Authors
Feng, J., Daly, S. E., Roth, K., Snyder, A. B.
Abstract
Studies investigating surface microbiota in food facilities often include estimates of relative abundance. However, obtaining accurate relative abundance values can be challenging. Differences among microbes can lead to different degrees of cell recovery from the surface and different DNA extraction yields that skew downstream relative abundance estimates. Here, we evaluated (1) the impact of cell recovery from surfaces using sponge swabs and (2) DNA extraction protocol on the relative abundance estimates of relative abundance on artificially inoculated surfaces. Our results showed that Escherichia coli (Gram-negative cell), Listeria monocytogenes (Gram-positive cell), Bacillus cereus (bacterial spore), Alicyclobacillus suci (bacterial spore), Exophiala phaeomuriformis (fungal cell), Aspergillus fischeri (fungal spore) differed significantly (p<0.05) in their recovery rates from stainless steel surfaces, ranging from 2.9%{+/-}3.0% recovery to 94.9%{+/-}3.0% recovery. Modification of the DNA extraction protocol by extending the bead-beating step by 10 min generally improved DNA yields, though the impact varied by organism. For example, DNA yields of E. coli increased from 70 to 84 ng/mL while that of L. monocytogenes increased only from 23.2 to 29.2 ng/mL. Amplicon sequencing results indicated that the differences in cell recovery and DNA extraction among microbial species skewed the relative abundance estimates from inoculated surfaces. For example, the estimated relative abundance of L. monocytogenes was 9-17%, which was lower than its actual relative abundance (25%). These results underscore the limitations of surface microbiota characterization in food facilities and highlighted the need to improve current recovery and DNA extraction methods.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 05 Nov 2025.
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