Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented 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.

Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.

Metagenome-assembled genomes for biomarkers of bio-functionalities in Laal dahi, an Indian ethnic fermented milk product

Laal dahi is a sweetened and soft pudding-like fermented milk product of the Eastern regions of India, which has not been studied for its microbial community structures and health promoting functionality in terms of 'omics' approaches. We applied metagenomic and metagenomes-assembled genomes (MAGs) tools to decipher the biomarkers for genes encoding for different health promoting functionalities in laal dahi. Abundance of bacterial domains was observed with negligible presence of eukaryotes and viruses. Bacillota was the most abundant phylum with different bacterial species viz., Enterococcus italicus, Lactococcus raffinolactis, Lactobacillus helveticus, Bifidobacterium mongoliense, Hafnia alvei, Lactococcus lactis, Acetobacter okinawensis, Streptococcus thermophilus, Thermus thermophilus, Leuconostoc citreum, Leuconostoc pseudomesenteroides, Acetobacter orientalis, Lactobacillus gallinarum, Lactococcus chungangensis and Lactobacillus delbrueckii. Comparison of laal dahi microbiome with that of similar fermented milk products was also carried out after retrieving the metagenomic datasets from public databases. Significant abundance of Lb. helveticus, E. italicus, Lc. raffinolactis and Lc. lactis in laal dahi. Interestingly, Bifidobacterium mongoliense, Lb. gallinarum, Lc. chungangensis and Acetobacter okinawensis were only detected in laal dahi but Streptococcus infantarius, Lacticaseibacillus rhamnosus and Lb. johnsonii were absent. Reconstruction of putative single environment-specific genomes from metagenomes in addition to subsampling of the abundant species resulted in five high-quality MAGs identified as Lactobacillus delbrueckii, Lactobacillus helveticus, Lactococcus chungangensis, Lactococcus lactis and Streptococcus thermophilus. All MAGs showed the presence of various genes with several putative functions corresponding to different probiotic and prebiotic functions, short-chain fatty acids production, immunomodulation, antitumor genes, essential amino acid and vitamin biosynthesis. Genes for γ-Aminobutyric acid (GABA) production were only detected in MAG of Lactococcus lactis. Gene clusters for secondary metabolites (antimicrobial peptides) were detected in all MAGs except Lc. chungangensis. Additionally, detection of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) elements was observed only in Lactobacillus delbrueckii and Streptococcus thermophilus. Annotation of several genes with potential health beneficial properties in all five MAGs may support the need to explore the culturability of these MAGs for future use in controlled fermentation of functional dairy products.

Antimicrobial Resistance of Lactic Acid Bacteria from Nono, a Naturally Fermented Milk Product

BACKGROUND

Antimicrobial resistance (AMR) is one of the biggest threats to public health. The food chain has been recognised as a vehicle for transmitting AMR bacteria. However, information about resistant strains isolated from African traditional fermented foods remains limited. Nono is a traditional, naturally fermented milk product consumed by many pastoral communities across West Africa. The main aim of this study was to investigate and determine the AMR patterns of lactic acid bacteria (LAB) involved in the traditional fermentation of milk for Nono production, and the presence of transferable AMR determinants.

METHODS

One hundred (100) LAB isolates from Nono identified in a previous study as Limosilactobacillus fermentum, Lactobacillus delbrueckii, Streptococcus thermophilus, Streptococcus infantarius, Lentilactobacillus senioris, Leuconostoc pseudomesenteriodes, and Enterococcus thailandicus were investigated. The minimum inhibitory concentration (MIC) was determined for 18 antimicrobials using the micro-broth dilution method. In addition, LAB isolates were screened for 28 antimicrobial resistance genes using PCR. The ability of LAB isolates to transfer tetracycline and streptomycin resistance genes to Enterococcus faecalis was also investigated.

