ArticleFrontiers in microbiology2021
An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
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- The Effects of Caloric Restriction and Clinical Psychological Intervention on the Interplay of Gut Microbial Composition and Stress in Women.Nutrients · 2024Trial
- Branched-chain amino acid assimilation enables mixotrophy of ammonia-oxidizing archaeal sponge symbionts.Science advances · 2026Article
- Crosstalk between CD8+ T cells and systemic bile acid metabolism shapes antiviral immunity and immunopathology.JCI insight · 2026Article
- Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults.Neurobiology of stress · 2026Article
- Seasonal differences and potential biological drivers of the methane paradox in two peri-Alpine lakes.Limnology and oceanography letters · 2026Article
- Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.Microbial ecology · 2026Article
- Vertically transmitted bacterivorous nematodes are consistent nest inhabitants in the Azteca-Cecropia ant-plant mutualism.Scientific reports · 2026Article
- Sulfoquinovose degradation by cow rumen microbiota.The ISME journal · 2026Article
- Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.The ISME journal · 2026Article
- Associations between gut microbiota and personality traits: insights from a captive common marmoset (Microbiology spectrum · 2026Article
- Longitudinal integration of microbiota and metabolomics reveals (poly)phenols-driven gut ecosystem dynamics.Frontiers in nutrition · 2026Article
- Shredder identity matters: taxon-specific gut microbiota in aquatic shredders drives bacterial diversity during leaf breakdown in streams.ISME communications · 2026Article
- Substrate complexity and species number jointly shift the balance between competition and facilitation in a chitin-degrading bacterial consortium.ISME communications · 2026Article
- Dynamic changes in protist community composition along a surface water-groundwater transect in the Danube wetland Lobau, Vienna, Austria.Frontiers in microbiology · 2026Article
- Model substrate particles uncover dynamics of microbial communities associated with particulate organic matter decomposition in soil.ISME communications · 2026Article
- Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments.ISME communications · 2026Article
- Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.ISME communications · 2026Article
- Lactulose selectively stimulates members of the gut microbiota, as determined by multi-modal activity-based sorting.Gut microbes · 2025Article
- Salinity Negatively Impacts Protistan and Fungal Community Stability and Shapes Assembly Processes in Freshwater Ecosystems.Environmental microbiology reports · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.
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