Comparison of the microbial composition of African fermented foods using amplicon sequencing

Microbiological evaluation of the indigenous fermented condiment okpeye available at various retail markets in the south-eastern region of Nigeria

In Africa, indigenous fermented condiments contribute to food security as a low-cost source of protein. Okpeye is an indigenous fermented condiment produced from Prosopis africana seeds. The reliance on spontaneous fermentation processes and unhygienic practices during production often results in the contamination of the final product with microbial hazards. A microbiological evaluation of 18 commercial samples of okpeye purchased from six markets in two cities in southeastern Nigeria was conducted. Fifty-nine (59) bacteria were isolated and identified at the species level by phenotyping and sequencing the 16S rRNA, gyrB and rpoB genes. Bacillus (47.4 %) and Staphylococcus (42.3 %) were the predominant bacterial genera in okpeye. Overall, B. amyloliquefaciens and S. simulans were the most frequently occurring bacteria and were present in all samples. In addition, B. cereus was isolated in samples obtained from all markets. Other bacterial species included B. velezensis, Oceanobacillus caeni, S. cohnii, Escherichia fergusonni and Vagacoccus lutrae. The B. cereus isolates (10) were screened for the presence of 8 enterotoxin genes (hblA, hblC, hblD, nheA, nheB, nheC, cytK, entFM) and one emetic gene (cesB). The non-haemolytic enterotoxin (nheABC) and haemolytic enterotoxin (hblABD) complexes were present in 70 % and 50 % of B. cereus respectively. The positive rate of cytK and entFM genes was 70 %, while the cesB gene was 30 %. Antibiotic susceptibility assessment showed that most of the isolates were susceptible to gentamicin, tetracycline, streptomycin, and erythromycin but resistant to ciprofloxacin and vancomycin. These findings highlight the need for further controls to reduce contamination with potential pathogenic bacteria in indigenous fermented condiments such as okpeye. There is also a need to educate producers regarding hygienic practices to safeguard public health and food security.

Draft genome of Lysinibacillus fusiformis PwPw_T2 isolated from Ananas comosus revealing acetic acid producing and xenobiotic degrading enzymes

Lysinibacillus fusiformis PwPw_T2 isolated from deteriorating Ananas comosus sample collected from Lagos State, Nigeria putatively possesses genomic features like potential enzymes catalyzing acetic acid production and xenobiotic compounds degradation via various pathways as indicated by its genome sequences. These could make the organism relevant in food waste valorization and micro-biotechnology.

Microbiological and physical-chemical characteristics of the Peruvian fermented beverage "Chicha de siete semillas": Towards the selection of strains with acidifying properties

Traditional fermented beverages have been consumed worldwide for centuries. Such is the case of "Chicha de siete semillas" which is originally from the province of Huanta, in Ayacucho, Peru. In this work we have analyzed the chemical composition and bacterial diversity of products manufactured from six producers, who have used different combinations of cereals, pseudocereals, legumes and aromatic herbs, although maize was present in all of them. The fermented beverages had a low pH, mainly due to the production of lactic acid, whereas ethanol was, in general, present in low concentrations. Most of the products were rich in GABA, the content of biogenic amines being very low, as corresponds to a product with a short maturation time (less than 4 days). A metataxonomic analysis revealed that Streptococcaceae and Leuconostocaceae families were dominant in the majority of the beverages, Streptococcus spp. and Leuconostoc spp. being the representative genera, respectively. The result was corroborated by culture-dependent techniques, since these were the most abundant genera isolated and identified in all samples, with Streptococcus macedonicus and Leuconostoc lactis as representative species. In lower proportions other isolates were identified as Lactobacillus delbrueckii, Lactiplantibacillus plantarum, Furfurilactobacillus rossiae, Weissella confusa and Enterococcus faecium. The genetic profile of 26 S. macedonicus isolates was determined by RAPD-PCR and REP-PCR, showing five different patterns distinguishable with the first technique. One representative strain from each genetic pattern was further characterized and used to ferment a maize-based matrix (with saccharose) in order to know their technological potential. All strains were able to ferment the beverage at 30 °C in a short time (about 6 h) reaching a pH below 4.5 and they remained viable after 24 h; the main organic acid contributing to the pH decrease was lactic acid. Therefore, S. macedonicus is a good candidate for being part of a putative starter culture, since it is a species well adapted to this cereal-based food niche.

