ArticleFrontiers in microbiomes2025
Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit's gut microbiota.
Article in Frontiers in microbiomes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Microbiome Dynamics of Camel Meat During Cold Storage Revealed by 16S rRNA Gene Sequencing.Biology · 2026Article
- eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.Journal of insect science (Online) · 2026Article
- Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.Microorganisms · 2026Review
- Omics Technologies in Molecular Biology.International journal of molecular sciences · 2026Article
- Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.Cancer reports (Hoboken, N.J.) · 2026Article
- Effects of combined Mediterranean diet and physical activity intervention on the gut microbiome and disease progression in individuals with Parkinson's disease: study protocol for a multicenter, randomized controlled pilot study (PRIME study).Frontiers in aging neuroscience · 2026Article
- Decoding the reproductive microbiome: enabling clinical and biological insights through machine and deep learning.Frontiers in endocrinology · 2026Review
- Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.Cancers · 2025Review
- Comparative evaluation of sequencing platforms: Pacific Biosciences, Oxford Nanopore Technologies, and Illumina for 16S rRNA-based soil microbiome profiling.Frontiers in microbiology · 2025Article
- Application and Limitations of 16S rRNA Gene Sequencing for Identifying WHO Priority Pathogenic Gram-Negative Bacilli.Infection and drug resistance · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial communities detected across the three platforms. The study employed DNA from four rabbit does' soft feces, sequenced using Illumina MiSeq for specific 16S rRNA gene regions V3-V4, and for the complete gene sequencing using PacBio HiFi and ONT MinION. Results highlight different levels of taxonomic resolution. At the species level, PacBio and ONT exhibited the better resolutions with 63% and 76% respectively, while 48% for Illumina. However, across all three platforms, the classification output at species level was mainly labeled as "
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Registered trials
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