Microbiome depiction through user-adapted bioinformatic pipelines and parameters
Open accessAbstract
Graphical Abstract: Determining microbiome composition is a multi-step process. The 16S rRNA gene is amplified from the extracted DNA, sequenced, and then metagenomic data are input into a bioinformatic workflow. This paper describes how choices of bioinformatic pipelines, databases, and parameter values, such as maxEE and QTrim, can impact microbial compositional output.
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In practice, gut microbiota profiling through 16S rRNA sequencing has become the gold standard for assessing ecological nutritional status.
“In practice, gut microbiota profiling through 16S rRNA sequencing has become the gold standard for assessing ecological nutritional status [78].”
From The Seven Methods for the Evaluation of Nutritional Status—ABCDEFG: Narrative Review (2026) · cites this paper as [78]
The graphical abstract describes 16S rRNA sequencing as a way to determine microbiome composition. The Abstract does not identify it as a gold standard or discuss assessing ecological nutritional status; it instead cautions that 16S-based compositions depend on the bioinformatic pipeline and should be interpreted carefully. (LLM, conf=0.86)
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References 135 · Cited by 6
- Authors
- Nayman, E. I., Schwartz, B. A., Polanco, F. C., Firek, A. K., Gumabong, A. C., Hofstee, N. J., Narasimhan, G., Cickovski, T., & Mathee, K.
- Affiliations
- Florida International University (US)
- Venue
- Journal of Medical Microbiology
- Publisher
- Microbiology Society
- Published
- 2023-10-12
- Volume
- 72
- Issue
- 10
- ISSN
- 0022-2615 (ISSN-L)
- 1473-5644
- OpenAlex
- W4387564027
- Cited by
- 6
- References
- 135
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 2
- FWCI
- 0.53
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Medical Microbiology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Florida International University Digital Commons (Florida International University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- microbiome, 16S rRNA, microbial community analysis, bioinformatics pipeline, taxonomic interpretation
- MeSH terms
- RNA, Ribosomal, 16S, Reproducibility of Results, Sequence Analysis, DNA, Computational Biology, Genomics, High-Throughput Nucleotide Sequencing, Microbiota
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