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In recent years, much attention has been directed towards the integration of dark fermentation process into a biorefinery concept to enhance the energetic gains, thereby improving the competitiveness of this process. The volatile fatty acids (VFAs) from dark fermentative H2-producing processes serve as precursors for the microbial synthesis of a broad spectrum of biotechnologically-important products such as biofuels and biocommodities. These products are desirable substrates for secondary bioprocesses due to their biodegradable nature and affordability. This short review discusses the use of acidogenic-derived VFAs in the production of value-added compounds such as polyhydroxyalkanoates (PHAs) alongside the microbial-based fuels (hydrogen, biogas, and electricity), and other valuable compounds (succinic acid, citric acid, and butanol). The review also highlights the strategies that have been used to enhance the extraction of VFAs from acidogenic effluents and other related waste streams. The application of novel enhancement techniques such as nanoparticles during VFAs recovery is also discussed in this work. Furthermore, the work highlights some of the recent advances in dark fermentation-based biorefinery, particularly the development of pilot-scale processes. Finally, the review provides some suggestions on the advancement of dark fermentation-based biorefineries using VFAs that are derived from acidogenic processes.

Introduction: Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types., Methods: Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline., Results: Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH 4, PO 4 , pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms., Discussion: Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces , Bacillus and Nocardioides . The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Raimi, Ezeokoli and Adeleke.)

The present study aimed to reveal the microbial (bacteria and yeast) composition of raw milk from dairy camel (n = 10), cow (n = 10) and goat (n = 10) in North-western Nigeria. High-throughput DNA metabarcoding was used to compare microbial compositions in raw milk among the three species. Although the three species had similar dominant bacterial (Firmicutes and Proteobacteria) and yeast (Ascomycota and Basidiomycota) phyla, their microbial compositions at the genus level were noticeably different. The top differentially abundant bacterial and yeast genera (percentage abundance) were Lactobacillus (36%), Streptococcus (34%), Enterococcus (12%), Kluyveromyces (28%), Saccharomyces (24%), and Candida (18%), respectively. Principal coordinate analysis based on unweighted UniFrac values revealed significant differences in the structure of bacterial communities and no differences in yeast communities in milk samples from the three species. This study provides insight into the rich and diverse bacterial and yeast communities in raw animal milk consumed in Nigeria, which could play beneficial roles or pose health threats to consumers. However, further research on the economic significance of the microbial community in animal milk consumed in Nigeria is required., (© The Author(s) 2022. Published by Oxford University Press on behalf of Applied Microbiology International.)

Amongst the biofuels described in the literature, biohydrogen has gained heightened attention over the past decade due to its remarkable properties. Biohydrogen is a renewable form of H 2 that can be produced under ambient conditions and at a low cost from biomass residues. Innovative approaches are continuously being applied to overcome the low process yields and pave the way for its scalability. Since the process primarily depends on the biohydrogen-producing bacteria, there is a need to acquire in-depth knowledge about the ecology of the various assemblages participating in the process, establishing effective bioaugmentation methods. This work provides an overview of the biofilm-forming communities during H 2 production by mixed cultures and the synergistic associations established by certain species during H 2 production. The strategies that enhance the growth of biofilms within the H 2 reactors are also discussed. A short section is also included, explaining techniques used for examining and studying these biofilm structures. The work concludes with some suggestions that could lead to breakthroughs in this area of research.

Vermicompost (VC) harbours diverse microbes, including plant growth-promoting microorganisms (PGPM) that are beneficial for sustainable crop production. Hence, this study aimed to analyse bacterial diversity of VC samples as a first high-throughput screening step towards subsequent targeted isolation of potential bacterial inoculum candidates. To achieve this, bacterial communities in VC collected from five production farms were enriched in nutrient-rich media before high-throughput sequence (HTS) analysis of the partial 16S rRNA gene. HTS analysis revealed 572 amplicon sequence variants (ASVs) in all enriched VC samples. Firmicutes, Proteobacteria, Planctomycetes and Bacteroidetes were the most dominant phyla, while Lysinibacillus, Escherichia-Shigella, Bacillus, Pseudomonas, Clostridium sensu stricto 1, Morganella, Vibrio and Aeromonas were the predominant genera across the enriched VC. The presence of Clostridium sensu stricto 1, Escherichia-Shigella and Vibrio genera, which are potentially pathogenic species, suggests the need to improve vermicomposting efficiency and safety. Predicted functional profiling of the bacterial communities using PICRUSt2 showed abundance profiles of nitrogenases, phosphatases and sulfatases. In addition, the potential to produce siderophore, indole acetic acids (IAA) and phytohormone regulator 1-aminocyclopropane-1-carboxylate (ACC) were predicted. Lysinibacillus, Bacillus, Paenibacillus and Pseudomonas were major bacterial communities with potential plant growth-promoting traits and could serve as resources in bacterial inoculum production. The findings in this study provide insight into the community composition, abundance and the potential functional capability of cultivable bacterial species of enriched VC. This study also points to VC as a suitable source of potentially beneficial bacterial candidates for inoculum production., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., (© 2021 The Society for Applied Microbiology.)

