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

Insights into the microbiota of raw milk from seven breeds animals distributing in Xinjiang China

Owing to its high nutritional content, raw milk contains a rich microbiota. Thus, to study microorganisms present in raw milk available in Xinjiang China, 142 raw milk samples from seven animal breeds (cow, sheep, goat, donkey, horse, camel, and yak) and four regions (Hami, Tarbagatay, Kashgar, and Ili) were analyzed by high-throughput DNA sequencing. These microorganisms were characterized by 10 dominant phyla. Proteobacteria (68.33%) was the major phylum, followed by Firmicutes (18.80%) and Thermi (3.16%). Horse milk contained more Bacteroidetes, sheep milk contained more Gammaproteobacteria, and donkey milk contained more unclassified sequences. Camel and donkey milk contained the highest and lowest bacterial diversity compared with that contained by the remaining milk samples, respectively. Additionally, spoilage microorganisms, including Chryseobacterium, Propionibacterium, and Flavobacterium, and pathogenic bacteria, including Ochrobactrum anthropi and Sphingomonas, were more prevalent in horse and yak milk, whereas probiotic lactic acid bacteria (LAB), such as Leuconostoc, Lactococcus, or Lactobacillus, were more prevalent in goat, donkey, and camel milk. Furthermore, Moraxella was abundantly present in goat, camel, and yak milk, Acinetobacter was more abundant in camel milk, and Pseudomonas was relatively abundant in sheep and donkey milk. Overall, specific harmful microorganisms and probiotic lactic acid bacteria were found in the raw milk samples obtained from different animals, which provided a basis for preventing and controlling the growth of harmful bacteria, as well as investigating probiotic resources in raw milk.

Comparative analyses of the bacterial communities present in the spontaneously fermented milk products of Northeast India and West Africa

Introduction

Spontaneous fermentation of raw cow milk without backslopping is in practice worldwide as part of the traditional food culture, including "Doi" preparation in earthen pots in Northeast India, "Kindouri" of Niger and "Fanire" of Benin prepared in calabash vessels in West Africa. Very few reports are available about the differences in bacterial communities that evolved during the spontaneous mesophilic fermentation of cow milk in diverse geographical regions.

Methods

In this study, we used high throughput amplicon sequencing of bacterial 16S rRNA gene to investigate 44 samples of naturally fermented homemade milk products and compared the bacterial community structure of these foods, which are widely consumed in Northeast India and Western Africa.

Results and discussion

The spontaneous milk fermentation shared the lactic acid bacteria, mainly belonging to Lactobacillaceae (Lactobacillus) and Streptococcaceae (Lactococcus) in these two geographically isolated regions. Indian samples showed a high bacterial diversity with the predominance of Acetobacteraceae (Gluconobacter and Acetobacter) and Leuconostoc, whereas Staphylococcaceae (Macrococcus) was abundant in the West African samples. However, the Wagashi cheese of Benin, prepared by curdling the milk with proteolytic leaf extract of Calotrophis procera followed by natural fermentation, contained Streptococcaceae (Streptococcus spp.) as the dominant bacteria. Our analysis also detected several potential pathogens, like Streptococcus infantarius an emerging infectious foodborne pathogen in Wagashi samples, an uncultured bacterium of Enterobacteriaceae in Kindouri and Fanire samples, and Clostridium spp. in the Doi samples of Northeast India. These findings will allow us to develop strategies to address the safety issues related to spontaneous milk fermentation and implement technological interventions for controlled milk fermentation by designing starter culture consortiums for the sustainable production of uniform quality products with desirable functional and organoleptic properties.

A Comparative Study of Skimmed Milk and Cassava Flour on the Viability of Freeze-Dried Lactic Acid Bacteria as Starter Cultures for Yogurt Fermentation

The purpose of this study was to evaluate the survival rates and fermentation performance of three freeze-dried lactic acid bacterial cultures previously isolated from Ghanaian traditional fermented milk. LAB cultures, i.e., Lactobacillus delbrueckii, Lactococcus lactis and Leuconostoc mesenteroides, were frozen in the chamber of a Telstar (Lyoquest) laboratory freeze dryer for 10 h at -55 °C (as single and combined cultures) using skimmed milk and cassava flour as cryoprotectants held in plastic or glass cryovials. For viability during storage, freeze-dried LAB cultures were stored in a refrigerator (4 °C) and at room temperature (25 °C) for 4 weeks. The survival of freeze-dried cultures was determined by growth kinetics at 600 nm (OD600). The performance of freeze-dried LAB cultures after 4 weeks of storage was determined by their growth, acidification of milk during yogurt fermentation and consumer sensory evaluation of fermented milk using a nine-point hedonic scale. The survival rates for LAB ranged between 60.11% and 95.4% following freeze-drying. For single cultures, the highest survival was recorded for Lactobacillus delbrueckii (L12), whereas for combined cultures, the highest survival was observed for Lactococcus lactis (L3) combined with Lactobacillus delbrueckii (L12). The consumer acceptability results showed that yogurts produced from a combined starter culture of Lactococcus lactis and Lactobacillus delbrueckii or from a single culture of Lactococcus lactis were the most preferred products with Lactococcus lactis and Lactobacillus delbrueckii possessing high survival rates and high consumer acceptability in yogurt production. These findings are crucial and can be adopted for large-scale production and commercialization of yogurt.

