2020 Volume 15 Issue 4
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Duan Yujing, Wu Xinyan, Chen Zeyou, Chen Ying, Li Linyun, Zhu Siyuan, Mao Daqing, Luo Yi. Advances in Human Gut Resistome[J]. Asian Journal of Ecotoxicology, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001
Citation: Duan Yujing, Wu Xinyan, Chen Zeyou, Chen Ying, Li Linyun, Zhu Siyuan, Mao Daqing, Luo Yi. Advances in Human Gut Resistome[J]. Asian Journal of Ecotoxicology, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001
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Advances in Human Gut Resistome

  • 1. Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China;

  • 2. State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China;

  • 3. School of Medicine, Nankai University, Tianjin 300071, China;

  • 4. College of Environment, Liaoning University, Shenyang 110036, China

  • Corresponding author: Luo Yi, luoy@nankai.edu.cn
  • Received Date: 25/03/2020
    Fund Project:
  • Human gut microbiota is the reservoir of antibiotic resistance genes (ARGs) and it plays an important role to human health. The abuse of antibiotics is still severe at present, which further aggravates the spread of ARGs. Bacterial resistance seriously affects human health, food safety and ecological safety, and pathogens carrying ARGs pose a great threat to clinical treatment. In combination with the research progress in China and abroad, this paper discussed in detail about gut resistome from the aspects including the composition, origin, propagation and evolution. In addition, the research methods of human gut resistome and the future prospect were summarized. This study could promote the public’s understanding of gut resistome and provide theoretical support for rational use of antibiotics.
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  • Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing[J]. Nature, 2010, 464(7285):59-65

    Google Scholar Pub Med

    郭慧玲, 邵玉宇, 孟和毕力格, 等. 肠道菌群与疾病关系的研究进展[J]. 微生物学通报, 2015, 42(2):400-410 Guo H L, Shao Y Y, Menghe B, et al. Research on the relation between gastrointestinal microbiota and disease[J]. Microbiology China, 2015, 42(2):400-410(in Chinese)

    Google Scholar Pub Med

    杨凤霞, 毛大庆, 罗义, 等. 环境中抗生素抗性基因的水平传播扩散[J]. 应用生态学报, 2013, 24(10):2993-3002 Yang F X, Mao D Q, Luo Y, et al. Horizontal transfer of antibiotic resistance genes in the environment[J].Chinese Journal of Applied Ecology, 2013, 24(10):2993-3002(in Chinese)

    Google Scholar Pub Med

    Allen H K, Donato J, Wang H H, et al. Call of the wild:Antibiotic resistance genes in natural environments[J]. Nature Reviews Microbiology, 2010, 8(4):251-259

    Google Scholar Pub Med

    Martinez J. Natural antibiotic resistance and contamination by antibiotic resistance determinants:The two ages in the evolution of resistance to antimicrobials[J]. Frontiers in Microbiology, 2012, 3(1):1

    Google Scholar Pub Med

    Cant ón R. Antibiotic resistance genes from the environment:A perspective through newly identified antibiotic resistance mechanisms in the clinical setting[J]. Clinical Microbiology and Infection, 2009, 15(s1):20-25

    Google Scholar Pub Med

    Wright G D. The antibiotic resistome:The nexus of chemical and genetic diversity[J]. Nature Reviews Microbiology, 2007, 5(3):175-186

    Google Scholar Pub Med

    李显志. 抗生素耐药基因古老起源与现代进化及其警示[J]. 中国抗生素杂志, 2013, 38(2):81-89 Li X Z. Ancient origin and modern evolution of antibiotic resistome and their implications[J]. Chinese Journal of Antibiotics, 2013, 38(2):81-89(in Chinese)

    Google Scholar Pub Med

    Hu Y, Yang X, Qin J, et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota[J]. Nature Communications, 2013, 4:2151

    Google Scholar Pub Med

    Salyers A A, Gupta A, Wang Y. Human intestinal bacteria as reservoirs for antibiotic resistance genes[J]. Trends in Microbiology, 2004, 12(9):412-416

    Google Scholar Pub Med

    Baron S A, Diene S M, Rolain J M. Human microbiomes and antibiotic resistance[J]. Human Microbiome Journal, 2018, 10:43-52

    Google Scholar Pub Med

    Lagier J C, Dubourg G, Million M, et al. Culturing the human microbiota and culturomics[J]. Nature Reviews Microbiology, 2018, 16:540-550

