The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Bacterial phylogeny structures soil resistomes across habitats
Open accessAbstract
Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.
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Cites
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
Self-citationPredictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
Self-citationAntibiotic resistance is ancient
D’Costa, V. M., King, C. E., Kalan, L., Morar, M., Sung, W. W. L., Schwarz, C., Froese, D., Zazula, G., Calmels, F., Debruyne, R., et al. (2011) · Nature · doi:10.1038/nature10388 · Cited by 2,720
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988
Self-citationThe shared antibiotic resistome of soil bacteria and human pathogens
Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O. A., & Dantas, G. (2012) · Science · doi:10.1126/science.1220761 · Cited by 1,650
Self-citationAntibiotic resistance in the environment: a link to the clinic?
Wright, G. D. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.08.005 · Cited by 831
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Self-citationMetagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota
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Metadata
- Authors
- Forsberg, K. J., Patel, S., Gibson, M. K., Lauber, C. L., Knight, R., Fierer, N., & Dantas, G.
- Venue
- Nature
- Published
- 2014-05-21
- Volume
- 509
- Issue
- 7502
- Pages
- 612-616
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2012365024
- Cited by
- 1,287
- References
- 6
- FWCI
- 40.47
- Type
- journal article
- Language
- en
- Open access
- green
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- Forsberg, K. J., Patel, S., Gibson, M. K., Lauber, C. L., Knight, R., Fierer, N., & Dantas, G. (2014). Bacterial phylogeny structures soil resistomes across habitats. Nature. https://doi.org/10.1038/nature13377
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