The presence of a genetically modified microorganism (GMM) or its DNA, often harboring antimicrobial resistance (AMR) genes, in microbial fermentation products on the market is prohibited by European regulations. GMMs are currently screened for through qPCR assays targeting AMR genes and vectors, and then confirmed by targeting known specific GM constructs/events. However, when the GMM was not previously characterized and an isolate cannot be obtained, its presence cannot be proven. We present a metagenomics approach capable of delivering the proof of presence of a GMM in a microbial fermentation product, with characterization based on the detection of AMR genes and vectors, species and unnatural associations in the GMM genome. In our proof-of-concept study, this approach was performed on a case with a previously isolated and sequenced GMM, an unresolved case for which no isolate was obtained, and a non-GMM-contaminated sample, all representative for the possible scenarios to occur in routine setting. Both short and long read sequencing were used. This workflow paves the way for a strategy to detect and characterize unknown GMMs by enforcement laboratories.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8991599PMC
http://dx.doi.org/10.1016/j.fochms.2021.100023DOI Listing

Publication Analysis

Top Keywords

microbial fermentation
12
amr genes
12
metagenomics approach
8
detect characterize
8
genetically modified
8
fermentation products
8
genes vectors
8
gmm
5
shotgun metagenomics
4
approach detect
4

Similar Publications

Managing infections caused by multidrug-resistant Gram-negative bacilli is a major public health concern, particularly in hospitals where surfaces can act as reservoirs for resistant microorganisms. Identifying these bacteria in hospital environments is crucial for improving healthcare safety. This study aimed to analyse environmental samples from a veterinary hospital to identify prevalent microorganisms and detect antimicrobial resistance patterns.

View Article and Find Full Text PDF

In vitro and in vivo analysis of rumen fermentation after supplementary niacin in high concentrated fed cattle.

Trop Anim Health Prod

December 2024

Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, 330045, China.

Rumen acidosis is a common nutritional metabolic disease in ruminants, and the developing of feed additives to prevent this disorder has great application prospect. This study was conducted to investigate the effects of dietary niacin supplementation with different concentrate to roughage ratio on rumen fermentation evaluated by simulated rumen fermentation in vitro and in vivo. The cattle fed with basal feed (dietary concentrate-to-forage ratio was 5: 5) and high concentrate feed (dietary concentrate-to-forage ratio was 8: 2) were defined as Control stage and HC stage, respectively.

View Article and Find Full Text PDF

Microcystin-LRs (MC-LR) produced by harmful cyanobacterial blooms (HCBs) pose significant hepatotoxic risks to both the environment and public health. Despite the identification and characterization of a limited number of MC-LR degrading bacteria, the challenge of safely removing MC-LRs from freshwater systems without disrupting aquatic ecosystems remains substantial. This study focused on the isolation of lactic acid bacteria from Bapshikhe, a traditional Korean fermented food, and investigated the mechanisms underlying the degradation of MC-LRs by these bacteria.

View Article and Find Full Text PDF

, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing , , JAAYZQ01, B4-G1, JAFGEY01, UCB3, and orders.

View Article and Find Full Text PDF

Positive regulation of a LuxR family protein, MilO, in mildiomycin biosynthesis.

Appl Environ Microbiol

December 2024

State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.

Mildiomycin is a representative peptidyl nucleoside antibiotic and was first isolated from , which has been used as an important biological agent to control powdery mildew in plants. Despite its importance, the biosynthetic pathways and regulatory mechanisms remain to be fully elucidated. In this study, we identified MilO as a positive pathway-specific regulator of mildiomycin biosynthesis in the heterologous host .

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!