Components of the iron reductive pathway of Candida albicans have been implicated in the production of prostaglandin E2 (PGE2) and virulence. However, it is unknown whether other components of this pathway influence PGE2. We investigated the role of the iron reductive pathway of C. albicans in biofilm formation, PGE2 production, and virulence in Caenorhabditis elegans. Additionally, as the co-occurrence of C. albicans and Pseudomonas aeruginosa in host tissues is frequent and involves competition for host-associated iron, we examined the effects of this interaction. Deletion of multicopper oxidase gene, FET99, and iron permease genes, FTH1 and FTH2, affected biofilm metabolic activity, and for the FTH2 mutant, also biofilm morphology. Deletion of CCC1 (vacuolar iron transporter) and CCC2 (P-type ATPase copper importer) also influenced biofilm morphology. For PGE2 production, deletion of FET99, FTH1, FTH2, CCC1, and CCC2 caused a significant reduction by monomicrobial biofilms, while FTH2deletion caused the highest reduction in polymicrobial biofilms. URA3 positive mutants of FET99 and FTH2 demonstrated attenuated virulence in C. elegans, potentially due to the inability of mutants to form hyphae in vivo. Deductively, the role of the iron reductive pathway in PGE2 synthesis is indirect, possibly due to their role in iron homeostasis., Lay Summary: Iron uptake is vital for disease-causing microbes like Candida albicans. Using strains deficient in some iron-uptake genes, we show that iron-uptake genes, especially FET99 and FTH2, play a role in biofilm formation, prostaglandin production, and virulence in the nematode infection model., (© The Author(s) 2021. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae , Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.

Severe cases of coronavirus disease 2019 (COVID-19) managed in the intensive care unit are prone to complications, including secondary infections with opportunistic fungal pathogens. Systemic fungal co-infections in hospitalized COVID-19 patients may exacerbate COVID-19 disease severity, hamper treatment effectiveness and increase mortality. Here, we reiterate the role of fungal co-infections in exacerbating COVID-19 disease severity as well as highlight emerging trends related to fungal disease burden in COVID-19 patients. Furthermore, we provide perspectives on the risk factors for fungal co-infections in hospitalized COVID-19 patients and highlight the potential role of prolonged immunomodulatory treatments in driving fungal co-infections, including COVID-19-associated pulmonary aspergillosis (CAPA), COVID-19-associated candidiasis (CAC) and mucormycosis. We reiterate the need for early diagnosis of suspected COVID-19-associated systemic mycoses in the hospital setting.

South African surface waters are subject to various forms of pollution. Recent findings in aquatic systems suggest an association exists between yeast diversity, chemical pollutants and land coverage, which are important water quality determinants. Yeast abundance and diversity, as well as antifungal agents in two river systems in South Africa, were investigated and related to the existing land coverage. Yeast abundance and diversity were determined from environmental DNA by quantitative polymerase chain reaction and next-generation sequencing, respectively, of the 26S ribosomal ribonucleic acid (rRNA) gene. Antifungal agents were qualitatively and/or quantitatively detected by ultra-high-pressure liquid chromatography-mass spectrometry. Analyses of 2 031 714 high-quality 26S rRNA sequences yielded 5554 amplicon sequence variants (ASVs)/species. ASV richness and Shannon-Wiener index of diversity reflected the southward flow of the river with higher values observed downstream compared to the upstream. Fluconazole concentrations were quantifiable in only two samples; 178 and 271 ng L -1 . Taxonomically, at least 20 yeast species were detected, including the dominant Candida tropicalis, Cryptococcus spp. as well as the lesser dominant Bensingtonia bomiensis, Fereydounia khargensis, Hericium erinaceus, Kondoa changbaiensi, Pseudozyma spp. and Sphacelotheca pamparum. The two dominant species are known opportunistic pathogens which had antifungal resistant traits in previous studies from the same rivers and therefore is a public health threat. The present study provides further evidence that yeasts should be included as part of water quality parameters, especially in developing countries where much of the population are economically disadvantaged, and also immunocompromised due to age and disease., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

