Combination of culture-independent and culture-dependent molecular methods for the determination of bacterial community of iru, a fermented Parkia biglobosa seeds

B-vitamins and heat processed fermented starchy and vegetable foods in sub-Saharan Africa: A review

Micronutrient deficiency still occurs in sub-Saharan Africa (SSA) despite the availability of several food resources, particularly fermented foods and vegetables, with high nutritional potential. Fermentation enhances the quality of food in several aspects. Organoleptically, certain taste, aroma, and textures are developed. Health and safety are improved by inhibiting the growth of several foodborne pathogens and removing harmful toxic compounds. Furthermore, nutrition is enhanced by improving micronutrient contents and bioavailability from the food, especially vitamin B content. However, during processing and before final consumption, many fermented foods are heat treated (drying, pasteurization, cooking, etc.) to make the food digestible and safe for consumption. Heat treatment improves the bioavailability of B-vitamins in some foods. In other foods, heating decreases the nutritional value because some B-vitamins are degraded. In SSA, cooked starchy foods are often associated with vegetables in household meals. This paper reviews studies that have focused fermented starchy foods and vegetable foods in SSA with the potential to provide B-vitamins to consumers. The review also describes the process of the preparation of these foods for final consumption, and techniques that can prevent or lessen B-vitamin loss, or enrich B-vitamins prior to consumption.

Plant-Based Alkaline Fermented Foods as Sustainable Sources of Nutrients and Health-Promoting Bioactive Compounds

Traditional food fermentation is a practice that precedes human history. Acidic products such as yogurts and sourdoughs or alcoholic beverages produced through lactic acid or yeast fermentations, respectively, are widely described and documented. However, a relatively less popular group of fermented products known as alkaline fermented foods are common traditional products in Africa and Asia. These products are so called “alkaline” because the pH tends to increase during fermentation due to the formation of ammonia resulting from protein degradation by Bacillus species. Plant-based alkaline fermented foods (AFFs) are generally produced from legumes including soybean, non-soybean leguminous seeds, and other non-legume plant raw materials. Alkaline fermented food products such as natto, douchi, kinema, doenjang, chongkukjang, thua nao, meitauza, yandou, dawadawa/iru, ugba, kawal, okpehe, otiru, oso, ogiri, bikalga, maari/tayohounta, ntoba mbodi, cabuk, and owoh are produced at small industrial scale or household levels and widely consumed in Asia and Africa where they provide essential nutrients and health-promoting bioactive compounds for the population. Alkaline food fermentation is important for sustainable food security as it contributes to traditional dietary diversity, significantly reduces antinutritional components in raw plant materials thereby improving digestibility, improves health via the production of vitamins, and may confer probiotic and post-biotic effects onto consumers. In this review, we present currently available scientific information on plant-based AFFs and their role as sustainable sources of nutrients and bioactive compounds for improved health. Finally, we provide perspectives on research needs required to harness the full potential of AFFs in contributing to nutrition and health.

Microbial Diversity and Quality-Related Physicochemical Properties of Spicy Cabbage in Northeastern China and Their Correlation Analysis

Chinese spicy cabbage (CSC) is a popular special fermented food in Northeast China. The bacterial community and quality of CSC from different regions of northeastern China (Group_J: Jilin province, Group_L: Liaoning province, Group_H: Heilongjiang province) at retail (Group_P) and home-made (Group_C) were investigated in this study. The determination of the microbial community was achieved using high-throughput sequencing and the quality-related physicochemical characteristics included pH, salinity, total acid (TA), amino acid nitrogen (AAN), reducing sugar (RS), nitrite, and biogenic amines (BAs). Based on OPLS-DA analysis, there was a difference between the quality of Group_C and Group_P. No significant difference was observed in province grouping. Proteobacteria and Firmicutes were the dominant phyla, and the dominant genera were Lactobacillus, Pantoea, Weissella, and Pseudomonas. All groups had significant differences in community structure (p < 0.05). Compared with Group_C, the relative abundance of opportunistic pathogens (Pseudomonas and Serratia) in Group_P was lower. Pseudomonas and Serratia were the biomarkers in Group_H. At the genus level, Lactobacilluss and Weissella had a positive correlation with pH, Cadaverrine, and salinity (p < 0.05), however, they were negatively related to tryptamine. Pseudomonas was negatively correlated with salinity (p < 0.05). Bacterial community and physicochemical parameters of CSC, as well as the correlation between them, were discussed in this study, providing a reference for future studies on CSC inoculation and fermentation.

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.

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

Background

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors.

Methods

We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms.

Results

We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.