RESULTS

The experiments revealed variable antimicrobial susceptibility according to the LAB isolate and the antimicrobial tested. The tetracycline resistance genes tet(S) and tet(M) were detected in isolates Ent. thailandicus 52 and S. infantarius 10. Additionally, aad(E) encoding resistance to streptomycin was detected in Ent. thailandicus 52. The conjugation experiments suggested that the tet(S) and aad(E) genes were transferable in vitro from isolate Ent. thailandicus 52 to Ent. faecalis JH2-2.

SIGNIFICANCE AND IMPACT

Traditional fermented foods play a significant role in the diet of millions of people in Africa, yet their contribution to the burden of AMR is largely unknown. This study highlights that LAB involved in traditionally fermented foods could be potential reservoirs of AMR. It also underscores the relevant safety issues of Ent. thailandicus 52 and S. infantarius 10 for use as starter cultures as they carry transferable AMR genes. Starter cultures are an essential aspect of improving the safety and quality attributes of African fermented foods. However, AMR monitoring is an important safety aspect in the selection of starter cultures for improving traditional fermentation technologies.

Adequate Dietary Intake and Consumption of Indigenous Fermented Products Are Associated with Improved Nutrition Status among Children Aged 6–23 Months in Zambia

Agroecological food systems and socioeconomic characteristics are known to influence household food security and food consumption patterns and consequently have an impact on child nutritional status. The present study examined food consumption patterns among children aged 6–23 months in two geographic regions of Zambia, with special focus on consumption of fermented products, and its association with illnesses and nutritional status. The cross-sectional survey enrolled a total of 213 children from Namwala and Mkushi districts of Zambia. A 24 h recall and food frequency questionnaire (FFQ) were used to determine the number of food groups consumed and consequently dietary diversity scores and food consumption patterns, respectively. Determinants of child’s linear growth as measured by Height-for-Age Z-scores (HAZ) were assessed via multiple linear regression analysis. In total, 54% of the children met the minimum dietary diversity by consuming food from at least 5+ food groups. Maize meal porridge, Mabisi (fermented milk), Chibwantu and Munkoyo (fermented beverages based on cereals) and groundnuts were among the frequently consumed foods. A higher consumption of fermented beverages was observed in Namwala compared to Mkushi district. A significant association was observed between HAZ score (rho = 0.198, p = 0.004), Weight-for-Age Z-score (WAZ) (rho = 0.142, p = 0.039) and consumption of mabisi. Dietary intake had a positive association with child nutritional status. The frequent consumption of traditional non-alcoholic cereal and milk-based fermented foods underpinned their contribution to the children’s dietary intake. Moreover, the trend would be viewed as an indicator to nutrition and policy actors on possible unoptimized potential of indigenous fermented foods’ influence in nutritional and health status among children at regional and national levels. Although Zambia has a wide range of traditional non-alcoholic fermented food products, their prospects in provision of macro- and micronutrients along with microbiota benefits remain scanty despite global efforts increasingly advocating for the inclusion of such traditional foods in food-based recommendations.

Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.

Composition and factors influencing community structure of lactic acid bacterial in dairy products from Nyingchi Prefecture of Tibet

This study investigated the community composition of lactic acid bacteria (LAB) from yaks' milk (YM) Tibetan yellow cattle milk (TM) and their fermented products from different counties in the Nyingchi Prefecture, Tibet using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. Sequencing revealed 26 genera and 94 species from 71 dairy samples; amongst these Lactobacillus delbrueckii (36.17%), Streptococcus thermophilus (19.46%) and Lactococcus lactis (18.33%) were the predominant species. This study also identified the main factors influencing LAB community composition by comparing amongst samples from different locations, from different milk types, and from different altitudes. The LAB communities in YM and TM were more diverse than in fermented yaks' milk (FYM) and fermented Tibetan yellow cattle milk (FTM) samples. Similarly, whether milk was fermented or not accounted for differences in LAB species composition while altitude of the dairy products had very little effect. Milk source and production process were the most likely causes of drastic shifts in microbial community composition. In addition, fermented dairy products were enriched in genes responsible for secondary metabolic pathways that were potentially beneficial for health. Comprehensive descriptions of the microbiota in different dairy products from the Nyingchi Prefecture, Tibet might help elucidate evolutionary and functional relationships amongst bacterial communities in these products.

