To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period

• Published in: BMC microbiology Vol. 22; no. 1; p. 34
• Main Authors: Duthoo, E, De Reu, K, Leroy, F, Weckx, S, Heyndrickx, M, Rasschaert, G
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 25-01-2022; BioMed Central; BMC
• Subjects: Atmosphere; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - growth & development; Bacteria - isolation & purification; Colony Count, Microbial; Contamination; Control; Deoxyribonucleic acid; Depletion; DNA; DNA barcoding; DNA Barcoding, Taxonomic - methods; DNA Barcoding, Taxonomic - standards; DNA Barcoding, Taxonomic - statistics & numerical data; Food; Food Microbiology - methods; Food Microbiology - standards; Food packaging; Food Packaging - methods; Food Packaging - standards; Food safety; Food spoilage; Food Storage - methods; Food Storage - standards; Food Storage - statistics & numerical data; Identification and classification; Lactic acid; Lactic acid bacteria; Meat; Meat Products - classification; Meat Products - microbiology; Meat substitutes; Methods; Microbial ecology; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Packaging; Refrigeration; RNA, Ribosomal, 16S - genetics; Safety and security measures; Shelf life; Spoilage; Vegetarian charcuterie; Vegetarianism; Vegetarians; Xanthan; Xanthan gum; United Kingdom; United Kingdom > UK; Belgium; Microbial ecology; Spoilage; Vegetarian charcuterie
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/s12866-022-02446-9

As the increased consumption of ready-to-eat meat alternatives is a fairly recent trend, little is known about the composition and dynamics of the microbiota present on such products. Such information is nonetheless valuable in view of spoilage and food safety prevention. Even though refrigeration and modified-atmosphere-packaging (MAP) can extend the shelf-life period, microbial spoilage can still occur in these products. In the present study, the microbiota of a vegetarian alternative to poultry-based charcuterie was investigated during storage, contrasting the use of a culture-dependent method to a culture-independent metagenetic method.
The former revealed that lactic acid bacteria (LAB) were the most abundant microbial group, specifically at the end of the shelf-life period, whereby Latilactobacillus sakei was the most abundant species. Metabarcoding analysis, in contrast, revealed that DNA of Xanthomonas was most prominently present, which likely was an artifact due to the presence of xanthan gum as an ingredient, followed by Streptococcus and Weissella.
Taken together, these results indicated that Lb. sakei was likely the most prominent specific spoilage organisms (SSO) and, additionally, that the use of metagenetic analysis needs to be interpreted with care in this specific type of product. In order to improve the performance of metagenetics in food samples with a high DNA matrix but a low bacterial DNA load, selective depletion techniques for matrix DNA could be explored.