ArticleMicrobiologyOpen2016
Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions.
Article in MicrobiologyOpen, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 72 citations in OpenAlex.
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- Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water.Scientific reports · 2024Article
- Effect of dietary calcium source, exogenous phytase, and formic acid on inositol phosphate degradation, mineral and amino acid digestibility, and microbiota in growing pigs.Journal of animal science · 2024Article
- Assessment of DNA extraction methods for human gut mycobiome analysis.Royal Society open science · 2024Article
- Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river.Environmental microbiome · 2023Article
- Effect of dietary calcium concentration and exogenous phytase on inositol phosphate degradation, mineral digestibility, and gut microbiota in growing pigs.Journal of animal science · 2023Article
- "Get the best out of what comes in" - adaptation of the microbiota of chamois (Frontiers in microbiology · 2023Article
- Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice.Animal microbiome · 2022Article
- The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.Microorganisms · 2022Article
- Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples.MicrobiologyOpen · 2022Article
- Cow's microbiome from antepartum to postpartum: A long-term study covering two physiological challenges.Frontiers in microbiology · 2022Article
- Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis.Microbiology spectrum · 2021Article
- Microbiome Clusters Disclose Physiologic Variances in Dairy Cows Challenged by Calving and Lipopolysaccharides.mSystems · 2021Article
- Screening of Rhizosphere Bacteria and Nematode Populations Associated with Soybean Roots in the Mpumalanga Highveld of South Africa.Microorganisms · 2021Article
- Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning.Animal microbiome · 2021Article
- Evaluation of Established Methods for DNA Extraction and Primer Pairs Targeting 16S rRNA Gene for Bacterial Microbiota Profiling of Olive Xylem Sap.Frontiers in plant science · 2021Article
- Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies.Frontiers in microbiology · 2021Article
- Quality assessment of DNA and hemoglobin by Fourier transform infrared spectroscopy in occupational exposure to extremely low-frequency magnetic field.Environmental science and pollution research international · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A robust DNA extraction method is important to identify the majority of microorganisms present in environmental microbial communities and to enable a consistent comparison between different studies. Here, 15 manual and four automated commercial DNA extraction kits were evaluated for their efficiency to extract DNA from porcine feces and ileal digesta samples. DNA yield, integrity, and purity varied among the different methods. Terminal restriction fragment length polymorphism (T-RFLP) and Illumina amplicon sequencing were used to characterize the diversity and composition of the microbial communities. We also compared phylogenetic profiles of two regions of the 16S rRNA gene, one of the most used region (V1-2) and the V5-6 region. A high correlation between community structures obtained by analyzing both regions was observed at genus and family level for ileum digesta and feces. Based on our findings, we want to recommend the FastDNA(™) SPIN Kit for Soil (MP Biomedical) as a suitable kit for the analyses of porcine gastrointestinal tract samples.
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Registered trials
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