Exploring the resistome of probiotics, starter cultures, and cheeses via metagenomic analysis

Rozman, Vita (author), Stopnišek, Nejc (author), Mohar Lorbeg, Petra (author), Obermajer, Tanja (author), Kušar, Darja (author), Bogovič Matijašić, Bojana (author)

The resistome of the food microbiota, which serves as a potential carrier for the transfer of antibiotic resistance genes (ARGs) to pathogenic bacteria, is a cause of concern for public health and food safety. From One Health’s perspective, the resistomes of humans, animals, and environment have been extensively studied, while the resistomes of different food systems remain largely unexplored. An important aspect of our study was to investigate the microbiomes of cheese (three groups), probiotic supplements and starter cultures (n = 75) using shotgun metagenome sequencing to gain new insights into their resistomes. In total, we identified 689 ARGs in 62 samples, mainly those conferring resistance to disinfectants, tetracyclines, aminoglycosides, and macrolides. Of these ARGs, 32.2 % (222) were carried on mobile genetic elements (MGEs). We observed significant differences in microbiome composition and resistome profiles among sample groups. In particular, raw milk cheeses without starter cultures were characterized by the highest abundance and diversity of ARGs and MGEs, while thermal treatment of milk and the addition of starter cultures led to a significant reduction in microbiome diversity as well as diversity and abundance of ARGs and MGEs in cheese. Significantly lower ARG loads were detected in starter cultures and probiotics than in raw milk cheeses. We also found that the bacterial composition correlated with the resistome. While the majority of ARG-carrying contigs originated from Bacillota, particularly from Enterococcus faecium and Lactococcus lactis, a considerable proportion of ARG hosts were also found within Pseudomonadota, including potentially pathogenic species found in raw milk cheeses. This study improves the understanding of resistomes in fermented dairy products, probiotics, and starter cultures, and sheds light on critical challenges related to antibiotic resistance in the food chain. Our data emphasize the role of raw milk cheese as a reservoir of antibiotic resistance and reveal that the production method is an important factor in shaping the microbiome and resistome of cheese. The low abundance of resistance genes and mobile genetic elements in commercial cultures supports the hypothesis that they contribute only marginally to resistomes within the food chain. We have also introduced new qPCR protocols for the rapid detection of high-risk ARGs in complex food samples.

• Language: English
• Keywords: food resistomes, antibiotic resistance, probiotics, starter cultures, cheeses, lactic acid bacteria, metagenomes
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty; VF - Veterinary Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 13 str.
• Numbering: Vol. 172, art. 111173
• PID: 20.500.12556/RUL-166864
• UDC: 637.3
• ISSN on article: 1873-7129
• DOI: 10.1016/j.foodcont.2025.111173
• COBISS.SI-ID: 223978755
• Publication date in RUL: 28.01.2025

Record is a part of a journal

• Title: Food control
• Publisher: Elsevier
• ISSN: 1873-7129
• COBISS.SI-ID: 23091461

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: mlečni izdelki, siri, probiotiki, starterske kulture, genetika, mikrobiomi, metagenomika, rezistomi, antibiotiki, rezistenca

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: J4-1769
• Name: Rezistomi probiotičnih in starterskih kultur kot potencialni dejavnik tveganja za širjenje odpornosti proti antibiotikom

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P4-0097
• Name: Prehrana in mikrobna ekologija prebavil