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., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Contamination of ready-to-eat (RTE) foods by pathogenic bacteria may predispose consumers to foodborne diseases. This study investigated the presence of bacterial contaminants and their antibiotic susceptibility patterns in three locally processed RTE foods (eko, fufu and zobo) vended in urban markets in Ogun state, Nigeria. Bacteria isolated from a total of 120 RTE food samples were identified by 16S rRNA gene phylogeny while susceptibility patterns to eight classes of antibiotics were determined by the disc diffusion method. Species belonging to the genera Acinetobacter and Enterobacter were recovered from all RTE food types investigated, Klebsiella and Staphylococcus were recovered from eko and fufu samples, while those of Shigella were recovered from eko samples. Enterobacter hormaechei was the most prevalent species in all three RTE food types. Precisely 99% of 149 isolates were multidrug-resistant, suggesting a high risk for RTE food handlers and consumers. Co-resistance to ampicillin and cephalothin was the most frequently observed resistance phenotype. Results demonstrate that improved hygiene practices by food processors and vendors are urgently required during RTE processing and retail. Also, adequate food safety guidelines, regulation and enforcement by relevant government agencies are needed to improve the safety of RTE foods and ensure the protection of consumer health., (© 2020 The Society for Applied Microbiology.)

Microbial lipids, also known as single-cell oils (SCOs), are highly attractive feedstocks for biodiesel production due to their fast production rates, minimal labor requirements, independence from seasonal and climatic changes, and ease of scale-up for industrial processing. Among the SCO producers, the less explored filamentous fungi (molds) exhibit desirable features such as a repertoire of hydrolyzing enzymes and a unique pellet morphology that facilitates downstream harvesting. Although several oleaginous filamentous fungi have been identified and explored for SCO production, high production costs and technical difficulties still make the process less attractive compared to conventional lipid sources for biodiesel production. This review aims to highlight the ability of filamentous fungi to hydrolyze various organic wastes for SCO production and explore current strategies to enhance the efficiency and cost-effectiveness of the SCO production and recovery process. The review also highlights the mechanisms and components governing lipogenic pathways, which can inform the rational designs of processing conditions and metabolic engineering efforts for increasing the quality and accumulation of lipids in filamentous fungi. Furthermore, we describe other process integration strategies such as the co-production with hydrogen using advanced fermentation processes as a step toward a biorefinery process. These innovative approaches allow for integrating upstream and downstream processing units, thus resulting in an efficient and cost-effective method of simultaneous SCO production and utilization for biodiesel production., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Mhlongo, Ezeokoli, Roopnarain, Ndaba, Sekoai, Habimana and Pohl.)