Cereal-based fermented foods as a source of folate and cobalamin: The role of endogenous microbiota

Folate (vitamin B9) and cobalamin (vitamin B12) deficiencies potentially affect millions of people worldwide, leading to different pathologies. In Ethiopia, the diet is characterized by high consumption of fermented cereal-based foods such as injera, a good source of folate but not of cobalamin, which is only found in foods of animal origin that are rarely consumed. Some of the bacteria responsible for the fermentation of cereals can synthesize cobalamin, but whether or not fermented cereal food products contain cobalamin remains underexplored. The objective of this study was to assess the folate and cobalamin content of injera collected from various households in Ethiopia at different stages of production. Global (16S rRNA gene sequencing) and specific (real-time PCR quantification of bacteria known for folate or cobalamin production) bacterial composition of these samples was assessed. UPLC-PDA was used to identify the cobalamin to see whether the active or inactive form was present. Surprisingly, teff flour contained 0.8 μg/100 g of cobalamin, most probably due to microbial contamination from the environment and the harvesting process. While fermentation increased the folate and cobalamin content in some households, their levels decreased in others. Conversely, cooking consistently reduced the level of the vitamins. Fresh injera contained, on average, 21.2 μg/100 g of folate and 2.1 μg/100 g of cobalamin, which is high, but with marked variation depending on the sample. However, the form of cobalamin was a corrinoid that is biologically inactive in humans. Injera fermentation was dominated by lactic acid bacteria, with significant correlations observed between certain bacterial species and folate and cobalamin levels. For example, a high proportion of Fructilactobacillus sanfranciscensis, a known folate consumer, was negatively correlated with the folate content of injera. On the contrary, Lactobacillus coryniformis, known for its cobalamin synthesis ability was present in high proportion in the cobalamin-rich samples. These findings highlight the complex interrelationship between microorganisms and suggest the involvement of specific bacteria in the production of folate and cobalamin during injera fermentation. Controlled fermentation using vitamin-producing bacteria is thus a promising tool to promote folate and cobalamin production in fermented food.

Microbial Diversity in African Foods and Beverages: A Systematic Assessment

This article provides a comprehensive and in-depth examination of the microbial diversity inherent in African food and beverages, with a particular emphasis on fermented products. It identifies and characterizes the dominant microorganisms, including both prokaryotes and yeasts, prevalent in these foods, and furthermore, critically analyzes the health benefits of these microbial strains, especially their probiotic properties, which could potentially improve digestion and contribute to human health. Notably, it underscores the vital role these microorganisms play in bolstering food security across Africa by enhancing and preserving food quality and safety. It also delves into the potential applications of microbial products, such as metabolites, in the food industry, suggesting their possible use in food processing and preservation. Conclusively, with a summarization of the key findings, emphasizing the importance of gaining a deep understanding of microbial diversity in African beverages and foods. Such knowledge is crucial not only in promoting food security but also in advancing public health.

Exploration of Infant Food Microbial Composition from Formal and Informal Settings Using Viable Counts and 16S rRNA Gene Amplicon Sequencing in Johannesburg, South Africa

Diarrhoea is a considerable agent of disease and loss of life in children below age five in South Africa. Soweto, South Africa is an urban township in Johannesburg, with most of its population living in informal settlements. Informal settlements in areas such as Soweto are often impoverished communities that do not get water easily, inadequate sanitation is pervasive, and poor hygiene common (risk factors for diarrhoeal diseases). Among the age groups, infants are most vulnerable to diarrhoeal infection, mainly through the ingestion of food and water. The presence of undesirable microbiota is a food safety and health challenge. This study investigated the microbiome of infant food samples collected from formal (n = 19) and informal (n = 11) households in Soweto. A non-culture-dependent technique was used to characterise the bacterial diversity and composition of the infant food samples. The results indicated that household type did not influence microbial diversity and composition in Soweto. South Africa. Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes dominated the phyla rank in food samples from formal and informal households. Potential pathogens of public health significance, including diarrhoeal disease agents such as Salmonella spp., E. coli, and Campylobacter spp., were detected within the foods. We concluded that the infant food samples showed rich bacterial diversity, and the presence of potential pathogens of public health significance suggests a disease risk that infants may face upon consuming the foods.

Technological variations, microbial diversity and quality characteristics of maize ogi used for akpan production in Benin

Fermented maize starch, called ogi in Benin, is used for preparing akpan, a traditional yoghurt-like food that contributes to the food and nutrition security of its consumers. Current ogi processing technologies used by two socio-cultural groups of Benin, namely the Fon and the Goun, and aspects of the quality of the fermented starches were studied to assess the current state-of-the-art, explore changes in key product characteristics over time and identify priorities for follow-up research to increase product quality and shelf life. A survey on processing technologies was conducted in five municipalities in south Benin and samples of maize starch were collected, which were analysed after the fermentation required to obtain ogi. Four processing technologies were identified, two from the Goun (G1, G2) and two from the Fon (F1, F2). The main difference between the four processing technologies was the steeping procedure used for the maize grains. The pH of the ogi samples ranged between 3.1 and 4.2, with the highest values for G1 samples, which also contained relatively higher concentrations of sucrose (0.05-0.3 g/L) than F1 samples (0.02-0.08 g/L), and lower citrate and lactate concentrations (0.2-0.3 and 5.6-16.9 g/L, respectively) than F2 samples (0.4-0.5 and 14-27.7 g/L, respectively). Fon samples collected in Abomey were particularly rich in volatile organic compounds and free essential amino acids. Members of the genera Lactobacillus (8.6-69.3%), Limosilactobacillus (5.4-79.1%), Streptococcus (0.6-59.3%) and Weissella (2.6-51.2%) dominated the bacterial microbiota of ogi with a significant abundance of Lactobacillus spp. in Goun samples. Sordariomycetes (10.6-81.9%) and Saccharomycetes (6.2-81.4%) dominated the fungal microbiota. The yeast community of ogi samples mainly consisted of the genera Diutina, Pichia, Kluyveromyces, Lachancea and unclassified members of the Dipodascaceae family. Hierarchical clustering of metabolic data showed similarities between samples from different technologies at a default threshold of 0.05. No obvious trend in the composition of the samples' microbial communities reflected the clusters observed for the metabolic characteristics. The results indicate that beyond the general impact of the use of Fon or Goun technologies on fermented maize starch, the individual contribution of processing practices warrants study, under controlled conditions, to determine the drivers of difference or similarity between maize ogi samples to further contribute to improving product quality and shelf life.

Traditional Fermentation Affects the Nutraceutical Properties of Parkia biglobosa Seeds

Parkia biglobosa seeds (African locust bean) play a crucial role in the diet and health of Western African populations. The seeds are spontaneously fermented to produce condiments used for food seasoning and stews preparation. Hence, to understand the health benefits of seed-based products from P. biglobosa, total polyphenol content, in vitro and ex vivo antioxidant properties, as well as antihypertensive activity, of fermented and non-fermented seeds were investigated. The Folin-Ciocalteu method was used to determine total polyphenol content; 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) tests were used to estimate the in vitro antioxidant activity. The ex vivo antioxidant and antihypertensive activities were evaluated by using cellular antioxidant activity in human red blood cells (CAA-RBC) and angiotensin-converting enzyme (ACE) inhibitory activity assays, respectively. The fermented seeds showed a huge increase in polyphenol content and in vitro antioxidant activities compared to non-fermented ones. The fermented seeds showed a higher potency of biological antioxidant activity than non-fermented ones by exhibiting greater protection of erythrocytes from oxidative damage at a very low dose of extracts. Both fermented and non-fermented seeds have been shown to contain peptides with ACE-inhibitory activity; however, the non-fermented seeds exerted a higher ACE-inhibitory activity than fermented ones. In conclusion, traditional fermentation positively impacted the nutraceutical and health benefits of P. biglobosa seeds. However, the non-fermented seeds should not be ignored. Both fermented and non-fermented seeds can be used as valuable ingredients for the formulation of functional foods.

Adaptations in the transformation of cassava (Manihot esculenta Crantz; Euphorbiaceae) for consumption in the dietary management of diabetes: the case of Palikur, or Parikwene People, from French Guiana

Introduction

In the French overseas department of French Guiana, in South America, nutrition therapy for the management of diabetes is based on French guidelines. However, this region is demographically diverse and includes several populations of Indigenous Peoples, Parikwene among others, also called Palikur. Due to socio-economical, cultural, and geographical differences, along with distinctions in the local food system, dietary recommendations, which many consider in the context of post-colonial power dynamics, are not well suited to local populations. In the absence of suitable recommendations, it is hypothesized that local populations will adapt their dietary practices considering diabetes as an emerging health problem.

Methods

Seventy-five interviews were conducted with community members and Elders, as well as healthcare professionals and administrators providing services to the Parikwene population of Macouria and Saint-Georges de l'Oyapock communes. Data regarding the representation of cassava (Manihot esculenta Crantz) consumption and diabetes were collected via semi-structured interviews and participant observation (i.e., observation and participation in community activities), namely via participating in activities related to the transformation of cassava tubers at swidden and fallow fields.

Results and Discussion

Parikwene have adapted the transformation of cassava tubers for their consumption in the management of diabetes.The importance of cassava tubers as a staple and core food to the Parikwene food system was established by identifying it as a cultural keystone species. Narratives illustrated conflicting perceptions regarding the implication of cassava consumption in the development of diabetes. Adaptations to the operational sequence involved in the transformation of cassava tubers led to the production of distinct cassava roasted semolina (i.e., couac), based on organoleptic properties (i.e., sweet, and acidic couac). Preferences for the consumption of acidic couac were grounded in the Parikwene knowledge system, as well as attention to diabetes related symptoms and glucometer readings.

Conclusion

These results provide important insights related to knowledge, attitudes, and practices in developing locally and culturally adapted approaches to providing dietary recommendations in the treatment of diabetes.

Promising Probiotic Properties of the Yeasts Isolated from Rabilé, a Traditionally Fermented Beer Produced in Burkina Faso

In recent years, research on yeasts as probiotics has gained more and more interest, which will allow the development of "new" products in the probiotics market. In this context, seventeen yeast strains isolated from Rabilé, a traditional beer produced in Burkina Faso, were assessed for their probiotic attributes. The yeast identification was performed by molecular methods, including PCR-RFLP and 5.8S-ITS region sequencing. Saccharomyces cerevisiae (14 strains) was the predominantly identified species, followed by Pichia kudriavzevii (2 strains) and Rhodotorula mucilaginosa (1 strain). Except for R. mucilaginosa, all yeast strains grew well at human temperature. The yeast strains showed high resistance when they were exposed to simulated gastrointestinal conditions. Auto-aggregation ability was between 70.20 ± 10.53% and 91.82 ± 1.96%, while co-aggregation with E. coli ranged from 24.92 ± 3.96% to 80.68 ± 9.53% and with S. enterica serovar Typhimurium from 40.89 ± 8.18% to 74.06 ± 7.94%. Furthermore, the hydrophobicity of isolated strains toward n-hexane was in the range from 43.17 ± 5.07% to 70.73 ± 2.42%. All yeast strains displayed high antioxidant capabilities, and the strains did not show hemolysis halos, such that they can be considered safe. Additionally, S. cerevisiae strains strongly inhibited the growth of foodborne pathogens. This is the first preliminary study to identify and characterize the yeast strains isolated from Rabilé with interesting probiotic properties.

Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes

Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.

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.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

Fermented Minor Grain Foods: Classification, Functional Components, and Probiotic Potential

Fermented minor grain (MG) foods often have unique nutritional value and functional characteristics, which are important for developing dietary culture worldwide. As a kind of special raw material in fermented food, minor grains have special functional components, such as trace elements, dietary fiber, and polyphenols. Fermented MG foods have excellent nutrients, phytochemicals, and bioactive compounds and are consumed as a rich source of probiotic microbes. Thus, the purpose of this review is to introduce the latest progress in research related to the fermentation products of MGs. Specific discussion is focused on the classification of fermented MG foods and their nutritional and health implications, including studies of microbial diversity, functional components, and probiotic potential. Furthermore, this review discusses how mixed fermentation of grain mixtures is a better method for developing new functional foods to increase the nutritional value of meals based on cereals and legumes in terms of dietary protein and micronutrients.

Development of mixed starter culture for the fermentation of Ethiopian honey wine, Tej

Ethiopian honey wine is one of the country's most popular spontaneously fermented traditional alcoholic beverages. However, the final product of this natural fermentation system is frequently of poor and inconsistent quality. Furthermore, it makes the process difficult to predict, control, and correct. Thus, the main aim of this study was to develop a direct fermentation system for Ethiopian honey wine, Tej. After isolating fermentative microbial strains from Tej samples, they were subjected to intensive screening to fit to its purpose. Later, phenotypic and genotypic characterization, and inoculation of isolates to honey-must were performed sequentially. Finally, microbial interaction and physicochemical analysis, including volatile compounds profiling, were done for the inoculated samples. The identified isolates were strains of Saccharomycetaceae and Lactobacillaceae families. These strains showed a good ability to tolerate osmotic stress and a lower pH environment. Tej sample produced by mixed culture inoculation of Saccharomyces and Lactobacillus species showed similar physicochemical, volatile compounds, and sensory attributes values with that of the control sample. Thus, a mixture of Saccharomyces and Lactobacillus strains could be used as a starter culture to produce Ethiopian honey, Tej, without scarifying of its major quality attributes.

