ArticleNPJ science of food2021
Monitoring the microbiome for food safety and quality using deep shotgun sequencing.
Article in NPJ science of food, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 43 citations in OpenAlex.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Genome editing and food safety: bridging the validation gap.NPJ science of food · 2026Review
- Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits.Environmental microbiome · 2026Article
- Diversity and selected functional traits of microbiota associated with traditional dried plant foods from South African informal markets.FEMS microbes · 2026Article
- Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends.Food science & nutrition · 2025Review
- Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.Microorganisms · 2025Article
- Can Metagenomic Analyses Be Used Effectively in Safe Food Production?Food science & nutrition · 2025Review
- Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.Applied and environmental microbiology · 2025Review
- Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.Pathogens (Basel, Switzerland) · 2025Article
- Development of a Novel Colorimetric pH Biosensor Based on A-Motif Structures for Rapid Food Freshness Monitoring and Spoilage Detection.Biosensors · 2024Article
- Article
- Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world.Nature reviews. Microbiology · 2024Review
- Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.Animal microbiome · 2023Article
- Application of Membrane Filtration to Cold Sterilization of Drinks and Establishment of Aseptic Workshop.Food and environmental virology · 2023Review
- Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.Foods (Basel, Switzerland) · 2023Review
- Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes.Journal of the Indian Institute of Science · 2023Review
- Article
- The microbiome and resistome of apple fruits alter in the post-harvest period.Environmental microbiome · 2022Article
- Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs.ISME communications · 2022Article
- Malnourishment affects gene expression along the length of the small intestine.Frontiers in nutrition · 2022Article
Corrections and comments
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Authors and funding
22 authors at 8 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.