High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage

Abstract

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 B1 (AFB1), AFB2, AFM1, 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.

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

“…Other genera, such as Acetobacter , were found at relatively high abundances in some of the dairy and cereal fermented samples. These observations agree with most of the previous studies that describe the microbial populations of dairy 6 and cereal 8,14,15 foods produced in Africa. Bacterial genera that include potential pathogenic species such as Escherichia or Clostridium (cluster I and XI) were found in several cereal and dairy samples.…”

Microbiological safety of ready‐to‐eat foods in low‐ and middle‐income countries: A comprehensive 10‐year (2009 to 2018) review

“…Processing techniques (such as grain washing, fermentation, dilution, and heat treatment) routinely applied during RTE production may influence mycotoxin levels in the finished product (Ezekiel, Ayeni, et al., ; Ezekiel, Sulyok, et al., ; Karlovsky et al., ; Okeke et al., , ). Nonetheless, mycotoxins in ingredients are commonly carried over to the final product albeit in varying concentrations depending on the toxin levels in the starting raw material (Ezekiel et al., ; Ezekiel, Ayeni, et al., ; Matumba et al., ; Okeke et al., ). Mycotoxin carry‐over is typical, particularly in resource scarce rural settings, where local food processors commonly apply low‐quality grains in the production of RTEs because high‐quality grains are often sold for household income (Ayalew et al., ; Misihairabgwi et al., ).…”

“…This technique revealed the V. cholerae strain(s) responsible for the outbreak may have been accidentally introduced from another geographical location (Chin et al, 2011;Hendriksen et al, 2011). Recently, molecular techniques including WGS have also been applied in other studies involving fermenters in traditional foods and pathogens in vegetable samples of LMIC origin (Adewumi, Oguntoyinbo, Keisam, Romi, & Jeyaram, 2013;Diaz et al, 2018;Ezekiel, Ayeni, et al, 2019;Igbinosa et al, 2018). These studies have mostly been conducted in collaboration with institutions in the North (Western world) where facilities and expertise are readily available; thus, technology and expertise transfer to LMICs are expected in the future.…”

Assessment of the Microbiome and Potential Aflatoxin Associated With the Medicinal Herb Platycladus orientalis

“…Given the continuous development in genomic technologies, high-throughput sequencing is widely applied in various areas. It provides insights into the diversity of microorganisms from different sources (Fan et al, 2018;Ezekiel et al, 2019). Traditionally, fungal identification from herbs has involved macro-and micro-morphological examinations through culture work and microscopy.…”