ArticleNature protocols2024
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.
Article in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows.Animal microbiome · 2026Article
- Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.Microbiome · 2026Article
- Food characterization in the omics era: current advances, analytical approaches, and future perspectives.Frontiers in nutrition · 2026Review
- Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems.Environmental microbiome · 2025Article
- Reshaped local microbiology metabolism by raw tea according to pile fermentation in the dark tea.Journal of advanced research · 2025Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- The food-associated resistome is shaped by processing and production environments.Nature microbiology · 2025Article
- Article
- Microbial dynamics in the ripening process of Vorarlberger Alpkäse: farm-specific variations at two Austrian alpine farms.Frontiers in microbiology · 2025Article
- Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges.Microbiome · 2024Article
- Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.MicrobiologyOpen · 2024Article
- In-depth characterization of food and environmental microbiomes across different meat processing plants.Microbiome · 2024Article
- Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.NPJ biofilms and microbiomes · 2024Article
- Article
- Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review.Foods (Basel, Switzerland) · 2024Review
- Persistence of microbiological hazards in food and feed production and processing environments.EFSA journal. European Food Safety Authority · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
29 authors.
Funding
Abstract
Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.
Indexed as
Identifiers
38267717What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.