Little is known of the mycobiota present in ready-to-eat peanuts consumed in Southern Africa. Knowledge of the mycobiota and aflatoxigenic species can elucidate potential health risks associated with consumption of ready-to-eat peanuts sold by supermarkets and roadside vendors. We investigated the culturable mycobiota diversity in supermarket and roadside-vended peanuts as well as the presence of five aflatoxin biosynthesis pathway-related genes ( aflR, aflJ, aflM, aflD , and aflP ) in 15 suspected aflatoxigenic isolates, with a focus on Mafikeng, South Africa. Mean colony-forming unit (CFU) counts of 288.7 and 619.7 CFU/g were observed in supermarket and roadside-vended peanuts, respectively. A total of 145 fungal isolates comprising 26 distinct taxa (based on 97% internal transcribed spacer region [ITS1-5.8S-ITS2] sequence similarity) were obtained, including strains representing Aspergillus, Acremonium, Alternaria, Bipolaris, Chaetomium, Ectophoma, Epicoccum, Hamigera, Leancillium, Monascus, Penicillium, Periconia, Talaromyces , and Trichoderma . Phylogenetic analyses of concatenated sequences of the ITS1-5.8S-ITS2, β-tubulin, and calmodulin genes delineated the species of As pergillus , which included A. flavus, A. fumigatus, A. hiratsukae, A. niger , and A. parasiticus . Higher species richness was obtained from supermarket peanuts compared with roadside-vended peanuts, with eight species common to both sources. Across supermarket or roadside-vended peanuts, A. fumigatus, A. niger , and A. flavus were prevalent (>40% incidence). In contrast, strains related to or representing Ectophoma multirostata, Aspergillus hiratsukae, Bipolaris zeae, Chaetomium bostrychodes, Epicoccum nigrum, Hamigera paravellanea, Lecanicillium aphanocladii, Monascus ruber, Periconia macrospinosa, Periconia lateralis, Talaromyces funiculosus, Talaromyces minioluteus, Talaromyces wortmannii, Talaromyces spp., and Trichoderma sp. were detected in either supermarket or roadside-vended peanuts. Among the five aflatoxin biosynthesis pathway-related genes, aflD and aflM were more prevalent (87%) and aflR was the least prevalent (40%). Findings suggest that roasted peanuts meant for human consumption and sold at supermarkets and by roadside vendors are contaminated with potential toxin-producing fungi. Hence, proper processing and packaging of peanuts before vending is recommended.

Fungal co-infections, especially with Aspergillus and Candida species, are prevalent in hospitalised COVID-19 patients, and could influence patient outcomes and hamper treatment efforts. However, information about and elucidation of the causal relationship between fungal co-infections and COVID-19 disease outcomes or severity in patients are still lacking. Such information, if and when available, will help facilitate appropriate case management.

Soil microbial communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and role in soil ecosystem processes. Presently, information on structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa is sparse. Here, bacterial communities in three post-coal mining reclamation soils were investigated using community-level physiological profiling (CLPP), enzyme activities, and next-generation sequencing of 16S rRNA gene. Inferences were drawn in reference to adjacent unmined soils. CLPP-based species diversity and proportionality did not differ significantly (P > 0.05) whereas activities of β-glucosidase, urease and phosphatases were significantly (P < 0.05) influenced by site and soil history (reclaimed vs unmined). Bacterial communities were influenced (PERMANOVA, P < 0.05) by soil history and site differences, with several phylotypes differentially abundant between soils. Contrastingly, predicted functional capabilities of bacterial communities were not different (PERMANOVA, P > 0.05), suggesting redundancy in bacterial community functions between reclamation and unmined soils. Silt content, bulk density, pH, electrical conductivity, Na and Ca significantly influenced soil bacterial communities. Overall, results indicate that bacterial community structure reflects underlying differences between soil ecosystems, and suggest the restoration of bacterial diversity and functions over chronological age in reclamation soils.

The genetic and predicted functional diversity of bacterial communities in 12 commercial biofertiliser products were evaluated using high-throughput sequencing of the 16S rRNA gene. Proteobacteria, Firmicutes and Bacteroides dominated the bacterial communities, with the genera Pseudomonas, Lactobacillus, Bacillus, Bradyrhizobium and Rhizobium being prevalent. The manufacturer-specified species were detected in relatively high abundance in two of the products while a few or none of the specified species were detected in some products. A number of unspecified microbes were detected, including potential human and crop pathogens such as Alcaligenes, Clostridium, Escherichia-Shigella and Proteus . The functional prediction unravelled high prevalence of enzyme-coding genes such as nitrogenase, NifT, alkaline phosphatase and reductases of nitric oxide, nitrate and nitrite which contribute to nitrogen-fixation, phosphorus solubilisation and degradation of nitrates and nitrites. In addition, toxins such as leukocidin/hemolysin and colicin V protein that cause product quality damage were highly predicted in over 67% of the products. Overall, high-throughput sequence analysis of bacterial communities in biofertiliser products revealed that majority of the products were of poor quality. This result justifies the need for regular quality assessment and improvement in quality control systems during biofertiliser formulation., Competing Interests: The authors declare that they have no conflict of interest.This article does not contain any studies with human participants or animals performed by any of the authors.

