Peter Markwell's research while affiliated with China National Center for Food Safety Risk Assessment and other places

Publications (4)

Article
Full-text available
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 mat...
Preprint
Full-text available
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 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...
Article
Full-text available
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 se...
Article
Full-text available
Under intense scrutiny for safety and authenticity, our food supply encompasses probiotic supplementation, fermentation organisms, pathogenic bacteria, and microbial toxins - in short, the microbiome and metabolome of food. Recent claims regarding probiotic supplements, additives, and cultured foods highlight the need for widely accepted protocols...

Citations

... Compared to other human-related environments, food microbiomes, including their resistance potential, are rarely investigated [10]. The microbiome of food is a decisive factor for food quality [11], shelf life [12] and fermentation process [13], and already highlighted as the "missing link" in food safety policies and standards [14]. ...
... The application of genomics in the microbiome of food has been used successfully to address some agronomic challenges and the challenges associated with food safety in developed countries. For example, the Food and Drug Administration (FDA), the Centre for Disease Control and Prevention, United States Department of Agriculture (USDA), the European Food safety authority (EFSA) The African Collaborative Centre for Microbiome and Genomics Research (ACCME) are relying on genomic technologies such as whole genomic sequencing in the detection of pathogens in food, in and outside of the human body [3], Beck et al. [9]. The initiation of the 100K pathogen genome project has made it possible to study the diversity of bacteria genome which is crucial in the investigation of disease-causing bacteria found in foodstuffs, bacteria likely to cause disease outbreaks and other microbiome studies directly related to agricultural productivity [83]. ...
... Similar to other meta-omic applications, the reliance on the completeness of reference databases together with the accuracy of food matrix authentication is important to avoid inaccurate conclusions. Haiminen et al. (2019) found both DNA and RNA shotgun sequencing to be accurate untargeted methods for food authentication and contaminant detection, which have been applied by Kamilari et al. (2019) to characterize Protected Designation of Origin (PDO) cheeses with complementary metabolomics to define product origin differentiating factors. ...
... The characterization of HPP food microbiomes leveraged current accepted public reference databases, yet it is known that these databases are still inadequate 1,2,11,56,57 . Furthermore, when considering congruence between Salmonella culturability and NGS read mapping techniques, the genetic breadth and depth of multi-genome reference sequences are essential. ...