State of the art of breeding, milking, and milk processing for the production of curdled milk and Wagashi Gassirè in Benin: Practices favoring the contamination of its dairy products

Introduction

This study aimed to identify the factors favoring the contamination of raw cow's milk, curdled milk, and Wagashi Gassirè cheese during their production and preservation in order to develop strategies to improve their quality.

Methods

A cross-sectional survey of 401 randomly selected stakeholders encompassing all levels of the dairy production chain in the Nikki and Dassa-Zoumé communes of Benin was conducted. The data obtained were analyzed using the SAS software for the calculation of frequencies and the R software for classifying the stakeholders based on the hygiene practices they adopted during the production and conservation of raw cow's milk, curdled milk, and Wagashi Gassirè.

Results and discussion

The study identified three types of dairy farmers based on how they medically treated their cattle and implemented hygiene practices, including farmers who (1) relied on themselves or received help from veterinarians trained in animal husbandry and milking to monitor the animals on their farms; (2) relied only on veterinarians; and (3) relied only on themselves. The majority of these dairy farmers felt that hygienic milking practices were very restrictive and difficult to implement. In addition, three groups of Wagashi Gassirè producers were identified: (1) producers trained in good hygiene practices who did not boil or sundry the cheese; (2) producers lacking the infrastructure to protect from weather exposure who used all parts of Calotropis procera for colored Wagashi Gassirè production; and (3) producers who did not often filter the milk and boiled the Wagashi Gassirè in bags before immersion in simple water or whey. The sanitary quality of milk and milk products is influenced by the diverse handling practices employed by producers. These practices must be considered according to the types of farmers and processors when suggesting improved intervention policies.

Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing

Background

The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated.

Methods

In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function.

Results

After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.

Progress of Molecular Display Technology Using Saccharomyces cerevisiae to Achieve Sustainable Development Goals

In the long history of microorganism use, yeasts have been developed as hosts for producing biologically active compounds or for conventional fermentation. Since the introduction of genetic engineering, recombinant proteins have been designed and produced using yeast or bacterial cells. Yeasts have the unique property of expressing genes derived from both prokaryotes and eukaryotes. Saccharomyces cerevisiae is one of the well-studied yeasts in genetic engineering. Recently, molecular display technology, which involves a protein-producing system on the yeast cell surface, has been established. Using this technology, designed proteins can be displayed on the cell surface, and novel abilities are endowed to the host yeast strain. This review summarizes various molecular yeast display technologies and their principles and applications. Moreover, S. cerevisiae laboratory strains generated using molecular display technology for sustainable development are described. Each application of a molecular displayed yeast cell is also associated with the corresponding Sustainable Development Goals of the United Nations.

Safety and Quality of Milk and Milk Products in Senegal—A Review

Historically, local milk production in Senegal has struggled to keep up with the demands of consumers, so there has been a heavy reliance on imported milk and milk products. More recently, efforts have been made to improve local dairy production by establishing large, organized dairies that collect milk from rural production areas and developing small-scale processing units, such as mini dairies. The local dairy value chain in Senegal consists of (1) informal collection systems where farmers commonly deliver milk directly to dairies; (2) traditional and artisanal processing using simple equipment and techniques; and (3) short local marketing and sale circuits. Most West African dairy sectors are dominated by raw, unpasteurized milk or traditional, spontaneously fermented milk products, such as lait caillé in Senegal, sold through small-scale channels without a cold chain, so the risk of food safety hazards may be increased. Microbiological, chemical, and physical hazards have been found in milk and milk products across West Africa. There is a need to educate milk producers, small-scale processors, and vendors on the importance of refrigerating milk immediately after milking as well as maintaining the cold chain until the milk is heat treated and, subsequently, until the milk is marketed to the consumer. However, without assistance, obtaining the equipment necessary for cold storage and processing of milk can be challenging.