Kunu is a traditional fermented single or mixed cereals-based beverage popularly consumed in many parts of West Africa. Presently, the bacterial community and mycotoxin contamination profiles during processing of various kunu formulations have never been comprehensively studied. This study, therefore, investigated the bacterial community and multi-mycotoxin dynamics during the processing of three kunu formulations using high-throughput sequence analysis of partial 16S rRNA gene (hypervariable V3-V4 region) and liquid chromatography tandem mass spectrometry (LC-MS/MS), respectively. A total of 2,303 operational taxonomic units (OTUs) were obtained across six processing stages in all three kunu formulations. Principal coordinate analysis biplots of the Bray-Curtis dissimilarity between bacterial communities revealed the combined influences of formulations and processing steps. Taxonomically, OTUs spanned 13 phyla and 486 genera. Firmicutes (phylum) dominated (relative abundance) most of the processing stages, while Proteobacteria dominated the rest of the stages. Lactobacillus (genus taxa level) dominated most processing stages and the final product ( kunu ) of two formulations, whereas Clostridium sensu stricto (cluster 1) dominated kunu of one formulation, constituting a novel observation. We further identified Acetobacter , Propionibacterium , Gluconacetobacter , and Gluconobacter previously not associated with kunu processing. Shared phylotypes between all communities were dominated by lactic acid bacteria including species of Lactobacillus , Lactococcus , Leuconostoc , Pediococcus , and Weissella . Other shared phylotypes included notable acetic acid bacteria and potential human enteric pathogens. Ten mycotoxins [3-Nitropropionic acid, aflatoxicol, aflatoxin B 1 (AFB 1 ), AFB 2 , AFM 1 , alternariol (AOH), alternariolmethylether (AME), beauvericin (BEAU), citrinin, and moniliformin] were quantified at varying concentrations in ingredients for kunu processing. Except for AOH, AME, and BEAU that were retained at minimal levels of < 2 μg/kg in the final product, most mycotoxins in the ingredients were not detectable after processing. In particular, mycotoxin levels were substantially reduced by fermentation, although simple dilution and sieving also contributed to mycotoxin reduction. This study reinforces the perception of kunu as a rich source of bacteria with beneficial attributes to consumer health, and provides in-depth understanding of the microbiology of kunu processing, as well as information on mycotoxin contamination and reduction during this process. These findings may aid the development of starter culture technology for safe and quality kunu production.

This study assessed, for the first time, the mycotoxicological risks from consumption of complementary foods by infants and young children in Nigeria. Molds belonging to Aspergillus aculeatinus, A. flavus, A. luchuensis, A. tubingensis, A. welwitschiae and Geotrichum candidum were recovered from the complementary foods. Twenty-eight major mycotoxins and derivatives, and another 109 microbial metabolites including chloramphenicol (a bacterial metabolite), were quantified in 137 food samples by LC-MS/MS. Aflatoxins and fumonisins co-contaminated 42% of the cereal- and nut-based food samples, at mean concentrations exceeding the EU limits of 0.1 and 200 μg/kg set for processed baby foods by 300 and six times, respectively. Milk contained mainly beauvericin, chloramphenicol and zearalenone. The trichothecenes, T-2 and HT-2 toxins, were quantified only in infant formula and at levels three times above the EU indicative level of 15 μg/kg for baby food. Chronic exposure estimate to carcinogenic aflatoxin was high causing low margin of exposure (MOE). Exposures to other mycotoxins either exceeded the established reference values by several fold or revealed low MOEs, pointing to important health risks in this highly vulnerable population. The observed mycotoxin mixtures may further increase risks of adverse health outcomes of exposure; this warrants urgent advocacy and regulatory interventions., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., (© 2018 The Society for Applied Microbiology.)

