ArticleMicroorganisms2019
The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical "Microscope" Affect the Biological Interpretation?
Article in Microorganisms, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.Nutrients · 2025Article
- Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition.mSystems · 2025Article
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
- Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies FecalInternational journal of molecular sciences · 2024Article
- A next-generation sequencing approach for the detection of mixed species in canned tuna.Food chemistry: X · 2023Article
- Alterations in gut microbiota caused by major depressive disorder or a low FODMAP diet and where they overlap.Frontiers in nutrition · 2023Review
- Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.Toxicological sciences : an official journal of the Society of Toxicology · 2022Review
- Article
- BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.BMC bioinformatics · 2020Article
- Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota.BMC microbiology · 2020Article
- Evolving Technologies in Gastrointestinal Microbiome Era and Their Potential Clinical Applications.Journal of clinical medicine · 2020Review
- Deep Insights into Gut Microbiota in Four Carnivorous Coral Reef Fishes from the South China Sea.Microorganisms · 2020Article
- Article
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Authors and funding
6 authors.
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Abstract
Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa
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