An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

Shotgun metagenomic analysis of microbiota dynamics during long-term backslopping fermentation of traditional fermented milk in a controlled laboratory environment

Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intra-population variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk.

Cutting edge tools in the field of soil microbiology

The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.

Metagenetic analysis of the bacterial diversity of Kazakh koumiss and assessment of its anti-Candida albicans activity

Koumiss, a five-thousand-year-old fermented mare's milk beverage, is widely recognized for its beneficial nutrient and medicinal properties. The microbiota of Chinese and Mongolian koumiss have been largely characterized in recent years, but little is known concerning Kazakh koumiss despite this drink historically originates from the modern Kazakhstan territory. In addition, while koumiss is regarded as a drink with therapeutic potential, there are also no data on koumiss anti-Candida activity. In this context, the aims of the present study were to investigate the bacterial diversity and anti-Candida albicans activity of homemade Kazakh koumiss samples as well as fermented whey and cow's milk, derived from koumiss and propagated for several months. Koumiss bacterial communities were largely dominated by lactic acid bacteria including Lactobacillus sensu lato spp. (69% of total reads), Streptococcus (8.0%) and Lactococcus (6.1%), while other subdominant genera included Acetobacter (2.6%), Enterobacter (2.4%), and Klebsiella (1.5%). Several but not all koumiss samples as well as fermented whey and cow's milk showed antagonistic activities towards C. albicans. Linear discriminant effect size (LEfSe) analysis showed that their bacterial communities were characterized by a significantly higher abundance of amplicon sequence variants (ASV) belonging to the genus Acetobacter. In conclusion, this study allowed to identify the key microorganisms of Kazakh koumiss and provided new information on the possible underestimated contribution of acetic acid bacteria to its probiotic properties.

A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan

Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.

Camel Milk: Antimicrobial Agents, Fermented Products, and Shelf Life

The camel milk (CM) industry has witnessed a notable expansion in recent years. This expansion is primarily driven by the rising demand for CM and its fermented products. The perceived health and nutritional benefits of these products are mainly responsible for their increasing popularity. The composition of CM can vary significantly due to various factors, including the breed of the camel, its age, the stage of lactation, region, and season. CM contains several beneficial substances, including antimicrobial agents, such as lactoferrin, lysozyme, immunoglobulin G, lactoperoxidase, and N-acetyl-D-glucosaminidase, which protect it from contamination by spoilage and pathogenic bacteria, and contribute to its longer shelf life compared to bovine milk (BM). Nevertheless, certain harmful bacteria, such as Listeria monocytogenes, Yersinia enterocolitica, and Escherichia coli, have been detected in CM, which is a significant public health concern. Therefore, it is crucial to understand and monitor the microbial profile of CM and follow good manufacturing practices to guarantee its safety and quality. This review article explores various aspects of CM, including the types of beneficial and harmful bacteria present in it, the composition of the milk, its antimicrobial properties, its shelf life, and the production of fermented CM products.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

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.

Microbial Communities in Home-Made and Commercial Kefir and Their Hypoglycemic Properties

Kefir is a popular traditional fermented dairy product in many countries. It has a complex and symbiotic culture made up of species of the genera Leuconostoc, Lactococcus, and Acetobacter, as well as Lactobacilluskefiranofaciens and Lentilactobacillus kefiri. Though kefir has been commercialized in some countries, people are still traditionally preparing kefir at the household level. Kefir is known to have many nutritious values, where its consistent microbiota has been identified as the main valuable components of the product. Type 2 diabetes mellitus (T2DM) is a common diet-related disease and has been one of the main concerns in the world’s growing population. Kefir has been shown to have promising activities in T2DM, mostly via hypoglycemic properties. This review aims to explain the microbial composition of commercial and home-made kefir and its possible effects on T2DM. Some studies on animal models and human clinical trials have been reviewed to validate the hypoglycemic properties of kefir. Based on animal and human studies, it has been shown that consumption of kefir reduces blood glucose, improves insulin signaling, controls oxidative stress, and decreases progression of diabetic nephropathy. Moreover, probiotic bacteria such as lactic-acid bacteria and Bifidobacterium spp. and their end-metabolites in turn directly or indirectly help in controlling many gut disorders, which are also the main biomarkers in the T2DM condition and its possible treatment.

Microbial Communities of Artisanal Fermented Milk Products from Russia

Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties.

