ArticleBMC genomics2021
Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 2 of them syntheses that pooled it.
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Who cites it
70 citing papers in PubMed, 2 syntheses or guidelines pooled it, 116 citations in OpenAlex.
- Changes in the gut microbiota of patients with sarcopenia based on 16S rRNA gene sequencing: a systematic review and meta-analysis.Frontiers in nutrition · 2024Pooled it
- Meta-analysis revealsGut microbesPooled it
- Trial
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- Antibiotic course frequency and recovery strategies alter gut microbial composition and metabolism.ISME communications · 2026Article
- Association of oral frailty and gut microbiota with hypertension: cross-sectional results in the Shika study.Frontiers of medicine · 2025Article
- Changes in the Anopheles arabiensis transcriptome and gut microbiota profiles associated with the endosymbiotic Microsporidia MB.BMC genomics · 2025Article
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- Distribution and antibiotic resistance patterns of airborne staphylococci in urban environments of Delhi, India.Scientific reports · 2025Article
- Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.Scientific reports · 2025Article
- Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.Microorganisms · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- The Skin Microbiome Profile of Contact Sports Athletes-Focus on Sexual Dimorphism and Athlete-Non-Athlete Differences.Sports (Basel, Switzerland) · 2025Article
- Harnessing dual-channel probiotics to synergistically correct intestinal and vaginal dysbiosis after antibiotic disruption.NPJ biofilms and microbiomes · 2025Article
- Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.BMC microbiology · 2025Article
- Transmission of maternal oral pathobionts to the infant gut predisposes offspring to exacerbated enteritis.Cell reports · 2025Article
- Bacteroides- and Prevotella-enriched gut microbial clusters associate with metabolic risks.Gut pathogens · 2025Article
- The Role of Microbiota in the Pathogenesis of Bullous Pemphigoid and Pemphigus Vulgaris: Evidence, Controversies, and Perspectives.International journal of molecular sciences · 2025Review
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
background16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol.
resultsQIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data.
conclusionsThese results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.
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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 Socratic graph.