Traditional Fermented Foods and Beverages from around the World and Their Health Benefits

Traditional fermented foods and beverages play an important role in a range of human diets, and several experimental studies have shown their potential positive effects on human health. Studies from different continents have revealed strong associations between the microorganisms present in certain fermented foods (e.g., agave fructans, kefir, yeats, kombucha, chungkookjang, cheeses and vegetables, among others) and weight maintenance, reductions in the risk of cardiovascular disease, antidiabetic and constipation benefits, improvement of glucose and lipids levels, stimulation of the immunological system, anticarcinogenic effects and, most importantly, reduced mortality. Accordingly, the aim of this review is to corroborate information reported in experimental studies that comprised interventions involving the consumption of traditional fermented foods or beverages and their association with human health. This work focuses on studies that used fermented food from 2014 to the present. In conclusion, traditional fermented foods or beverages could be important in the promotion of human health. Further studies are needed to understand the mechanisms involved in inflammatory, immune, chronic and gastrointestinal diseases and the roles of fermented traditional foods and beverages in terms of preventing or managing those diseases.

Co-occurrence of Lactobacillus Species During Fermentation of African Indigenous Foods: Impact on Food Safety and Shelf-Life Extension

The benefits derived from fermented foods and beverages have placed great value on their acceptability worldwide. Food fermentation technologies have been employed for thousands of years and are considered essential processes for the production and preservation of foods, with the critical roles played by the autochthonous fermenting food-grade microorganisms in ensuring food security and safety, increased shelf life, and enhanced livelihoods of many people in Africa, particularly the marginalized and vulnerable groups. Many indigenous fermented foods and beverages of Africa are of plant origin. In this review, the predominance, fermentative activities, and biopreservative role of Lactobacillus spp. during production of indigenous foods and beverages, the potential health benefit of probiotics, and the impact of these food-grade microorganisms on food safety and prolonged shelf life are discussed. During production of African indigenous foods (with emphasis on cereals and cassava-based food products), fermentation occurs in succession; the first group of microorganisms to colonize the fermenting substrates are lactic acid bacteria (LAB) with the diversity and dominance of Lactobacillus spp. The Lactobacillus spp. multiply rapidly in the fermentation matrix, by taking up nutrients from the surrounding environments, and cause rapid acidification in the fermenting system via the production of organic compounds that convert fermentable sugars into mainly lactic acid. Production of these compounds in food systems inhibits spoilage microorganisms, which has a direct effect on food quality and safety. The knowledge of microbial interaction and succession during food fermentation will assist the food industry in producing functional foods and beverages with improved nutritional profiling and technological attributes, as Lactobacillus strains isolated during fermentation of several African indigenous foods have demonstrated desirable characteristics that make them safe for use as probiotic microorganisms and even as a starter culture in small- and large-scale/industrial food production processes.

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.

Potential Role of African Fermented Indigenous Vegetables in Maternal and Child Nutrition in Sub-Saharan Africa

Hunger and malnutrition continue to affect Africa especially the vulnerable children and women in reproductive age. However, Africa has indigenous foods and associated traditional technologies that can contribute to alleviation of hunger, malnutrition, and communicable and noncommunicable diseases. The importance of African indigenous vegetables is undeniable, only that they are season-linked and considered as "food for poor" despite their high nutritional contents. The utilization of African indigenous vegetables (AIVs) is hindered by postharvest losses and antinutrients affecting the bioavailability of nutrients. In Africa, fermentation is among the oldest food processing technologies with long history of safe use. Apart from extending shelf life and improving food organoleptic properties, fermentation of African indigenous vegetables (AIVs) is known to improve food nutritional values such as proteins, minerals, vitamins, and other beneficial phytochemicals. It can also increase bioavailability of various vitamins, minerals, and phytochemicals and increase synthesis of vital blood pressure regulators thus protecting against cardiovascular diseases and cancer and further helping fight certain malnutrition deficiencies. Some lactic acid bacteria (LAB) involved in food fermentation are known to produce exopolysaccharides with cholesterol-lowering, immunomodulator, antioxidant, and anticancer properties. Fermented foods (vegetables) are superior in quality and safety since most microorganisms involved in fermentation are good starter cultures that can inhibit the growth of foodborne pathogens and detoxify harmful compounds in foods. Thus, fermented foods can boost growth and well-being in children and women due to their higher nutritional contents. Therefore, fermentation of AIVs can contribute to the attainment of food and nutrition security especially among women and children who rely on these vegetables as a staple source of micronutrients and income. These benefits have a positive impact on the implementation of the second sustainable development goals and African Union agenda 2063. This review is aimed at shedding light on the potential of African fermented indigenous vegetables in combating maternal and child malnutrition in Sub-Sahara Africa.

