Profiling of bacterial and fungal communities of Mexican cheeses by high throughput DNA sequencing

Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing

Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.

Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity?

The microbial diversity of artisanal cheeses has been ever more extensively explored over recent years. Many new studies have been particularly focused on the detection and identification of fungi associated with cheese rinds. This is not surprising given that the composition and abundance of fungi on the cheese surface can significantly contribute to desirable sensory qualities, while also contributing to defects, particularly during ripening, and risks associated with the production of mycotoxins. Here we critically review the impact of fungi on the quality of artisanal cheeses, as well as the risks associated with the presence of particular species or strains with specific phenotypes. Ultimately, we address the question; should fungi be predominantly considered villains when it comes to artisanal cheese safety or could their presence be better exploited by producers in order to generate innovative products with greater added value? Such discussions will be increasingly important from the perspective of the future commercialization and regulation of artisanal cheeses that frequently contain a high abundance of moulds.

Fungal communities on alpine cheese rinds in Southern Switzerland

BACKGROUND

The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region.

RESULTS

Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars.

CONCLUSIONS

Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors.

Universal drivers of cheese microbiomes

The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Use of Autochthonous Lactic Acid Bacteria as Starter Culture of Pasteurized Milk Adobera Cheese

Adobera, a genuine, brick-shaped, lightly ripened, unstretched pasta filata-like cheese from Western México, is one of the most important market-share wise but is usually made with raw milk and prepared following artisanal procedures. A pasteurized milk cheese is needed to assess its safety and guarantee standardized quality features. However, no commercial Adobera cheese culture is available, as specific lactic acid bacteria relevant for its production have not been thoroughly identified. This study is aimed at comparing the technological and quality features of Adobera cheeses made with pasteurized milk inoculated with a mixture of autochthonous lactic acid bacteria (Lactobacillus and Leuconostoc strains) to those of traditional raw milk cheeses, hypothesizing that no significant differences would be found between them. Milk pasteurization promoted water retention into the cheese matrix, impacting its texture and color profiles. Raw milk cheeses were harder, more cohesive, and less elastic than pasteurized milk cheeses. Ripening markers were significantly higher in raw milk cheeses at all sampling times, although its evolution over time showed that the starter culture could exhibit similar proteolytic activity than that of native milk microbiota under favorable ripening conditions. The principal component analysis revealed apparent overall differences between raw Adobera cheeses and those made with pasteurized cheese milk.

Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing

Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00963-3.

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.

Illumina MiSeq sequencing reveals microbial community succession in salted peppers with different salinity during preservation

Chopped pepper is one of the traditional fermented pepper products in China. At present, the industrial production method is mainly to preserve the peppers with high salt about 1 year, and then make the product after desalination and seasoning when it is processed. However, the composition and succession of the bacterial community involved in the long-term preservation of salted pepper was complex. In this study, Illumina Miseq sequencing technology was used to reveal the succession in the bacterial community structure of different salted pepper within 10 months of preservation. The results showed that Firmicutes and Proteobacteria were dominant bacteria in all samples at the Phylum level. At the Genus level, among fresh unsalted capsicum, Fructobacillus (44.66%), Enterobacteriaceae unclassified (26.78%), Leuconostoc (12.04%) and Lactococcus (8.45%) had relatively high abundance. Enterobacteriaceae unclassified, Lactobacillus, Marinospirillum and Halomonas were identified as the main dominant bacteria in the samples with 6%-12% (w/w) salinity, and Enterobacteriaceae unclassified mainly appeared in the early stage of preservation. In 15% and 18%(w/w) salinity samples, with the increase of preservation time, the dominant genus was changed from Enterobacteriaceae unclassified to Chromohalobacterter, Tetragenococcus, Halomonas, Halovibrio, etc., while the relative abundance of Lactobacillus remained at an extremely low level. The bacterial structure of 6% (w/w) salinity samples changed significantly during preservation, while the distribution in PCoA analysis of salinity samples of 9% was similar to that of 12%. In the high-salinity samples (15%-18%), the composition of the community was highly similar in 0-6 months, but the composition changed significantly with the increase of the preservation time and the growth of halophilic bacteria (p < 0.01). Pearson correlation analysis was used to investigate that Lactobacillus exhibited a negative correlation with salinity (p < 0.01). And the salinity had a positive correlation with both the species richness and evenness in the samples, which might be the key factor for the change of the microbial community.

