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Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
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Cites
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Self-citationA metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Self-citationHost-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis
Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251
SOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,760
Self-citationMeyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Outpatient antibiotic use in Europe and association with resistance: a cross-national database study
Goossens, H., Ferech, M., Vander Stichele, R., & Elseviers, M. (2005) · The Lancet · doi:10.1016/s0140-6736(05)17907-0 · Cited by 3,359
MEGAN analysis of metagenomic data
Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007) · Genome Research · doi:10.1101/gr.5969107 · Cited by 3,312
DNA recovery from soils of diverse composition
Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.2.316-322.1996 · Cited by 2,880
Tackling the widespread and critical impact of batch effects in high-throughput data
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2825 · Cited by 2,196
Cited by
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315
Self-citationAn integrated catalog of reference genes in the human gut microbiome
MetaHIT Consortium, Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2942 · Cited by 2,164
Self-citationLloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016) · Genome Medicine · doi:10.1186/s13073-016-0307-y · Cited by 1,891
Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J. M., & Zhang, T. (2015) · The ISME Journal · doi:10.1038/ismej.2015.59 · Cited by 1,238
Antibiotic-Resistance Genes in Waste Water
Karkman, A., Do, T. T., Walsh, F., & Virta, M. P. J. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2017.09.005 · Cited by 955
An omics-based framework for assessing the health risk of antimicrobial resistance genes
Zhang, A.-N., Gaston, J. M., Dai, C. L., Zhao, S., Poyet, M., Groussin, M., Yin, X., Li, L.-G., van Loosdrecht, M. C. M., Topp, E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25096-3 · Cited by 939
Self-citationPärnänen, K., Karkman, A., Hultman, J., Lyra, C., Bengtsson-Palme, J., Larsson, D. G. J., Rautava, S., Isolauri, E., Salminen, S., Kumar, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06393-w · Cited by 678
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
Pasolli, E., Truong, D. T., Malik, F., Waldron, L., & Segata, N. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004977 · Cited by 659
Karkman, A., Pärnänen, K., & Larsson, D. G. J. (2019) · Nature Communications · doi:10.1038/s41467-018-07992-3 · Cited by 628
Interconnected microbiomes and resistomes in low-income human habitats
Pehrsson, E. C., Tsukayama, P., Patel, S., Mejía-Bautista, M., Sosa-Soto, G., Navarrete, K. M., Calderon, M., Cabrera, L., Hoyos-Arango, W., Bertoli, M. T., et al. (2016) · Nature · doi:10.1038/nature17672 · Cited by 607
How to select a probiotic? A review and update of methods and criteria
de Melo Pereira, G. V., de Oliveira Coelho, B., Magalhães Júnior, A. I., Thomaz-Soccol, V., & Soccol, C. R. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2018.09.003 · Cited by 523
Huddleston, J. R. (2014) · Infection and Drug Resistance · doi:10.2147/idr.s48820 · Cited by 522
Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach
Yang, Y., Li, B., Zou, S., Fang, H. H. P., & Zhang, T. (2014) · Water Research · doi:10.1016/j.watres.2014.05.019 · Cited by 512
Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., & Alvarez-Cohen, L. (2015) · mBio · doi:10.1128/mbio.02288-14 · Cited by 474
Probiotic supplements might not be universally-effective and safe: A review
Kothari, D., Patel, S., & Kim, S.-K. (2019) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.12.104 · Cited by 445
Metagenome-wide association studies: fine-mining the microbiome
Wang, J., & Jia, H. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.83 · Cited by 429
Self-citationMa, L., Xia, Y., Li, B., Yang, Y., Li, L.-G., Tiedje, J. M., & Zhang, T. (2016) · Environmental Science & Technology · doi:10.1021/acs.est.5b03522 · Cited by 423
Self-citationHorizontal transfer of antibiotic resistance genes in the human gut microbiome
McInnes, R. S., McCallum, G. E., Lamberte, L. E., & van Schaik, W. (2020) · Current Opinion in Microbiology · doi:10.1016/j.mib.2020.02.002 · Cited by 401
Application of metagenomics in the human gut microbiome
Wang, W.-L., Xu, S.-Y., Ren, Z.-G., Tao, L., Jiang, J.-W., & Zheng, S.-S. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i3.803 · Cited by 397