Changes and Driving Mechanism of Microbial Community Structure during Paocai Fermentation

Fermentation of paocai is a dynamic process of the microbial community structure, and the interaction between community structure and physicochemical factors endows paocai with unique taste and flavor. The study of bacterial and fungal community structure changes and the driving mechanism of physicochemical factors induced changes in community structure, showing that Pseudomonas belonging to Proteobacteria and Lactobacillus belonging to Firmicutes were the dominant bacteria in the process of paocai fermentation. The correlation analysis of physicochemical factors with bacterial community showed that titratable acid was significantly positively correlated with Lactobacillus and negatively correlated with Pseudomonas, while nitrite was the opposite. Redundancy analysis (RDA) showed that pH was positively correlated with the bacterial community in the early fermentation stage, amino acid nitrogen was positively correlated with the bacterial community in the middle fermentation stage, and titratable acid was positively correlated with the bacterial community in the late fermentation stage. Variance partitioning analysis (VPA) showed that environmental factors, pH and metabolites, were the main driving forces of bacterial community diversity, which jointly explained 32.02% of the bacterial community structure variation. To study the glucolysis and nitrogen metabolism in the process of paocai fermentation, we found that in the early stage of the fermentation, the nitrite reductase enzyme of Pseudomonas activity was high, with high nitrite content in the prophase, but by the end of fermentation, lactic acid bacteria rapidly increased, the content of L−lactic acid through the glycolysis pathway, making paocai fermentation environment become acidic, then Pseudomonas decreased. Ascomycota and Basidiomycota were the main phylum fungi in the fermentation process. RDA analysis showed that the fungal community was positively correlated with pH, nitrite, and soluble protein at the early fermentation stage, amino acid nitrogen was positively correlated with the fungal community at the middle fermentation stage, titratable acid and reducing sugar were positively correlated with the fungal community at the late fermentation stage. VPA analysis showed that metabolites were the main driving force of fungal community diversity and accounted for 45.58% of fungal community diversity. These results had a certain guiding significance for the production and preservation of naturally fermented paocai.

Assessment of the clinical and laboratorial profile of patients with obesity and asymptomatic COVID-19 undergoing bariatric surgery in Brazil

Purpose

to outline the clinical and laboratorial profile of patients with obesity undergoing bariatric surgery who presented positive reverse transcription-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (Sars-CoV-2) in the preoperative period without symptoms presentation.

Methods

Case series of 17 patients undergoing bariatric surgery who presented positive RT-PCR for Sars-CoV-2 in the preoperative period, with no reported symptoms. Data collected included demographic characteristics, length of hospital stay, waiting time for surgery, inflammatory markers, serum levels of micronutrients and dengue virus (DENV) serology.

Results

In total, 219 patients underwent bariatric surgery in our institution during the study period. The incidence of asymptomatic cases was 7.7%. The sample comprised 88.2% of women, with mean age of 39.3 years and mean preoperative body mass index (BMI) of 37.7 kg/m2. Thirty five percent of the sample had previous diagnosis of diabetes and 29.4% had hypertension. The mean time elapsed between positive RT-PCR and the operation was 17 ± 7.5 days and the mean length of postoperative hospital stay was 1.9 ± 0.43 day. Mean lymphocytes count was 2,409.7/mm3 and the mean platelet-to-lymphocyte ratio was 126.3. Mean C-reactive protein value was 5.8 mg/dL, while ferritin marked 107.4 µg/L. DENV IgG was identified in all patients who tested for it. Mean levels of vitamin D and zinc were 25.6 ng/mL and 79.9 µg/dL, respectively. There were no postoperative complications reported.

Conclusion

None of the included patients presented any of the laboratory markers related to disease severity. Moreover, it is important to notice that all patients who tested for DENV, had the specific IgG detected in their serum.

Graphical abstract

Preventive and Therapeutic aspects of Fermented Foods

In recent times, the status of some fermented foods which are considered as functional foods that confer health benefits in certain disease conditions has grown rapidly. The health benefits of fermented foods are due to the presence of probiotic microbes and the bioactive compound formed during fermentation. Microbes involved and metabolites produced by them are highly species-specific and contribute to the authenticity of the fermented foods. Several studies pertaining to the effect of fermented foods on various disease conditions have been conducted in recent years using both animal models and clinical trials on humans. This review focuses on the impact of fermented foods on conditions like diabetes, cardiovascular disease (CVD), obesity, gastrointestinal disorder, cancer and neurodegenerative disorders.

Lactobacillus kefiranofaciens: From Isolation and Taxonomy to Probiotic Properties and Applications

One of the main lactic acid bacterial species found in the kefir grain ecosystem worldwide is Lactobacillus kefiranofaciens, exhibiting strong auto-aggregation capacity and, therefore, being involved in the mechanism of grain formation. Its occurrence and dominance in kefir grains of various types of milk and geographical origins have been verified by culture-dependent and independent approaches using multiple growth media and regions of the 16S rRNA gene, respectively, highlighting the importance of their combination for its taxonomic identification. L. kefiranofaciens comprises two subspecies, namely kefiranofaciens and kefirgranum, but only the first one is responsible for the production of kefiran, the water-soluble polysaccharide, which is a basic component of the kefir grain and famous for its technological as well as health-promoting properties. L. kefiranofaciens, although very demanding concerning its growth conditions, can be involved in mechanisms affecting intestinal health, immunomodulation, control of blood lipid levels, hypertension, antimicrobial action, and protection against diabetes and tumors. These valuable bio-functional properties place it among the most exquisite candidates for probiotic use as a starter culture in the production of health-beneficial dairy foods, such as the kefir beverage.

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

Viruses in fermented foods: are they good or bad? Two sides of the same coin

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.