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri)

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Relevance of organ(s)-on-a-chip systems to the investigation of food-gut microbiota-host interactions

The ever greater understanding of the composition and function of the gut microbiome has provided new opportunities with respect to understanding and treating human disease. However, the models employed for in vitro and in vivo animal studies do not always provide the required insights. As a result, one such alternative in vitro cell culture based system, organ-on-a-chip technology, has recently attracted attention as a means of obtaining data that is representative of responses in humans. Organ-on-a-chip systems are designed to mimic the interactions of different tissue elements that were missing from traditional two-dimensional tissue culture. While they do not traditionally include a microbiota component, organ-on-a-chip systems provide a potentially valuable means of characterising the interactions between the microbiome and human tissues with a view to providing even greater accuracy. From a dietary perspective, these microbiota-organ-on-a-chip combinations can help researchers to predict how the consumption of specific foods and ingredients can impact on human health and disease. We provide an overview of the relevance and interactions of the gut microbiota and the diet in human health, we summarise the components involved in the organ-on-a-chip systems, how these systems have been employed for microbiota based studies and their potential relevance to study the interplay between food-gut microbiota-host interactions.

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.

Microbial Diversity and Metabolite Profile of Fermenting Millet in the Production of Hausa koko, a Ghanaian Fermented Cereal Porridge

Hausa koko is an indigenous porridge processed from millet in Ghana. The process involves fermentation stages, giving the characteristic organoleptic properties of the product that is produced largely at a small-scale household level and sold as a street food. Like many other indigenous foods, quality control is problematic and depends on the skills of the processor. In order to improve the quality of the product and standardize the process for large-scale production, we need a deeper understanding of the microbial processes. The aim of this study is to investigate the microbial community involved in the production of this traditional millet porridge and the metabolites produced during processing. High-throughput amplicon sequencing was used to identify the bacterial (16S rRNA V4 hypervariable region) and fungal [Intergenic Transcribed Spacer (ITS)] communities associated with the fermentation, while nuclear magnetic resonance (NMR) was used for metabolite profiling. The bacterial community diversity was reduced during the fermentation processes with an increase and predominance of lactobacilli. Other dominant bacteria in the fermentation included Pediococcus, Weissella, Lactococcus, Streptococcus, Leuconostoc, and Acetobacter. The species Limosilactobacillus fermentum and Ligilactobacillus salivarius accounted for some of the diversities within and between fermentation time points and processors. The fungal community was dominated by the genus Saccharomyces. Other genera such as Pichia, Candida, Kluyveromyces, Nakaseomyces, Torulaspora, and Cyberlindnera were also classified. The species Saccharomyces cerevisiae, Stachybotrys sansevieriae, Malassezia restricta, Cyberlindnera fabianii, and Kluyveromyces marxianus accounted for some of the diversities within some fermentation time points. The species S. sansevieria and M. restricta may have been reported for the first time in cereal fermentation. This is the most diverse microbial community reported in Hausa koko. In this study, we could identify and quantify 33 key different metabolites produced by the interactions of the microbial communities with the millet, composed of organic compounds, sugars, amino acids and intermediary compounds, and other key fermentation compounds. An increase in the concentration of organic acids in parallel with the reduction of sugars occurred during the fermentation process while an initial increase of amino acids followed by a decrease in later fermentation steps was observed.

Augmenting Clinical Interventions in Psychiatric Disorders: Systematic Review and Update on Nutrition

There is a strong relationship between a healthy diet and mental well-being. Several foods and food compounds are known to modulate biomarkers and molecular mechanisms involved in the aetiogenesis of several mental disorders, and this can be useful in containing the disease progression, including its prophylaxis. This is an updated systematic review of the literature to justify the inclusion and recognition of nutrition in the management of psychiatric illnesses. Such foods and their compounds include dietary flavanols from fruits and vegetables, notable antioxidant and anti-inflammatory agents, probiotics (fermented foods) known to protect good gut bacteria, foods rich in polyunsaturated fatty acids (e.g., Omega-3), and avoiding diets high in saturated fats and refined sugars among others. While the exact mechanism(s) of mitigation of many nutritional interventions are yet to be fully understood, the evidence-based approach warrants the inclusion and co-recognition of nutrition in the management of psychiatric illnesses. For the greater public health benefit, there is a need for policy advocacy aimed at bridging the knowledge gap and encouraging the integration of nutritional intervention with contemporary therapies in clinical settings, as deficiencies of certain nutrients make therapy difficult even with appropriate medication.

Significance of African Diets in Biotherapeutic Modulation of the Gut Microbiome

Diet plays an essential role in human development and growth, contributing to health and well-being. The socio-economic values, cultural perspectives, and dietary formulation in sub-Saharan Africa can influence gut health and disease prevention. The vast microbial ecosystems in the human gut frequently interrelate to maintain a healthy, well-coordinated cellular and humoral immune signalling to prevent metabolic dysfunction, pathogen dominance, and induction of systemic diseases. The diverse indigenous diets could differentially act as biotherapeutics to modulate microbial abundance and population characteristics. Such modulation could prevent stunted growth, malnutrition, induction of bowel diseases, attenuated immune responses, and mortality, particularly among infants. Understanding the associations between specific indigenous African diets and the predictability of the dynamics of gut bacteria genera promises potential biotherapeutics towards improving the prevention, control, and treatment of microbiome-associated diseases such as cancer, inflammatory bowel disease, obesity, type 2 diabetes, and cardiovascular disease. The dietary influence of many African diets (especially grain-base such as millet, maize, brown rice, sorghum, soya, and tapioca) promotes gut lining integrity, immune tolerance towards the microbiota, and its associated immune and inflammatory responses. A fibre-rich diet is a promising biotherapeutic candidate that could effectively modulate inflammatory mediators' expression associated with immune cell migration, lymphoid tissue maturation, and signalling pathways. It could also modulate the stimulation of cytokines and chemokines involved in ensuring balance for long-term microbiome programming. The interplay between host and gut microbial digestion is complex; microbes using and competing for dietary and endogenous proteins are often attributable to variances in the comparative abundances of Enterobacteriaceae taxa. Many auto-inducers could initiate the process of quorum sensing and mammalian epinephrine host cell signalling system. It could also downregulate inflammatory signals with microbiota tumour taxa that could trigger colorectal cancer initiation, metabolic type 2 diabetes, and inflammatory bowel diseases. The exploitation of essential biotherapeutic molecules derived from fibre-rich indigenous diet promises food substances for the downregulation of inflammatory signalling that could be harmful to gut microbiota ecological balance and improved immune response modulation.

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.

Metataxonomic analysis of bacterial communities and mycotoxin reduction during processing of three millet varieties into ogi, a fermented cereal beverage

Ogi is a fermented cereal beverage, made primarily from maize (Zea mays) and rarely from millets. Unlike maize-based ogi, little is known about the bacterial community and mycotoxin profile during the production of millet-based ogi. Therefore, the bacterial community dynamics and mycotoxin reduction during ogi processing from three millet varieties were investigated using next-generation sequencing of the 16S rRNA gene and liquid chromatography-tandem mass spectrometry, respectively. A total of 1163 amplicon sequence variants (ASVs) were obtained, with ASV diversity across time intervals influenced by processing stage and millet variety. ASV distribution among samples suggested that the souring stage was more influenced by millet variety than the steeping stage, and that souring may be crucial for the quality attributes of the ogi. Furthermore, bacterial community structure during steeping and souring was significantly differentiated (PERMANOVA, P < 0.05) between varieties, with close associations observed for closely-related millet varieties. Taxonomically, Firmicutes, followed by Actinobacteria, Bacteroidetes, Cyanobacteria and Proteobacteria phyla were relatively abundant (>1%). Lactic acid bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Lactobacillus, Lactococcus and Pediococcus, dominated most fermentation stages, suggesting their roles as key fermentative and functional bacteria in relation to mycotoxin reduction. About 52-100%, 58-100% and 100% reductions in mycotoxin (aflatoxins, beauvericin, citrinin, moniliformin, sterigmatocystin and zearalenone) concentrations were recorded after processing of white fonio, brown fonio and finger millet, respectively, into ogi. This study provides new knowledge of the dominant bacterial genera vital for the improvement of millet-based ogi through starter culture development and as well, elucidates the role of processing in reducing mycotoxins in millet ogi.

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.

Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues

Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

Technologically relevant Bacillus species and microbial safety of West African traditional alkaline fermented seed condiments

Fermented food condiments serve as a major source of nutrients to many homes in West Africa, especially among the rural poor who use these condiments as a cheap source of protein substitute for milk and other animal protein sources. Traditional fermented West African condiments are produced by spontaneous fermentation of legumes and protein-rich seeds of both cultivated and wild plant species. These fermented condiments are culturally accepted and widely produced in the West African sub-region, and rely on indigenous microbiota responsible for taste, texture, aroma development and the overall unique product characteristics. Detailed understanding of fermentation microbiota and their unique technological and functional properties are fundamental in developing products with enhanced quality and safety, as well as development of specific locally adapted starter cultures. Technologically relevant Bacillus spp., mainly Bacillus subtilis, are the predominant fermentative bacteria responsible for the natural fermentation of condiments across West Africa. Other species of Bacillus including B. amyloliquefaciens, B. licheniformis, B. pumilus, B. megaterium, B. sphaericus, B. cereus, B. badius and B. fusiformis are also frequently involved in the fermentation process. These bacterial species are responsible for flavor development, bio-conversion of complex food molecules, and production of antimicrobial compounds that impact shelf-life and safety, and in some instances, may confer host-beneficial health effects beyond basic nutrition. First, this review provides currently available information on the technologically relevant Bacillus species isolated from fermented food condiments in nine (9) West African countries. In addition, perspectives on harnessing the potentials of the technologically beneficial bacterial strains in fermented condiments in West Africa for enhanced food safety, quality and overall food security is presented.

Pyrosequencing scrutiny of bacterial and fungal communities in two Sudanese sorghum-based fermented foods

Purpose

Several fermented foods are produced from sorghum flour in Africa, especially in the dryland regions where it is the principal crop. It is important to explore the microbial communities in these foods to improve their quality and organoleptic properties. In this study, the bacterial and fungal communities of two popular sorghum-based fermented foods in Sudan (kisra and hulumur) were analyzed, for the first time, using a culture-independent method of next-generation sequencing.

Methods

Fermented doughs for kisra and hulumur production were prepared according to the traditional approach, and then the bacterial and fungal communities were investigated using high-throughput sequencing.

Results

Firmicutes and Proteobacteria phyla were the predominant bacteria in both fermented doughs. At the genus level, the bacterial community was dominated by lactic acid bacteria, primarily Lactobacillus and Pediococcus, which represented 95.7% and 72% of the bacterial population in kisra and hulumur, respectively. Next, acetic acid bacteria (Gluconobacter and Acetobacter) were subdominant in hulumur. The fungal community was more heterogeneous among the fermented doughs. Zygomycota (85.5%) comprised the major phylum in kisra fermented dough, whereas Ascomycota (99.5%) was predominant in hulumur. The major fungal genera, Rhizopus, Alternaria, Penicillium, Gibberella, Lasiodiplodia, and Aspergillus, were extremely varied between the fermented doughs.

Conclusion

Exploration of kisra and hulumur microbial community structure will expand the knowledge about their microbiota to manipulate the microbial community and improve their quality and organoleptic properties using different microbial recipes.

Traditional and Artisanal Beverages in Nigeria: Microbial Diversity and Safety Issues

A review of up to 90 articles on the microorganisms associated with important artisanal or traditional beverages in Nigeria was carried out. This resulted in an overview of the prevalent microorganisms associated with soymilk, nono (fermented cow milk), tiger nut milk, yoghurt, kunu, zobo, palm wine and the local beers pito and brukutu. The bacteria genera, namely Bacillus, Escherichia, Lactobacillus, Staphylococcus, and Streptococcus, were detected in all nine beverages. On the contrary, this survey resulted in finding that the genera Saccharomyces, Aspergillus, Candida, and Penicillium were the eukaryotic microorganisms isolated in all beverages. The occurrence of fungal isolates, which can be responsible for producing mycotoxins, is a concern and shows the need for post-production tests. Overall, there is a low prevalence of bacteria associated with hygiene, especially the Escherichia genus in alcoholic beverages such as palm wine, pito and burukutu, which may be due both to a low acidity and high ethanol content. However, the prevalence of hygiene indicator genera was higher in nonalcoholic drinks, probably because of incorrect practices during processing. The magnitude of the production and sales of unregulated local beverages in Nigeria has reached the stage where significant regulation and food safety standards are required to safeguard public health. An opportunity exists to monitor and characterize the microbial flora of the artisanal beverages using molecular methods at all stages of production and storage.