In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species’ viability from total RNA sequencing.

The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA sequencing. Our comprehensive database includes >6000 plants and animals that may be present in food. FASER accurately identified eukaryotic species with 0.4% median absolute difference between observed and expected proportions on sequence data from various sources including sausage meat, plants, and fish. FASER was applied to 31 high protein powder raw factory ingredient total RNA samples. The samples mostly contained the expected source ingredient, chicken, while three samples unexpectedly contained pork and beef. Our results demonstrate that DNA/RNA sequencing of food ingredients, combined with a robust analysis, can be used to find contaminants and authenticate food ingredients in a single assay.

This study investigated the effects of high intensity ultrasound (temperature, amplitude, and time) on the inactivation of indigenous bacteria in pasteurized milk,Bacillus atrophaeusspores inoculated into sterile milk, andSaccharomyces cerevisiaeinoculated into sterile orange juice using response surface methodology. The variables investigated were sonication temperature (range from 0 to 84°C), amplitude (range from 0 to 216 μm), and time (range from 0.17 to 5 min) on the response, log microbe reduction. Data were analyzed by statistical analysis system software and three models were developed, each for bacteria, spore, and yeast reduction. Regression analysis identified sonication temperature and amplitude to be significant variables on microbe reduction. Optimization of the inactivation of microbes was found to be at 84.8°C, 216 μm amplitude, and 5.8 min. In addition, the predicted log reductions of microbes at common processing conditions (72°C for 20 sec) using 216 μm amplitude were computed. The experimental responses for bacteria, spore, and yeast reductions fell within the predicted levels, confirming the accuracy of the models.

Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANEL ^TM data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e ⁻⁷ and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to trace the mode by which characteristics have spread across breeds during historical breed formation; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial. Author Summary: From the sleek Doberman Pinscher to the coifed Poodle, the sunny Golden Retriever to the aristocratic Pekingese, the world of purebred dogs offers options that appeal to nearly all aesthetics. Pure dog breeds, of which there are over 400 worldwide, are created through selective breeding over multiple generations, toward an ideal goal of temperament, behavior, and physical appearance. Written descriptions of these breed-specific ideals are produced and maintained by dedicated breed enthusiasts, and provide guidelines that direct breeders in their selection choices. However, the genetic mechanisms that produce the spectrum of canine colors and patterns, sculpt the small triangular ears of a Siberian Husky or the long soft ears of a Basset Hound, are complicated and intertwined. This means that some breeds can carry rare, hidden traits for many generations, hampering selection efforts toward uniformity. We have determined the genotypes of >11,000 dogs, representing >200 breeds, at 12 genes that impact coat color and physical characteristics. In doing so, we can now present realistic trait frequencies within each breed, report occurrences of gene variants that can produce undesirable traits, and draw conclusions about the historic spread of characteristics across modern related breeds and those with distant shared ancestry.

Increased interest in reduced and low sodium dairy foods generates flavor issues for cheeses. Sodium is partly replaced with potassium or calcium to sustain the salty flavor perception, but the other cations may also alter metabolic routes and the resulting flavor development in aged cheeses. The effect of some cations on selected metabolic enzyme activity and on lactic acid bacterial physiology and enzymology has been documented. Potassium, for example, is an activator of 40 enzymes and inhibits 25 enzymes. Currently, we can visualize the effects of these cations only as lists inside metabolic databases such as MetaCyc. By visualizing the impact of these activating and inhibitory activities as biochemical pathways inside a metabolic database, we can understand their relevance, predict, and eventually dictate the aging process of cheeses with cations that replace sodium. As examples, we reconstructed new metabolic databases that illustrate the effect of potassium on flavor-related enzymes as microbial pathways. After metabolic reconstruction and analysis, we found that 153 pathways of lactic acid bacteria are affected due to enzymes likely to be activated or inactivated by potassium. These pathways are primarily linked to sugar metabolism, acid production, and amino acid biosynthesis and degradation that relate to Cheddar cheese flavor.