Analysis of fungal dynamic changes in the natural fermentation broth of 'Hongyang' kiwifruit

'Hongyang' kiwifruit (Actinidia chinensis Planch.) is an ideal kiwifruit wine variety. At present, there is no research on the dynamic changes of yeast during the natural fermentation of kiwifruit wine. In this study, a high-throughput was employed to analyze the fungal population composition and diversity in the samples cultured in yeast extract peptone dextrose (YPD) medium and enriched in the natural fermentation process of 'Hongyang' kiwifruit at four time points, day one (D1T), day three (D3T), day five (D5T), and day fifteen (D15T). Five hundred and eighty-two operational taxonomic units (OTUs) were obtained from 131 genera and 178 species samples. The diversity analysis results showed that in the early natural fermentation stage, the dominant species was Aureobasidium pullulans, and as natural fermentation proceeded, the genus Pichia became the dominant species. Pichia kluyveri was an important species at the later stages of natural fermentation. An analysis of the metabolic pathways shows that P. kluyveri plays an aromatic-producing role in the natural fermentation of 'Hongyang' kiwifruit. These results could provide a theoretical basis for the studies of kiwifruit fungal diversity and fungal changes during fermentation. The findings could fix a major deficiency in the production of kiwifruit fruit wine, which lacks a specific flavor-producing yeast species or strain.

Deciphering the Microbiota and Volatile Profiles of Algerian Smen, a Traditional Fermented Butter

In Algeria, Smen is a fermented butter produced in households using empirical methods. Smen fermentation is driven by autochthonous microorganisms; it improves butter shelf-life and yields highly fragrant products used as ingredients in traditional dishes as well as in traditional medicine. The present study is aimed at investigating microbial diversity and dynamics during Algerian Smen fermentation using both culture-dependent and culture-independent approaches, as well as by monitoring volatile organic compound production. To reach this goal, fifteen Smen samples (final products) produced in households from different regions in Algeria were collected and analyzed. In addition, microbial and volatile compound dynamics at the different stages of Smen manufacturing were investigated for one Smen preparation. The results showed that Smen is a microbiologically safe product, as all hygiene and safety criteria were respected. The dominant microorganisms identified by both techniques were LAB and yeasts. Lactococcus spp. and Streptococcus thermophilus were the main bacterial species involved in spontaneous raw milk fermentation preceding butter-making, while lactobacilli and enterococci were the only bacteria found to be viable during Smen maturation. Regarding fungal diversity, yeast species were only recovered from two mature Smen samples by culturing, while different species (e.g., Geotrichum candidum, Moniliella sp.) were identified in all samples by the culture-independent approach. Using microbial analysis of a single batch, many of these were found viable during manufacturing. Concerning the volatile profiles, they were highly diverse and characterized by a high prevalence of short chain fatty acids, methylketones, and esters. Correlation analysis between microbial diversity and volatile profiles showed that several yeast (Moniliella sp., K. marxianus) and LAB (e.g., Lactococcus spp., S. thermophilus) species were strongly correlated with one or more volatile organic compound families, including several ethyl esters and methyl ketones that can be linked to pleasant, sweetly floral, fruity, buttery, and creamy odors. This study clearly identified key microorganisms involved in Smen fermentation and maturation that could be used in the future for better fermentation control and improvement of quality attributes.

A review of microbes and chemical contaminants in dairy products in sub-Saharan Africa

Animal milk types in sub-Saharan Africa (SSA) are processed into varieties of products using different traditional methods and are widely consumed by households to support nutritional intake and diet. Dairy products contain several microorganisms, their metabolites, and other chemical compounds, some with health benefits and many others considered as potential health hazards. Consumption of contaminated milk products could have serious health implications for consumers. To access the safety of milk products across SSA, studies in the region investigating the occurrences of pathogens as well as chemical compounds such as heat stable toxins and veterinary drug residues in animal milk and its products were reviewed. This is done with a holistic view in light of the emerging exposome paradigm for improving food safety and consumer health in the region. Herein, we showed that several published studies in SSA applied conventional and/or less sensitive methods in detecting microbial species and chemical contaminants. This has serious implications in food safety because the correct identity of a microbial species and accurate screening for chemical contaminants is crucial for predicting the potential human health effects that undermine the benefits from consumption of these foods. Furthermore, we highlighted gaps in determining the extent of viral and parasitic contamination of milk products across SSA as well as investigating multiple classes of chemical contaminants. Consequently, robust studies should be conducted in this regard. Also, efforts such as development cooperation projects should be initiated by all stakeholders including scientists, regulatory agencies, and policy makers to improve the dairy product chain in SSA in view of safeguarding consumer health.

Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes

With the emergence of next-generation sequencing (NGS) technology, there have been a large number of metagenomic studies that estimated the bacterial composition via 16S ribosomal RNA (16S rRNA) amplicon sequencing. In particular, subsets of the hypervariable regions in 16S rRNA, such as V1-V2 and V3-V4, are targeted using high-throughput sequencing. The sequences from different taxa are assigned to a specific taxon based on the sequence homology. Since such sequences are highly homologous or identical between species in the same genus, it is challenging to determine the exact species using 16S rRNA sequences only. Therefore, in this study, homologous species groups were defined to obtain maximum resolution related with species using 16S rRNA. For the taxonomic assignment using 16S rRNA, three major 16S rRNA databases are independently used since the lineage of certain bacteria is not consistent among these databases. On the basis of the NCBI taxonomy classification, we re-annotated inconsistent lineage information in three major 16S rRNA databases. For each species, we constructed a consensus sequence model for each hypervariable region and determined homologous species groups that consist of indistinguishable species in terms of sequence homology. Using a k-nearest neighbor method and the species consensus sequence models, the species-level taxonomy was determined. If the species determined is a member of homologous species groups, the species group is assigned instead of a specific species. Notably, the results of the evaluation on our method using simulated and mock datasets showed a high correlation with the real bacterial composition. Furthermore, in the analysis of real microbiome samples, such as salivary and gut microbiome samples, our method successfully performed species-level profiling and identified differences in the bacterial composition between different phenotypic groups.

Occurrence of Yeasts in White-Brined Cheeses: Methodologies for Identification, Spoilage Potential and Good Manufacturing Practices

Yeasts are generally recognized as contaminants in the production of white-brined cheeses, such as Feta and Feta-type cheeses. The most predominant yeasts species are Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Kluyveromyces lactis, Rhodotorula mucilaginosa, and Trichosporon spp. Although their spoilage potential varies at both species and strain levels, yeasts will, in case of excessive growth, present a microbiological hazard, effecting cheese quality. To evaluate the hazard and trace routes of contamination, the exact taxonomic classification of yeasts is required. Today, identification of dairy yeasts is mainly based on DNA sequencing, various genotyping techniques, and, to some extent, advanced phenotypic identification technologies. Even though these technologies are state of the art at the scientific level, they are only hardly implemented at the industrial level. Quality defects, caused by yeasts in white-brined cheese, are mainly linked to enzymatic activities and metabolism of fermentable carbohydrates, leading to production of metabolites (CO2, fatty acids, volatile compounds, amino acids, sulfur compounds, etc.) and resulting in off-flavors, texture softening, discoloration, and swelling of cheese packages. The proliferation of spoilage yeast depends on maturation and storage conditions at each specific dairy, product characteristics, nutrients availability, and interactions with the co-existing microorganisms. To prevent and control yeast contamination, different strategies based on the principles of HACCP and Good Manufacturing Practice (GMP) have been introduced in white-brined cheese production. These strategies include milk pasteurization, refrigeration, hygienic sanitation, air filtration, as well as aseptic and modified atmosphere packaging. Though a lot of research has been dedicated to yeasts in dairy products, the role of yeast contaminants, specifically in white-brined cheeses, is still insufficiently understood. This review aims to summarize the current knowledge on the identification of contaminant yeasts in white-brined cheeses, their occurrence and spoilage potential related to different varieties of white-brined cheeses, their interactions with other microorganisms, as well as guidelines used by dairies to prevent cheese contamination.

Microbial Diversity and Metabolite Profiles of Palm Wine Produced From Three Different Palm Tree Species in Côte d'Ivoire

Palm wine, the most commonly consumed traditional alcoholic beverage in Western Africa, harbours a complex microbiota and metabolites, which plays a crucial role in the overall quality and value of the product. In the present study, a combined metagenomic and metabolomic approach was applied to describe the microbial community structure and metabolites profile of fermented saps from three palm species (Elaeis guineensis, Raphia hookeri, Borassus aethiopum) in Côte d'Ivoire. Lactobacillaceae (47%), Leuconostocaceae (16%) and Acetobacteriaceae (28%) were the most abundant bacteria and Saccharomyces cerevisiae (87%) the predominant yeasts in these beverages. The microbial community structure of Raphia wine was distinctly different from the others. Multivariate analysis based on the metabolites profile clearly separated the three palm wine types. The main differentiating metabolites were putatively identified as gevotroline hydrochloride, sesartemin and methylisocitrate in Elaeis wine; derivative of homoserine, mitoxantrone in Raphia wine; pyrimidine nucleotide sugars (UDP-D-galacturonate) and myo-Inositol derivatives in Borassus wine. The enriched presence of gevotroline (an antipsychotic agent) and mitoxantrone (an anticancer drug) in palm wine supports its therapeutic potential. This work provides a valuable insight into the microbiology and biochemistry of palm wines and a rationale for selecting functional microorganisms for potential biotechnology applications.