Environmental Selection Shapes Bacterial Community Composition in Traditionally Fermented Maize-Based Foods from Benin, Tanzania and Zambia

Natural (microbial) communities are complex ecosystems with many interactions and cross-dependencies. Among other factors, selection pressures from the environment are thought to drive the composition and functionality of microbial communities. Fermented foods, when processed using non-industrial methods, harbor such natural microbial communities. In non-alcoholic fermented foods the fermenting microbiota is commonly dominated by 4–10 species of bacteria, which make them suitable model systems to study ecosystem assembly and functioning. In this study, we assess the influence of the environment on the composition of microbial communities of traditional fermented products from Africa. We compare differences between microbial communities that are found in similar products but come from different countries, hypothesizing they experience different environmental selection pressures. We analyzed bacterial community composition in 36 samples of various cereal-based fermented foods from Benin, Tanzania and Zambia using 16S rDNA amplicon sequencing. The differential abundance analysis indicates that the bacterial communities of fermented foods from the three countries are dominated by mostly lactic acid bacteria belonging to the genera of Lactobacillus, Weisella and Curvibacter. The samples from Zambia contain the most dissimilar microbial communities in comparison with samples from Benin and Tanzania. We propose this is caused by the relatively low temperature in Zambia, suggesting that indeed environmental selection can shape community composition of fermenting microbes.

Contribution of traditional fermented foods to food systems transformation: value addition and inclusive entrepreneurship

To date, many efforts to eradicate hunger include increasing agricultural production, processing of raw materials and supplementation, and fortification of foods. Locally produced foods represent a significant part of Food Systems as they contribute to tackling hunger and malnutrition. However, few studies have investigated the processing of traditional fermented foods at household level as a means to improve nutrition and triggering inclusive entrepreneurship, two crucial dimensions Food Systems build on. Fermentation is an ancient processing technique that relies on transformation of raw materials by microbial activity and is mainly undertaken by women. This paper posits that upscaling small scale fermented food processing activities while enhancing functional food properties and fostering women entrepreneurship contributes to prevention of food losses, promotion of nutrition and health, and entrepreneurial opportunities for current processors. This is key for effective policy interventions to foster food security in challenging contexts.⨪.

Microbial population dynamics during traditional production of Mabisi, a spontaneous fermented milk product from Zambia: a field trial

Mabisi is a fermented milk product, traditionally produced in a calabash by uncontrolled fermentation. Due to high costs and a reduced availability of calabashes, nowadays plastic containers are also used for Mabisi production. However, the effect of this change in production practice on the properties of the product has not been documented. Therefore, we aimed at determining the effect of fermentation vessels and types of back-slopping on acidification and microbial communities during fermentation. A series of fifteen experiments using two types of fermentation vessels (plastic buckets and calabashes) in combination with different types of back-slopping (no back-slopping, passive back-slopping, and active back-slopping) were set up at a field site in rural Zambia. In each of the fifteen fermentations we analysed acidification rate of traditional Mabisi fermentation and bacterial diversity over time. No significant difference was found in terms of microbial diversity during and at the end of fermentation between fermentations performed in buckets or previously used calabashes. Bacterial communities in general decreased in diversity over time, where the drop in pH correlated with a decrease in Shannon Index. In case of active back-slopping, the pH drop started right after inoculation while in the no back-slopping and passive back-slopping fermentations, there was a clear lag phase before acidification started. All experimental series resulted in a microbial community dominated by Lactococcus lactis and a Shannon Index, as a measure for diversity, between 0.6 and 2.0. The use of plastic buckets for Mabisi fermentation can be a valuable alternative to the use of calabashes as this study showed no biological and physico-chemical differences between Mabisi resulting from both fermentation vessels, although the reason for perceived differences should be further investigated.