ArticleBMC genomic data2024
An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.
Article in BMC genomic data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.BMC microbiology · 2026Article
- Biofilm formation on venovenous ECMO cannulas can lead to re-introduction of pathogens during the decannulation process - a small-scale study reveals new insights when combining cultures and molecular results.BMC infectious diseases · 2026Observational
- Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.International journal of genomics · 2026Review
- Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents.One health (Amsterdam, Netherlands) · 2025Article
- Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.Frontiers in microbiomes · 2025Article
- Comparative evaluation of sequencing platforms: Pacific Biosciences, Oxford Nanopore Technologies, and Illumina for 16S rRNA-based soil microbiome profiling.Frontiers in microbiology · 2025Article
- Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.Frontiers in microbiology · 2025Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Barley farmland harbors a highly homogeneous soil bacterial community compared to wild ecosystems in the Qinghai-Xizang Plateau.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
backgroundRecent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms.
resultsWe have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run.
conclusionsThe unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.
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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.