ArticlemSystems
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.The ISME journal · 2026Article
- Effect of perinatal ampicillin or amoxicillin/clavulanate exposure on maternal and infant gut microbiome, metabolome, and infant responses to the 20-valent pneumococcal conjugate vaccine.Gut microbes reports · 2026Article
- A comparison of microbial community composition in two alpine springs in southern Nevada.PloS one · 2026Article
- Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine.bioRxiv : the preprint server for biology · 2025Article
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.Microbiology spectrum · 2025Article
- Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.Microbiology (Reading, England) · 2025Article
- Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine.Scientific reports · 2025Article
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- ReBiA-Robotic Enabled Biological Automation: 3D Epithelial Tissue Production.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- Gut pathobiome mediates behavioral and developmental disorders in biotoxin-exposed amphibians.Environmental science and ecotechnology · 2024Article
- Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses.Microbiology spectrum · 2024Article
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- Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution.mSystems · 2023Article
- Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses.mSystems · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (
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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.