Microbiomes in light of traits: a phylogenetic perspective
Abstract
A focus on the phenotypic characteristics of microorganisms-their traits-offers a path for interpreting the growing amount of microbiome data. We review key aspects of microbial traits, as well as approaches used to assay their phylogenetic distribution. Recent studies reveal that microbial traits are differentially conserved across the tree of life and appear to be conserved in a hierarchical fashion, possibly linked to their biochemical complexity. These results suggest a predictive framework whereby the genetic (or taxonomic) resolution of microbiome variation among samples provides information about the traits under selection. The organizational parallels seen among human and free-living microbiomes seem to support this idea. Developments in this framework may offer predictions not only for how microbial composition responds to changing environmental conditions, but also for how these changes may alter the health or functioning in human, engineered, and environmental systems.
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Network-based approaches are likely to provide the best hope of integrating all this information by allowing a complete overview of the rumen microbiome because they can capture fundamental properties including taxonomy, functional similarity, metabolic processes, co-expression, and gene-sharing.
“Network-based approaches are likely to provide the best hope of integrating all this information by allowing a complete overview of the rumen microbiome as they are capable of capturing the fundamental properties of the microbial ecosystem including taxonomy (Barberan et al., 2012), functional similarity (Martiny et al., 2015), metabolic processes (Shlomi et al., 2008), co-expression (Zhang and”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Martiny et al., 2015
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Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891 · see citing works
The ecology and biogeochemistry of stream biofilms
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The Syntrophy hypothesis for the origin of eukaryotes revisited
López-García, P., & Moreira, D. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0710-4 · Cited by 201 · see citing works
- Authors
- Martiny, J. B. H., Jones, S. E., Lennon, J. T., & Martiny, A. C.
- Affiliations
- University of California, Irvine (US)
- University of Notre Dame (US)
- Indiana University Bloomington (US)
- Corresponding author
- Martiny, Jennifer B. H.
- Venue
- Science
- Published
- 2015-11-06
- Volume
- 350
- Issue
- 6261
- Pages
- aac9323-aac9323
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2156546195
- Cited by
- 834
- References
- 120
- Citations by year
- 2026: 68 · 2025: 87 · 2024: 71 · 2023: 83 · 2022: 113 · 2021: 85 · 2020: 81 · 2019: 72 · 2018: 84 · 2017: 52 · 2016: 36 · 2015: 1
- FWCI
- 5.31
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Science Foundation (DEB-1442230, DEB-144246, OCE-1332740, OCE-1046297)
- U.S. Army Research Office (W911NF-14-1-0411)
- Office of Biological and Environmental Research (BER) (DE-PS02-09ER09-25)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- 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
- Keywords
- microbiological properties, trait selection, microbiome, microbial community composition, human microbiome
- MeSH terms
- Environment, Humans, Phylogeny, Genetic Variation, Gene Transfer, Horizontal, Prochlorococcus, Genetic Loci, Phylogeography, Gene-Environment Interaction, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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