Characterization of Diversity and Probiotic Efficiency of the Autochthonous Lactic Acid Bacteria in the Fermentation of Selected Raw Fruit and Vegetable Juices

The diversity of indigenous lactic acid bacteria (LAB) in fermented broccoli, cherry, ginger, white radish, and white-fleshed pitaya juices was analyzed using culture-independent and -dependent approaches. The major properties of selected probiotic strains, including dynamic variations in pH, viable cell counts, antibiotic resistance, bacterial adhesion to hydrophobic compounds, and survivability during simulated gastrointestinal transit, were investigated using broccoli as the fermentation substrate. In broccoli and ginger juices, the genus Lactobacillus occupied the dominant position (abundances of 79.0 and 30.3%, respectively); in cherry and radish juices, Weissella occupied the dominant position (abundances of 78.3 and 83.2%, respectively); and in pitaya juice, Streptococcus and Lactococcus occupied the dominant positions (52.2 and 37.0%, respectively). Leuconostoc mesenteroides, Weissella cibaria/soli/confusa, Enterococcus gallinarum/durans/hirae, Pediococcus pentosaceus, Bacillus coagulans, and Lactococcus garvieae/lactis subspecies were identified by partial 16S rRNA gene sequencing. In general, the selected autochthonous LAB isolates displayed no significant differences in comparison with commercial strains with regard to growth rates or acidification in fermented broccoli juice. Among all the isolates, L. mesenteroides B4-25 exhibited the highest antibiotic resistance profile (equal to that of L. plantarum CICC20265), and suitable adhesion properties (adhesion of 13.4 ± 5.2% ∼ 36.4 ± 3.2% and 21.6 ± 1.4% ∼ 69.6 ± 2.3% to ethyl acetate and xylene, respectively). Furthermore, P. pentosaceus Ca-4 and L. mesenteroides B-25 featured the highest survival rates (22.4 ± 2.6 and 21.2 ± 1.4%, respectively), after simulated gastrointestinal transit. These results indicated a high level of diversity among the autochthonous bacterial community in fermented fruit and vegetable juices, and demonstrated the potential of these candidate probiotics for applications in fermentation.

Screening of a beta-cypermethrin-degrading bacterial strain Brevibacillus parabrevis BCP-09 and its biochemical degradation pathway

A novel beta-cypermethrin (Beta-CP)-degrading strain isolated from activated sludge was identified as Brevibacillus parabrevis BCP-09 based on its morphological and physio-biochemical characteristics, and 16S rRNA gene analysis. Strain BCP-09 could effectively degrade Beta-CP at pH 5.0-9.0, 20-40 °C, and 10-500 mg L^-1 Beta-CP. Under optimal conditions (pH 7.41, 38.9 °C, 30.9 mg L^-1 Beta-CP), 75.87% Beta-CP was degraded within 3 days. Beta-CP degradation (half-life, 33.45 h) and strain BCP-09 growth were respectively described using first-order-kinetic and logistic-kinetic models. Seven metabolites were detected by high-performance liquid chromatography and gas chromatography-mass spectrometry- methyl salicylate, catechol, phthalic acid, salicylic acid, 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylic acid, 3-phenoxybenzaldehyde, and 3-phenoxybenzoic acid (3-PBA). The major Beta-CP metabolite, 3-PBA was further degraded into phenol, benzoic acid, and 4-methylhexanoic acid. BCP-09 also degraded aromatic compounds such as phenol, catechol, and protocatechuic acid. Beta-CP appears to be mainly degraded into 3-PBA, which is continuously degraded into smaller benzene or chain compounds. Thus, strain BCP-09 could form a complete degradation system for Beta-CP and might be considered a promising strain for application in the bioremediation of environments and agricultural products polluted by Beta-CP.

Phylogenetic analyses of bacteria associated with the processing of iru and ogiri condiments

Analysis of the bacterial community dynamics during the production of traditional fermented condiments is important for food safety assessment, quality control and development of starter culture technology. In this study, bacteria isolated during the processing of iru and ogiri, two commonly consumed condiments in Nigeria, were characterized based on phylogenetic analyses of the bacterial 16S rRNA gene. A total of 227 isolates were obtained and clustered into 12 operational taxonomic units (OTUs) based on 97% 16S rRNA gene similarity. The OTUs spanned three phyla (Firmicutes, Actinobacteria and Proteobacteria), and nine genera: Acinetobacter, Aerococcus, Bacillus, Enterococcus, Enterobacter, Lysinibacillus, Micrococcus, Proteus and Staphylococcus. OTUs closely related to species of Bacillus dominated the processing stages of both condiments. Although no single OTU occurred throughout iru processing stages, an OTU (mostly related to B. safensis) dominated the ogiri processing stages indicating potentials for the development of starter culture. However, other isolates such as those of Enterococcus spp. and Lysinibacillus spp. may be potential starters for iru fermentation. Presumptive food-borne pathogens were also detected at some stages of the condiments' processing, possibly due to poor hygienic practices.

SIGNIFICANCE AND IMPACT OF THE STUDY

Iru and ogiri are important condiments used for flavour enhancement in foods and serve as protein substitutes in diets among rural populations across West Africa. Consumption of these condiments is growing, reinforcing the need to scale up their production. Production of these condiments includes spontaneous fermentation, which often leads to inconsistent product quality and unguaranteed safety. This study has demonstrated the bacterial succession in iru and ogiri processing and highlights species that could be selected and exploited for starter culture development. This study provides a starting point to produce quality and microbiologically safe iru and ogiri condiments.