Caselli, E., Fabbri, C., D’Accolti, M., Soffritti, I., Bassi, C., Mazzacane, S., & Franchi, M. (2020) · BMC Microbiology · doi:10.1186/s12866-020-01801-y · Cited by 391
Zhao, R., Feng, J., Liu, J., Fu, W., Li, X., & Li, B. (2019) · Water Research · doi:10.1016/j.watres.2018.12.034 · Cited by 383
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes
Hu, Y., Yang, X., Li, J., Lv, N., Liu, F., Wu, J., Lin, I. Y. C., Wu, N., Weimer, B. C., Gao, G. F., et al. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.01802-16 · Cited by 371
Self-citationvan Schaik, W. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0087 · Cited by 364
Kim, D.-W., & Cha, C.-J. (2021) · Experimental & Molecular Medicine · doi:10.1038/s12276-021-00569-z · Cited by 355
Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341
Self-citationSpecies- and site-specific genome editing in complex bacterial communities
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., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01014-7 · Cited by 322
Tan, B., Ng, C., Nshimyimana, J. P., Loh, L. L., Gin, K. Y.-H., & Thompson, J. R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01027 · Cited by 297
Li, S., Zhang, C., Li, F., Hua, T., Zhou, Q., & Ho, S.-H. (2021) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2021.125148 · Cited by 267
Dissemination of the mcr-1 colistin resistance gene
Zhi, C., Lv, L., Yu, L.-F., Doi, Y., & Liu, J.-H. (2016) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(16)00063-3 · Cited by 258
Phylogeny, culturing, and metagenomics of the human gut microbiota
Walker, A. W., Duncan, S. H., Louis, P., & Flint, H. J. (2014) · Trends in Microbiology · doi:10.1016/j.tim.2014.03.001 · Cited by 239
Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome
Crits-Christoph, A., Hallowell, H. A., Koutouvalis, K., & Suez, J. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2055944 · Cited by 156
Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria
Casaburi, G., Duar, R. M., Vance, D. P., Mitchell, R., Contreras, L., Frese, S. A., Smilowitz, J. T., & Underwood, M. A. (2019) · Antimicrobial Resistance & Infection Control · doi:10.1186/s13756-019-0583-6 · Cited by 101
Lu, N., Hu, Y., Zhu, L., Yang, X., Yin, Y., Lei, F., Zhu, Y., Du, Q., Wang, X., Meng, Z., et al. (2014) · Scientific Reports · doi:10.1038/srep04302 · Cited by 84
Antibiotic resistance propagation through probiotics
Daniali, M., Nikfar, S., & Abdollahi, M. (2020) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1080/17425255.2020.1825682 · Cited by 90
Probiotics, mechanisms of action, and clinical perspectives for diarrhea management in children
do Carmo, M. S., Santos, C. I. D., Araújo, M. C., Girón, J. A., Fernandes, E. S., & Monteiro-Neto, V. (2018) · Food & Function · doi:10.1039/c8fo00376a · Cited by 75
Hu, Y., Yang, X., Lu, N., & Zhu, B. (2014) · Gut Microbes · doi:10.4161/gmic.27916 · Cited by 70
Targeting the Microbiota in Pharmacology of Psychiatric Disorders
Pascale, A., Marchesi, N., Govoni, S., & Barbieri, A. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104856 · Cited by 67
Fu, Y., Dou, Q., Smalla, K., Wang, Y., Johnson, T. A., Brandt, K. K., Mei, Z., Liao, M., Hashsham, S. A., Schäffer, A., et al. (2023) · mLife · doi:10.1002/mlf2.12101 · Cited by 65
Klopper, K. B., Deane, S. M., & Dicks, L. M. T. (2018) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-017-9307-5 · Cited by 53
Accounting for the health risk of probiotics
Liu, X., Zhao, H., & Wong, A. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e27908 · Cited by 44
Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria
Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Janežič, S., Rupnik, M., & Bogovič Matijašić, B. (2023) · Life Science Alliance · doi:10.26508/lsa.202201637 · Cited by 36
Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Golob, M., Zdovc, I., & Bogovič Matijašić, B. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2127438 · Cited by 21
Field, W., & Hershberg, R. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv102 · Cited by 19
Wang, C., Wang, C., Chen, S., Shi, K., Yu, J., Ding, Y., Yue, Y., Hua, Y., Wang, H., & Chen, J. (2025) · BMC Microbiology · doi:10.1186/s12866-025-04586-0 · Cited by 6
Metadata
- Authors
- Hu, Y., Yang, X., Qin, J., Lu, N., Cheng, G., Wu, N., Pan, Y., Li, J., Zhu, L., Wang, X., Meng, Z., Zhao, F., Liu, D., Ma, J., Qin, N., Xiang, C., Xiao, Y., Li, L., Yang, H., Wang, J., Yang, R., Gao, G. F., Wang, J., & Zhu, B.
- Venue
- Nature Communications
- Published
- 2013-07-23
- Volume
- 4
- Issue
- 1
- Pages
- 2151-2151
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2027951608
- Cited by
- 781
- References
- 36
- FWCI
- 15.77
- Type
- journal article
- Language
- en
- Open access
- bronze
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