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.

Microbial diversity of representative traditional fermented sausages in different regions of China

AIMS

The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.

METHODS AND RESULTS

The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78·39, 13·13 and 7·14% in SC, 35·47, 30·36 and 28·04% in GD, 54·81, 28·91 and 14·00% in HN, 20·20, 58·16 and 17·31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.

CONCLUSIONS

The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.

Characterisation of fungal contamination sources for use in quality management of cheese production farms in Korea

OBJECTIVE

This study was conducted to determine the composition and diversity of the fungal flora at various control points in cheese ripening rooms of 10 dairy farms from six different provinces in the Republic of Korea.

METHODS

Floor, wall, cheese board, room air, cheese rind and core were sampled from cheese ripening rooms of ten different dairy farms. The molds were enumerated using YM petrifilm, while isolation was done on yeast extract glucose chloramphenicol agar plates. Morphologically distinct isolates were identified using sequencing of internal transcribed spacer region.

RESULTS

The fungal counts in 8 out of 10 dairy farms were out of acceptable range, as per hazard analysis critical control point regulation. A total of 986 fungal isolates identified and assigned to the phyla Ascomycota (14 genera) and Basidiomycota (3 genera). Of these Penicillium, Aspergillus, and Cladosporium were the most diverse and predominant. The cheese ripening rooms was overrepresented in 9 farms by Penicillium (76%), while Aspergillusin a single farm. Among 39 species, the prominent members were Penicillium commune, P. oxalicum, P. echinulatum, and Aspergillus versicolor. Most of the mold species detected on surfaces were the same found in the indoor air of cheese ripening rooms.

CONCLUSION

The environment of cheese ripening rooms persuades a favourable niche for mold growth. The fungal diversity in the dairy farms were greatly influenced by several factors (exterior atmosphere, working personnel etc.,) and their proportion varied from one to another. Proper management of hygienic and production practices and air filtration system would be effective to eradicate contamination in cheese processing industries.

Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd

BACKGROUND

Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter. In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation.

RESULTS

During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>10⁵  CFU g^-1 ) indicate a potential hazard to consumers.

CONCLUSION

The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products. © 2019 Society of Chemical Industry.

Amplicon sequencing reveals the bacterial diversity in milk, dairy premises and Serra da Canastra artisanal cheeses produced by three different farms

In this work, the amplicon sequencing of the 16 S rRNA gene was employed to investigate the bacterial diversity in ingredients, processing environment, and ripened cheeses collected from three farms producing Serra da Canastra artisanal cheese. The data obtained indicated a remarkable variability in the bacteria consortia of the milk, whey, and environmental samples collected in farms 1, 2, and 3, despite their location in the same city. On the other hand, the starter culture and final product (ripened cheese) presented more constant and similar microbiota no matter the farm. The findings suggest that Streptococcus and Lactococcus have competitive advantages throughout Serra da Canastra cheese-making/ripening, which is crucial for their high relative abundance in the final products. An exploratory assessment based on sequencing data available in the literature showed that the Serra da Canastra cheeses sequences clustered with specific cheese varieties that are also made from raw milk but ripened for very different periods. The findings of this study highlight that despite the variability of milk and whey microbiota among the three farms, the starter culture ("pingo") has strong relevance in shaping the microbiota of the final product.

Bifidobacterial Distribution Across Italian Cheeses Produced from Raw Milk

Cheese microbiota is of high industrial relevance due to its crucial role in defining the organoleptic features of the final product. Nevertheless, the composition of and possible microbe-microbe interactions between these bacterial populations have never been assessed down to the species-level. For this reason, 16S rRNA gene microbial profiling combined with internally transcribed spacer (ITS)-mediated bifidobacterial profiling analyses of various cheeses produced with raw milk were performed in order to achieve an in-depth view of the bifidobacterial populations present in these microbially fermented food matrices. Moreover, statistical elaboration of the data collected in this study revealed the existence of community state types characterized by the dominance of specific microbial genera that appear to shape the overall cheese microbiota through an interactive network responsible for species-specific modulatory effects on the bifidobacterial population.