Influence of soy fortification on microbial diversity during cassava fermentation and subsequent physicochemical characteristics of garri

This study investigated the influence of the addition of soy products on the microbiology, nutritional and physico-chemical characteristics of garri, a fermented cassava product. Malted soy flour (MSF) and soy protein (SP) were separately added (12% w/w) to cassava mash prior to controlled fermentation, while non-supplemented cassava mash served as a control. Identification of lactic acid bacteria (LAB) and aerobic mesophilic bacteria was accomplished by repetitive sequence based (rep)-PCR analysis and 16S rRNA gene sequencing. Physicochemical, nutritional and sensory characterisation of control and soy-fortified garri was performed using conventional methods. rep-PCR allowed differentiation of 142 isolates into 41 groups corresponding to 6 species of LAB and 25 species of aerobic mesophiles. LAB isolates belonged to the genera Lactobacillus, Weissella, Leuconostoc and Lactococcus with Leuconostoc mesenteroides being the dominant species in control and MSF-cassava while Weissella cibaria dominated SP-cassava fermentation. Aerobic mesophiles included Gram positive and negative bacteria including species of the genera Bacillus, Clostridium, Staphylococcus, Serratia, Acinetobacter and Raoultella. Diversity of aerobic mesophiles varied between control, MSF- and SP- cassava mash. Protein content of soy-fortified garri increased from 0.73% to 10.17% and 10.05% in MSF and SP garri respectively with a significant decrease in total cyanide from 26 to 11 ppm. Results from physicochemical and organoleptic evaluation indicate that supplementation of cassava with soy products prior to fermentation can produce acceptable garri. Soy products can be considered a viable option for protein fortification of garri, a low protein food with the aim of combating malnutrition.

Molecular analysis of bacterial community dynamics during the fermentation of soy-daddawa condiment

Bacterial community dynamics during soy-daddawa fermentation was investigated using culture-dependent and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) molecular methods. The total titratable acidity (TTA), pH, and bacterial counts (BCs) were monitored daily during a 72-h fermentation period. Bacteria were characterized based on 16S rRNA gene sequencing. TTA ranged from 0.08 to 0.26 mg lactic acid/g, whereas pH ranged from 7.01 to 8.19. BCs increased from 3.9 to 10.61 log CFU/g. Fifty-eight isolates were obtained by culture method and clustered into seven operational taxonomic units (OTUs) at 97% sequence similarity, whereas four OTUs were obtained from the PCR-DGGE method. Taxonomic identification revealed that bacteria belonged to the genera Bacillus, Enterobacter, Enterococcus, and Staphylococcus with B. subtilis being present throughout fermentation. Medically significant isolates, including B. anthracis, Enterococcus casseliflavus, and Enterobacter hormaechei were detected. These results emphasize the need for starter culture utilization and offer a platform for starter culture screening and selection.

Produce from Africa's Gardens: Potential for Leafy Vegetable and Fruit Fermentations

A rich variety of indigenous fruits and vegetables grow in Africa, which contribute to the nutrition and health of Africa's populations. Fruits and vegetables have high moisture and are thus inherently prone to accelerated spoilage. Food fermentation still plays a major role in combating food spoilage and foodborne diseases that are prevalent in many of Africa's resource disadvantaged regions. Lactic acid fermentation is probably the oldest and best-accepted food processing method among the African people, and is largely a home-based process. Fermentation of leafy vegetables and fruits is, however, underutilized in Africa, although such fermented products could contribute toward improving nutrition and food security in this continent, where many are still malnourished and suffer from hidden hunger. Fermentation of leafy vegetables and fruits may not only improve safety and prolong shelf life, but may also enhance the availability of some trace minerals, vitamins and anti-oxidants. Cassava, cow-peas, amaranth, African nightshade, and spider plant leaves have a potential for fermentation, as do various fruits for the production of vinegars or fruit beers and wines. What is needed to accelerate efforts for production of fermented leaves and vegetables is the development of fermentation protocols, training of personnel and scale-up of production methods. Furthermore, suitable starter cultures need to be developed and produced to guarantee the success of the fermentations.

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment

Soy-daddawa, a fermented soybean (Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3-V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria, and included species from the genera Atopostipes, Bacillus, Brevibacterium and Nosocomiicoccus. Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota, and included species from the genera, Alternaria, Aspergillus, Candida, Cladosporium, Dokmaia, Issatchenkia, Kodamaea, Lecythophora, Phoma, Pichia, Rhizopus, Saccharomyces and Starmerella. The majority of fungal species have not been previously reported in soy-daddawa. Potential opportunistic human pathogens such as Atopostipes suicloacalis, Candida rugosa, Candida tropicalis, and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing.