ArticleCurrent microbiology2021
Effect of Amplicon Sequencing Depth in Environmental Microbiome Research.
Article in Current microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut microbiota and type 2 diabetes associations: a meta-analysis of 16S studies and their methodological challenges.Frontiers in microbiomes · 2025Pooled it
- The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.Molecular ecology resources · 2025Article
- Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.Scientific reports · 2025Article
- Insights from a Long-Term Outdoor Mesocosm Study: eDNA Metabarcoding Reveals Exacerbated but Transient Impacts from a Nanoenabled Pesticide Formulation (Nano-TiOACS ES&T water · 2025Article
- Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments.Environmental microbiology · 2025Article
- More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.Microbial ecology · 2025Article
- Composite quantile regression approach to batch effect correction in microbiome data.Frontiers in microbiology · 2025Article
- Don't let valuable microbiome data go to waste: combined usage of merging and direct-joining of sequencing reads for low-quality paired-end amplicon data.Biotechnology letters · 2024Article
- Existence of rare actinobacterial forms in the Indian sector of Southern Ocean: 16 S rRNA based metabarcoding study.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Rodents consuming the same toxic diet harbor a unique functional core microbiome.Animal microbiome · 2024Article
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- Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples.PloS one · 2023Article
- Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research.Biotechnology letters · 2022Article
- Correlation Between Salivary Microbiome of Parotid Glands and Clinical Features in Primary Sjögren's Syndrome and Non-Sjögren's Sicca Subjects.Frontiers in immunology · 2022Article
- 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
- Defining and quantifying the core microbiome: Challenges and prospects.Proceedings of the National Academy of Sciences of the United States of America · 2021Review
- Article
- A comprehensive evaluation of single-end sequencing data analyses for environmental microbiome research.Archives of microbiology · 2021Article
- Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index-A Pilot Study.Microorganisms · 2021Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplicon sequencing approach is commonly employed in microbiome studies and sequencing depth is considered as a major factor influencing the outcome of data analyses. As of now, the effect of amplicon sequencing depth in environmental microbiome analyses is not explicitly illustrated. In this study, microbiome data of nine aquatic samples from Sundarbans mangrove region, obtained from SRA, were analyzed to explain the influence of sequencing depth variation in environmental microbiome data analyses. Briefly, four groups based on number of reads (NOR) were created comprising of, total NOR, 75 k, 50 k and 25 k, followed by data analyses. The results showed that the observed ASVs among four groups were significantly different (P value 1.094e-06). The Bray-Curtis dissimilarity analysis showed differences in microbiome composition and also, each group exhibited slightly different core-microbiome structure. Importantly, the variation in sequencing depth was found to affect the predictions of environmental drivers associated with microbiome composition. Thus, this study emphasizes that the microbiome data are compositional and the NOR in the data could affect the microbial composition. In summary, this study demonstrates the consequences of sequencing depth variation on microbiome data analyses and suggests the researchers to take proper cautions to avoid misleading results due to sequencing depth variation.
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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.