acid.IMPORTANCE We present an advance in the understanding of meat fermentation by coupling DNA sequencing metagenomics and metabolomics approaches to describe the microbial function during this process. Very few studies using this global approach have been dedicated to food, and none have examined sausage fermentation, underlying the originality of the study. The starter culture drastically affected the organoleptic properties of the products. This finding underlines the importance of starter culture selection that takes into consideration the functional characteristics of the microorganism to optimize production efficiency and product quality.

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.

Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation

The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO₂, mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.

Fungi as a Source of Food

In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.

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.

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese.

IMPORTANCE

This study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria.

Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis

The microbial communities in cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a surface-ripened cheese by means of metatranscriptomic analysis. The cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of cheese microorganisms.

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipid catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. The results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.