ArticleScientific reports2021
Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Secondary analysis of the intestinal microbiota of healthy chickens.Poultry science · 2026Article
- Gut check: Exploring tools, techniques, and future directions in microbiome research.Poultry science · 2026Article
- The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.Animal microbiome · 2026Article
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Core-Periphery Microbiota Organization Is Associated with Functional Resilience in High Arctic Svalbard Soils.Computational and structural biotechnology journal · 2026Article
- Differentiated short- and long-term impacts of a starter stimbiotic supplementation on gut health in broilers fed wheat and rye-based diets at homeostasis and underAnimal nutrition (Zhongguo xu mu shou yi xue hui) · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Animals : an open access journal from MDPI · 2024Article
- Modulation of chicken gut microbiota for enhanced productivity and health: A review.Veterinary world · 2024Review
- Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs.Journal of animal science and technology · 2024Article
- Article
- Prophylactic influences of prebiotics on gut microbiome and immune response of heat-stressed broiler chickens.Scientific reports · 2023Article
- Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project.Phenomics (Cham, Switzerland) · 2023Article
- Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources.Applied and environmental microbiology · 2023Article
- Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the JellyfishMicroorganisms · 2023Article
- An Environmental DNA Primer for Microbial and Restoration Ecology.Microbial ecology · 2023Review
- Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems.Environmental microbiome · 2023Article
- Microbiome-Based Stain Analyses in Crime Scenes.Applied and environmental microbiology · 2023Review
- RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4-V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1-V3(1) and (2), and V3-V4 and V3-V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.
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