Microbiomes Associated With Foods From Plant and Animal Sources.

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PubMed ID: 30405589

Imagen Publicación

Jarvis KG, Daquigan N, White JR, Morin PM, Howard LM, Manetas JE, Ottesen A, Ramachandran P, Grim CJ

Front Microbiol. 2018. doi: 10.3389/fmicb.2018.02540

COMMENT: Detection of foodborne pathogens is frequently hampered by the indigenous microbiota of the food. Characterizing baseline microbiomes in foods is important for the implementation of microbiome profiling methods for detecting pathogens in food. In addition, food microbiome profiling can help to improve the methods of preservation.


The aim of the study was to define baseline microbiomes of several plant-derived commodities employing 16S rRNA gene sequencing (V1-V3 hypervariable regions). A non-plant-derived commodity was also included for comparison, smoked salmon samples were analyzed. The commodities analyzed represent the global nature of food supply and have been linked to foodborne outbreaks in the past.

Main results:

16S rRNA gene sequence data from this study has been submitted to the FDA MetaGenomeTraker Project (NCBI Accession PRJNA390622).

The masala spice mixes, which had the highest alpha diversity in our study, harbored 19 unique genera including food spoilage associated bacteria such as Bacillus, and Cronobacter which are known foodborne pathogens, and Pediococcus that is used in food fermentations

The cilantro microbiota consists primarily of Proteobacteria (54–99%), followed by Bacteroidetes (0.83–46%), Actinobacteria (0.03–5%) and Firmicutes (0–2%)

The cucumber microbiota is comprised of Proteobacteria (45–85%), followed by Firmicutes (2–40%), Actinobacteria (8–31%), and Bacteroidetes (0–2%).

Smoked salmon species diversity was lower than plant derived food species diversity. The microbiomes were comprised almost entirely of Proteobacteria and Firmicutes at proportional abundances.

The Firmicutes identified in smoked salmon: Lactobacillus, Brochothrix, Carnobacterium, Leuconostoc, Vagococcus, and Lactococcus, are commonly associated with spoilage of refrigerated high-protein foods, such as meat and fish.


Sequencing food microbiomes reveals key features about food safety and quality.

All of the foods in this study harbored microbiome profiles that would eventually lead to bacterial spoilage.

The presence of Flavobacterium, Erwinia, Pantoea, Acinetobacter, and Pseudomonas species in all plant food microbiomes supports the notion that spoilage can be predicted by assessing food microbiome profiles.


Diana López-Farfán