ArticleFrontiers in cellular and infection microbiology2021
Impact of Bead-Beating Intensity on the Genus- and Species-Level Characterization of the Gut Microbiome Using Amplicon and Complete 16S rRNA Gene Sequencing.
Article in Frontiers in cellular and infection microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Separating extracellular from intracellular fecal metabolites exposes cross-feeding architecture in the gut: exploring metabolite partitioning and ecological associations.Gut microbes · 2026Article
- Impact of the anti-inflammatory macrolide glasmacinal on the gut microbiota of healthy adults: an open-label trial.Nature communications · 2026Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Ig-microbiota binding patterns in mothers and infants: a scoping review.Gut microbiome (Cambridge, England) · 2026Review
- Development and optimization of host DNA depletion in blood cultures using a saponin and salt-activated nuclease-based method.Frontiers in microbiology · 2026Article
- Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.Nature communications · 2025Article
- Tunable lysis of functionalized nanocultures for efficient microbial and nucleic acid recovery.Chemical engineering journal (Lausanne, Switzerland : 1996) · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Impact of Pre-Extraction Methods on Apple Blossom Microbiome Analysis.Microorganisms · 2025Article
- De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.Microbiome · 2025Article
- Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.Phenomics (Cham, Switzerland) · 2025Article
- Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis.Pediatric rheumatology online journal · 2025Article
- Microbiome differences between trauma- and caries-derived periapical lesions using next-generation sequencing.Journal of oral microbiology · 2025Article
- Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections.Frontiers in cellular and infection microbiology · 2025Article
- Article
- Comparing Gene Expression Between Planktonic and Biofilm Cells of Foodborne Bacterial Pathogens Through RT-qPCR.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings.Frontiers in microbiology · 2025Article
- Optimizing Production Conditions of a Caspian SeaInternational journal of molecular and cellular medicine · 2025Article
- A Comparison of Three Automated Nucleic Acid Extraction Systems for Human Stool Samples.Microorganisms · 2024Article
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Authors and funding
7 authors.
Funding
Abstract
Bead-beating within a DNA extraction protocol is critical for complete microbial cell lysis and accurate assessment of the abundance and composition of the microbiome. While the impact of bead-beating on the recovery of OTUs at the phylum and class level have been studied, its influence on species-level microbiome recovery is not clear. Recent advances in sequencing technology has allowed species-level resolution of the microbiome using full length 16S rRNA gene sequencing instead of smaller amplicons that only capture a few hypervariable regions of the gene. We sequenced the v3-v4 hypervariable region as well as the full length 16S rRNA gene in mouse and human stool samples and discovered major clusters of gut bacteria that exhibit different levels of sensitivity to bead-beating treatment. Full length 16S rRNA gene sequencing unraveled vast species diversity in the mouse and human gut microbiome and enabled characterization of several unclassified OTUs in amplicon data. Many species of major gut commensals such as
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