Balance Trees Reveal Microbial Niche Differentiation
Open accessAbstract
By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss.
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Several developed methods exist to find changes in compositional data between cases and controls that avoid biases caused by the compositional nature of metagenomic sequencing data (e.g., ALDEx2, ANCOM, Gneiss).
“There already exist several developed methods to find changes in compositional data between cases and controls that avoid the biases caused by the compositional nature of metagenomic sequencing data (for example, ALDEx263, ANCOM64 and Gneiss65).”
From Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma (2024) · cites this paper as [65]
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References 28 · Cited by 254
- Authors
- Morton, J. T., Sanders, J., Quinn, R. A., McDonald, D., Gonzalez, A., Vázquez-Baeza, Y., Navas-Molina, J. A., Song, S. J., Metcalf, J. L., Hyde, E. R., Lladser, M., Dorrestein, P. C., & Knight, R.
- Affiliations
- University of California San Diego (US)
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- University of Colorado Boulder (US)
- Corresponding author
- Knight, Rob
- ORCID
- Venue
- mSystems
- Publisher
- American Society for Microbiology
- Published
- 2017-02-28
- Volume
- 2
- Issue
- 1
- ISSN
- 2379-5077 (ISSN-L)
- PMC
- PMC5264246
- OpenAlex
- W2573450200
- Cited by
- 254
- References
- 28
- Citations by year
- 2026: 6 · 2025: 9 · 2024: 15 · 2023: 14 · 2022: 25 · 2021: 40 · 2020: 72 · 2019: 37 · 2018: 24 · 2017: 12
- FWCI
- 29.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mSystems (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Science Foundation (DGE-1144086, 1144807)
- HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669)
- Alfred P. Sloan Foundation (G-2015-13933, G-2015-13979)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- compositional data, microbial community composition, microbial ecology
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