Monitoring the microbiome for food safety and quality using deep shotgun sequencing.
Journal
NPJ science of food
ISSN: 2396-8370
Titre abrégé: NPJ Sci Food
Pays: England
ID NLM: 101739627
Informations de publication
Date de publication:
08 Feb 2021
08 Feb 2021
Historique:
received:
14
01
2020
accepted:
24
11
2020
entrez:
9
2
2021
pubmed:
10
2
2021
medline:
10
2
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33558514
doi: 10.1038/s41538-020-00083-y
pii: 10.1038/s41538-020-00083-y
pmc: PMC7870667
doi:
Types de publication
Journal Article
Langues
eng
Pagination
3Références
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