ArticlemSphere2018
Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products.
Article in mSphere, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- Impact of Glucosamine Supplementation on Gut Health.Nutrients · 2021Trial
- Variations in cow milk and teat skin microbiota across the lactation cycle with intramammary cephalosporin use at dry-off.Applied and environmental microbiology · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Microbiota profiling in esophageal diseases: Novel insights into molecular staining and clinical outcomes.Computational and structural biotechnology journal · 2024Review
- The Investigation of Changes in Bacterial Community of Pasteurized Milk during Cold Storage.Foods (Basel, Switzerland) · 2024Article
- Analysis of the Nasal Microbiota in Healthy and Diseased Pigs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Variable Region Sequences Influence 16S rRNA Performance.Microbiology spectrum · 2023Article
- Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort.Microbiome · 2023Article
- The Contribution of the Human Oral Microbiome to Oral Disease: A Review.Microorganisms · 2023Review
- Article
- Cholesteatoma has an altered microbiota with a higher abundance ofLaryngoscope investigative otolaryngology · 2022Article
- Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates.Microorganisms · 2022Article
- High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.BMC microbiology · 2022Article
- Article
- Patterns of Relative Bacterial Richness and Community Composition in Seawater and Marine Sediment Are Robust for Both Operational Taxonomic Units and Amplicon Sequence Variants.Frontiers in microbiology · 2022Article
- Article
- Impact of Feeding Postbiotics and Paraprobiotics Produced FromFrontiers in veterinary science · 2022Article
- Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods.PloS one · 2022Article
- Characteristics of Vaginal Microbiome in Reproductive-Age Females with HPV Infection in Xinjiang, China.Evidence-based complementary and alternative medicine : eCAM · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA sequencing and analysis methods were compared for 16S rRNA V4 PCR amplicon and genomic DNA (gDNA) mock communities encompassing nine bacterial species commonly found in milk and dairy products. The two communities comprised strain-specific DNA that was pooled before (gDNA) or after (PCR amplicon) the PCR step. The communities were sequenced on the Illumina MiSeq and Ion Torrent PGM platforms and then analyzed using the QIIME 1 (UCLUST) and Divisive Amplicon Denoising Algorithm 2 (DADA2) analysis pipelines with taxonomic comparisons to the Greengenes and Ribosomal Database Project (RDP) databases. Examination of the PCR amplicon mock community with these methods resulted in operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) that ranged from 13 to 118 and were dependent on the DNA sequencing method and read assembly steps. The additional 4 to 109 OTUs/ASVs (from 9 OTUs/ASVs) included assignments to spurious taxa and sequence variants of the 9 species included in the mock community. Comparisons between the gDNA and PCR amplicon mock communities showed that combining gDNAs from the different strains prior to PCR resulted in up to 8.9-fold greater numbers of spurious OTUs/ASVs. However, the DNA sequencing method and paired-end read assembly steps conferred the largest effects on predictions of bacterial diversity, with effect sizes of 0.88 (Bray-Curtis) and 0.32 (weighted Unifrac), independent of the mock community type. Overall, DNA sequencing performed with the Ion Torrent PGM and analyzed with DADA2 and the Greengenes database resulted in the most accurate predictions of the mock community phylogeny, taxonomy, and diversity.
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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.