ArticlemSystems
Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Human gut microbiome as a composite health biomarker.Gut microbes · 2026Article
- Microbiome Dynamics in Early Life Stages of the Precious Mediterranean Red Coral Corallium rubrum.Environmental microbiology reports · 2025Article
- Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.Nature communications · 2024Article
- Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies.Frontiers in veterinary science · 2024Article
- Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2023Article
- Forensic DNA Analysis of Mixed Mosquito Blood Meals: STR Profiling for Human Identification.Insects · 2023Article
- A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis.mSystems · 2021Article
- Taxonomy, not locality, influences the cloacal microbiota of two nearctic colubrids: a preliminary analysis.Molecular biology reports · 2021Article
- Article
- Determination of human identity from Anopheles stephensi mosquito blood meals using direct amplification and massively parallel sequencing.Forensic science international. Genetics · 2020Article
- A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.mSystems · 2019Article
- Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer.FEBS open bio · 2019Article
- Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.Comparative medicine · 2018Article
- Root Microbiota in Primary and Secondary Apical Periodontitis.Frontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (
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