Investigation of physicochemical composition and microbial communities in traditionally fermented vrum from Inner Mongolia

Mongolian traditionally fermented vrum is known for its functional characteristics, and indigenous microbial flora plays a critical role in its natural fermentation. However, studies of traditionally fermented vrum are still rare. In this study, we investigated the artisanal production of traditionally fermented vrum from Inner Mongolia. In general, its physicochemical composition was characterized by 34.5 ± 8% moisture, 44.9 ± 12.1% fat, 10.6 ± 3.2% protein, and 210 ± 102°T. The total lactic acid bacteria and yeast counts ranged from 50 to 2.8 × 10⁸ cfu/g and from 0 to 1.1 × 10⁶ cfu/g, respectively. We studied bacterial and fungal community structures in 9 fermented vrum; we identified 5 bacterial phyla represented by 11 genera (an average relative abundance >1%) and 8 species (>1%), and 3 fungal phyla represented by 8 genera (>1%) and 8 species (>1%). Relative abundance values showed that Lactococcus and Lactobacillus were the most common bacterial genera, and Dipodascus was the predominant fungal genus. This scientific investigation of the nutritional components, microbial counts, and community profiles in Mongolian traditionally fermented vrum could help to develop future functional biomaterials and probiotics.

Microbial Profile of the Leachate from Mexico City’s Bordo Poniente Composting Plant: An Inoculum to Digest Organic Waste

In recent years, municipal solid waste (MSW) management has become a complex problem worldwide. Similarly, Mexico City is facing such a situation for the management and treatment of organic fraction of municipal solid waste (OFMSW). Therefore, in this work, we investigated whether leachate from the composting plant, Bordo Poniente, located in Mexico City can be used as an inoculum for the treatment of OFMSW using thermophilic anaerobic digestion (AD) with a hydraulic retention time of 30 days. We analyzed the physicochemical properties of the leachate and performed a biochemical methane potential test. Archaeal and bacterial diversity was also identified using high throughput DNA sequencing of 16S rDNA libraries. Methane yield was 0.29 m3 CH4/kg VSadded in the positive control and 0.16 m3 CH4/kg VSadded in the treatment group. The phylum, Bacteroidetes, and genus, Methanosarcina, prevailed in the leachate. However, in thermophilic conditions, the microbial communities changed, and the phylum, Firmicutes, genera, Methanoculleus, and candidate genus, vadinCA11, were dominant in the treatment group. We concluded that the leachate contains a suitable initial charge of many active bacteria and methanogenic archaea which contribute to the AD process, hence it can be used as an inoculum for the treatment of OFMSW.

High-Throughput Illumina MiSeq Amplicon Sequencing of Yeast Communities Associated With Indigenous Dairy Products From Republics of Benin and Niger

Traditional Wagashi cheese and fermented cow milk are among the most popular dairy products appreciated by people from Benin, Niger, and the neighboring region. These products are the main source of protein in the diet of the low-income population in the region. The fermented milk is prepared by spontaneous fermentation without back-slopping. Whereas, the leaf extract of Calotropis procera is used for curdling the milk to prepare the soft Wagashi cheese. The present study aims to provide in-depth analysis of yeast communities associated with these traditional milk products by high-throughput Illumina MiSeq amplicon sequencing of internal transcribed spacer (ITS) region of fungal rRNA genes. A total of 60 samples, 20 samples of fermented milk each from Benin and Niger, and 20 samples of Wagashi cheese from Benin were used for analysis. The metagenomic investigation revealed that Kluyveromyces marxianus, Saccharomyces cerevisiae, Candida parapsilosis, and Sagenomella keratitidis were the predominant yeast species present in the traditional milk products. Furthermore, we noticed a high presence of K. marxianus (61.1% relative abundance) in the Wagashi cheese and S. cerevisiae (28.4% relative abundance) in the fermented milk of Niger. The presence of potential pathogenic yeast C. parapsilosis and S. keratitidis in these African milk products calls for further investigation to assess their safety. The predominant yeast K. marxianus and S. cerevisiae, recognized with generally regarded as safe (GRAS) status, could be further selected as starter culture along with lactic acid bacteria for developing controlled fermentation processes with enhanced product quality and safety.