The US Food Safety Modernization Act (FSMA) of September 2015 requires food facilities to have a food safety plan in place that includes an analysis of hazards and risk-based preventive controls to minimize or prevent the identified hazards.

However, issues such as antibiotic resistance, biogenic amines, acid-resistant pathogens, low availability of essential minerals and nutrients and shelf life remain to be challenging with burning issues that consistently call for research solutions to guarantee human health.



Studies in our lab focus on global food safety and security issues by addressing many unanswered research questions through an understanding of the genetic diversity of bacteria, yeast and viruses in fermented foods and beverages and knowing the genetic basis for surviving under acidic or alkaline pH and alcohol regimes.

Food and drug administration (FDA) described fermented foods as food with pH 4.6 or below, although outbreaks reported from consumption of fermented foods in the US are considerably lower than other foods.

Fermented foods and beverages constitute a significant part of diet around the world. They are made from different substrates ranging from milk, meat, cereal, tubers, fruits and produce. These substrates transfer microbes into the fermentation vessels and determine their metabolic signature and sensory profile.

Many fermented products consumed globally are produced with deliberate inoculation while some that are industrialized use starter cultures or backslopping techniques.

Deciphering diversity

Our studies use metagenomics amplicon and shotgun sequencing to decipher strain-level microbial diversity (alpha and beta), relative abundance and taxonomy of culturable and uncultured microbes. We also characterize gene coding for important functions such as antimicrobial compounds, antibiotic resistance, quorum sensing, biofilm formation and transposable genetic elements. These are helping us to use the fermentation system as a simple ecosystem that can be used to study genetic transfer and metabolic exchanges in an ecosystem.

We are pursuing strain-level whole genome sequencing to support the selection of strains that can be used for the industrial production of fermented beverages. Here we are combining epigenetic and pan-genomic tools for comparative strain-level characterization to support taxonomy, the impact of fermentation conditions on gene expression and to maximize functional advantages of novel strains.

We are also utilizing metabolomic techniques such HPLC and H1 NMR to determine novel metabolites that contribute to the flavour, aroma, antimicrobial and rheological properties of fermented foods and beverages. Recently, we identified strains of fructophilic lactic acid bacteria that can reduce residual fructose in wine and still perform a malolactic fermentation without the production of mannitol.

Fermented foods

On the other hand, we have shown genetic variation among viral stains associated with fermented foods and beverages. We recently characterized a novel Lactobacillus delbrueckii bacteriophage PMBT4 in fermented African dairy food and are currently studying molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages as well as conducting global-scale virome studies of fermented foods and beverages.

This is enabling us to better understand the roles that viruses play during fermentation, especially how they affect cellular functions, such as carbohydrate metabolism, translation, signal transduction and nucleotide metabolism, as well as how we could utilize phages for biocontrol during the fermentation of beer to remove spoilage bacteria such as Levilactobacillus brevis and biogenic amines such as Lentilactobacillus hilgardii.