The DOI matches its Crossref record; 68 of the 68 references it cites were found in a registry or an index.
Design of synthetic bacterial communities for predictable plant phenotypes
Open accessAbstract
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Solymos, P., Stevens, M. H. H., Szoecs, E., et al. (2001) · CRAN: Contributed Packages · doi:10.32614/cran.package.vegan · Cited by 22,615
Multilayer feedforward networks are universal approximators
Hornik, K., Stinchcombe, M., & White, H. (1989) · Neural Networks · doi:10.1016/0893-6080(89)90020-8 · Cited by 21,728
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Regularization and Variable Selection Via the Elastic Net
Zou, H., & Hastie, T. (2005) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.1467-9868.2005.00503.x · Cited by 20,957
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
Visualizing and understanding convolutional networks
Zeiler, M. D., & Fergus, R. (2014) · Lecture Notes in Computer Science · doi:10.1007/978-3-319-10590-1_53 · Cited by 15,839
Cited by
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application
Compant, S., Samad, A., Faist, H., & Sessitsch, A. (2019) · Journal of Advanced Research · doi:10.1016/j.jare.2019.03.004 · Cited by 1,643
Harnessing the plant microbiome for sustainable crop production
Compant, S., Cassan, F., Kostić, T., Johnson, L., Brader, G., Trognitz, F., & Sessitsch, A. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-024-01079-1 · Cited by 365
Data-driven prediction of colonization outcomes for complex microbial communities
Wu, L., Wang, X.-W., Tao, Z., Wang, T., Zuo, W., Zeng, Y., Liu, Y.-Y., & Dai, L. (2024) · Nature Communications · doi:10.1038/s41467-024-46766-y · Cited by 44
Metadata
- Authors
- Herrera Paredes, S., Gao, T., Law, T. F., Finkel, O. M., Mucyn, T., Teixeira, P. J. P. L., Salas González, I., Feltcher, M. E., Powers, M. J., Shank, E. A., Jones, C. D., Jojic, V., Dangl, J. L., & Castrillo, G.
- Venue
- PLOS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-02-20
- Volume
- 16
- Issue
- 2
- Pages
- e2003962
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2788354600
- Cited by
- 267
- References
- 68
- FWCI
- 21.24
- Type
- journal article
- Language
- en
- Open access
- gold
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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Design of synthetic bacterial communities for predictable plant phenotypes. https://app.cochat.ai/papers/10.1371/journal.pbio.2003962
- The paper
- Herrera Paredes, S., Gao, T., Law, T. F., Finkel, O. M., Mucyn, T., Teixeira, P. J. P. L., Salas González, I., Feltcher, M. E., Powers, M. J., Shank, E. A., Jones, C. D., Jojic, V., Dangl, J. L., & Castrillo, G. (2018). Design of synthetic bacterial communities for predictable plant phenotypes. PLOS Biology. https://doi.org/10.1371/journal.pbio.2003962
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.