The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Species- and site-specific genome editing in complex bacterial communities
Open accessAbstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR–Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control. A suite of methods enables programmable species- and locus-specific editing of bacteria in 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
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
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
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,587
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 10,905
Cited by
Phage therapy: From biological mechanisms to future directions
Strathdee, S. A., Hatfull, G. F., Mutalik, V. K., & Schooley, R. T. (2023) · Cell · doi:10.1016/j.cell.2022.11.017 · Cited by 817
The CRISPR-Cas toolbox and gene editing technologies
Liu, G., Lin, Q., Jin, S., & Gao, C. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.002 · Cited by 404
Microbiota succession throughout life from the cradle to the grave
Martino, C., Dilmore, A. H., Burcham, Z. M., Metcalf, J. L., Jeste, D., & Knight, R. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00768-z · Cited by 275
Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes
Russell, B. J., Brown, S. D., Siguenza, N., Mai, I., Saran, A. R., Lingaraju, A., Maissy, E. S., Dantas Machado, A. C., Pinto, A. F. M., Sanchez, C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.050 · Cited by 151
Harnessing the potential: Advances in cyanobacterial natural product research and biotechnology
Baunach, M., Guljamow, A., Miguel-Gordo, M., & Dittmann, E. (2024) · Natural Product Reports · doi:10.1039/d3np00045a · Cited by 66
Metadata
- Authors
- Rubin, B. E., Diamond, S., Cress, B. F., Crits-Christoph, A., Lou, Y. C., Borges, A. L., Shivram, H., He, C., Xu, M., Zhou, Z., Smith, S. J., Rovinsky, R., Smock, D. C. J., Tang, K., Owens, T. K., Krishnappa, N., Sachdeva, R., Barrangou, R., Deutschbauer, A. M., Banfield, J. F., & Doudna, J. A.
- Venue
- Nature Microbiology
- Published
- 2021-12-06
- Volume
- 7
- Issue
- 1
- Pages
- 34-47
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W4200576031
- Cited by
- 322
- References
- 62
- FWCI
- 13.69
- Type
- journal article
- Language
- en
- Open access
- green
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: Species- and site-specific genome editing in complex bacterial communities. https://app.cochat.ai/papers/10.1038/s41564-021-01014-7
- The paper
- Rubin, B. E., Diamond, S., Cress, B. F., Crits-Christoph, A., Lou, Y. C., Borges, A. L., Shivram, H., He, C., Xu, M., Zhou, Z., Smith, S. J., Rovinsky, R., Smock, D. C. J., Tang, K., Owens, T. K., Krishnappa, N., Sachdeva, R., Barrangou, R., Deutschbauer, A. M., . . . Doudna, J. A. (2021). Species- and site-specific genome editing in complex bacterial communities. Nature Microbiology. https://doi.org/10.1038/s41564-021-01014-7
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.
