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.
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http://dx.doi.org/10.1016/j.fochms.2021.100023 | DOI Listing |
Environ Microbiol Rep
December 2024
Facultad de Ciencias de la Salud, Universidad Alfonso X el Sabio, Madrid, Spain.
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 PDFTrop 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 PDFArch Microbiol
December 2024
Global Leadership School, Handong Global University, Pohang, 37554, South Korea.
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 PDFmSystems
December 2024
Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA.
, 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 PDFAppl 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 .
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