Response and growth kinetics of microbes in contaminated medium are useful indices for the screening and selection of tolerant species for eco-friendly bio-augmentative remediation of polluted environments. In this study, the heavy metal (HM) tolerance, bioaccumulation and growth kinetics of seven bacterial strains isolated from mining sites to 10 HMs (Cd, Hg, Ni, Al, Cr, Pb, Cu, Fe, Mn and Zn) at varied concentrations (25-600 mgL -1 ) were investigated. The isolates were phylogenetically (16S rRNA gene) related to Lysinibacillus macroides, Achromobacter spanius, Bacillus kochii, B. cereus, Klebsiella pneumoniae, Pseudomonas mosselii and P. nitroreducens. Metal tolerance, effects on lag phase duration and growth rates were assessed using the 96-well micro-titre method. Furthermore, metal bioaccumulation and quantities within cells were determined by transmission electron microscopy and electron dispersive x-ray analyses. Tolerance to Ni, Pb, Fe and Mn occurred at highest concentrations tested. Growth rates increased with increasing Fe concentrations, but reduced significantly (p < .05) with increasing Zn, Cu, Hg, Cd and Al. Significantly higher (p < .05) growth rates (compared to controls) was found with some isolates in Hg (25 mgL -1 ), Ni (100 mgL -1 ), Cr (150 mgL -1 ), Mn (600 mgL -1 ), Pb (100 mgL -1 ), Fe (600 mgL -1 ) and Al (50 mgL -1 ). Lag phase urations were isolate- and heavy metal-specific, in direct proportion to concentrations. A. spanius accumulated the most Mn and Zn, while B. cereus accumulated the most Cu. Metals accumulated intra-cellularly without cell morphology distortions. The isolates' multi-metal tolerance, intra-cellular metal bioaccumulation and growth kinetics suggest potentials for application in the synergetic biodegradation and bioremediation of polluted environments, especially HM-rich sites., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The microbiological safety of spontaneously fermented foods is not always guaranteed due to the undefined fermenting microbial consortium and processing materials. In this study, two commonly consumed traditional condiments (iru and ogiri) and their respective raw seeds (locust bean and melon) purchased from markets in south-western Nigeria were assessed for bacterial diversity and mycotoxin contamination using 16S rRNA gene sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS), respectively. Two hundred isolates obtained from the raw seeds and condiments clustered into 10 operational taxonomic units (OTUs) and spanned 3 phyla, 10 genera, 14 species and 2 sub-species. Bacillus (25%) and Staphylococcus (23.5%) dominated other genera. Potentially pathogenic species such as Alcaligenes faecalis, Bacillus anthracis, Proteus mirabilis and Staphylococcus sciuri subsp. sciuri occurred in the samples, suggesting poor hygienic practice during production and/or handling of the condiments. A total of 48 microbial metabolites including 7 mycotoxins [3-nitropropionic acid, aflatoxin B 1 (AFB 1 ), AFB 2 , beauvericin, citrinin, ochratoxin A and sterigmatocystin] were quantified in the food samples. Melon and ogiri had detectable aflatoxin levels whereas locust bean and iru did not; the overall mycotoxin levels in the food samples were low. There is a need to educate processors/vendors of these condiments on good hygienic and processing practices., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Genetic modification of maize with Bacillus thuringiensis (Bt) cry proteins may predispose shifts in the bacterial endophytes' community associated with maize shoots. In this study, the diversity of bacterial endophytes associated with a Bt maize genotype (Mon810) and its isogenic non-transgenic parental line were investigated at pre-flowering (50 days) and post-flowering (90 days) developmental stages. PCR-DGGE and high throughput sequencing on the Illumina MiSeq sequencer were used to characterize bacterial 16S rRNA gene diversity in leaves, stems, seeds and tassels. PCR-DGGE profile revealed similarity as well as differences between bacterial communities of shoots in both cultivars and at both developmental stages. A total of 1771 operational taxonomic units (OTUs) were obtained from the MiSeq and assigned into 14 phyla, 27 classes, 58 orders, 116 families and 247 genera. Differences in alpha and beta diversity measures of OTUs between the phyllospheres of both genotypes were not significant (P > .05) at all developmental stages. In all cultivars, OTU diversity reduced with plant development. OTUs belonging to the phyla Proteobacteria were dominant in all maize phyllospheres. The class Gammaproteobacteria was dominant in Bt maize while, Alphaproteobacteria and Actinobacteria were dominant in non-Bt maize phyllospheres. Differences in the abundance of some genera, including Acidovorax, Burkerholderia, Brachybacterium, Enterobacter and Rhodococcus, whose species are known beneficial endophytes were observed between cultivars. Hierarchical cluster analysis further suggests that the bacterial endophyte communities of both maize genotypes associate differently (are dissimilar). Overall, the results suggest that bacterial endophytes community differed more across developmental stages than between maize genotypes.

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., (Copyright © 2016 Elsevier B.V. All rights reserved.)