    Google Scholar Pub Med

    Van Schaik W. The human gut resistome[J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2015, 370(1670):doi.org/10.1098/rstb.2014.0087

    Google Scholar Pub Med

    Mcarthur A G, Waglechner N, Nizam F, et al. The comprehensive antibiotic resistance database[J]. Antimicrobial Agents and Chemotherapy, 2013, 57(7):3348-3357

    Google Scholar Pub Med

    Liu B, Pop M. ARDB-Antibiotic resistance genes database[J]. Nucleic Acids Research, 2008, 37(suppl_1):D443-D447

    Google Scholar Pub Med

    Zhou C E, Smith J, Lam M, et al. MvirDB-A microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications[J]. Nucleic Acids Research, 2006, 35(suppl_1):D391-D394

    Google Scholar Pub Med

    Scaria J, Chandramouli U, Verma S K. Antibiotic resistance genes online (ARGO):A database on vancomycin and beta-lactam resistance genes[J]. Bioinformation, 2005, 1(1):5-7

    Google Scholar Pub Med

    Kleinheinz K A, Joensen K G, Larsen M V. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences[J]. Bacteriophage, 2014, 4(2):e27943

    Google Scholar Pub Med

    Gibson M K, Forsberg K J, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology[J]. The ISME Journal, 2015, 9(1):207-216

    Google Scholar Pub Med

    Gupta S K, Padmanabhan B R, Diene S M, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes[J]. Antimicrobial Agents and Chemotherapy, 2014, 58(1):212-220

    Google Scholar Pub Med

    Li L G, Yin X, Zhang T. Tracking antibiotic resistance gene pollution from different sources using machine-learning classification[J]. Microbiome, 2018, 6(1):93

    Google Scholar Pub Med

    Ufarté L, Potocki-Veronese G, Laville É. Discovery of new protein families and functions:New challenges in functional metagenomics for biotechnologies and microbial ecology[J]. Frontiers in Microbiology, 2015, 6:563

    Google Scholar Pub Med

    Verastegui Y, Cheng J, Engel K, et al. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities[J]. mBio, 2014, 5(4):e01157-14

    Google Scholar Pub Med

    王淑娴, 刁菁, 樊英, 等. MALDI-TOF MS技术用于细菌鉴定的研究进展[J]. 农业灾害研究, 2019, 9(5):20-23 Wang S X, Diao J, Fan Y, et al. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacterial srain identification[J]. Journal of Agricultural Catastrophology, 2019, 9(5):20-23(in Chinese)

    Google Scholar Pub Med

    Yatsunenko T, Rey F E, Manary M J, et al. Human gut microbiome viewed across age and geography[J]. Nature, 2012, 486:222-227

    Google Scholar Pub Med

    Lu N, Hu Y, Zhu L, et al. DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related[J]. Scientific Reports, 2014, 4(1):4302

    Google Scholar Pub Med

    Ruppé E, Ghozlane A, Tap J, et al. Prediction of the intestinal resistome by a three-dimensional structure-based method[J]. Nature Microbiology, 2019, 4(1):112-123

    Google Scholar Pub Med

    Feng J, Li B, Jiang X, et al. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses[J]. Environmental Microbiology, 2018, 20(1):355-368

    Google Scholar Pub Med

    Duan Y, Chen Z, Tan L, et al. Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals[J]. The Science of the Total Environment, 2019, 705:135674

    Google Scholar Pub Med

    Scott K P, Melville C M, Barbosa T M, et al. Occurrence of the new tetracycline resistance gene tet (W) in bacteria from the human gut[J]. Antimicrobial Agents and Chemotherapy, 2000, 44(3):775-777

    Google Scholar Pub Med

    Moore A M, Ahmadi S, Patel S, et al. Gut resistome development in healthy twin pairs in the first year of life[J]. Microbiome, 2015, 3(1):27

    Google Scholar Pub Med

    Bäckhed F, Roswall J, Peng Y, et al. Dynamics and stabilization of the human gut microbiome during the first year of life[J]. Cell Host & Microbe, 2015, 17(5):690-703

    Google Scholar Pub Med

    Vangay P, Ward T, Gerber Jeffrey S, et al. Antibiotics, pediatric dysbiosis, and disease[J]. Cell Host & Microbe, 2015, 17(5):553-564

    Google Scholar Pub Med

    Palleja A, Mikkelsen K H, Forslund S K, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure[J]. Nature Microbiology, 2018, 3(11):1255-1265

    Google Scholar Pub Med

    Raymond F, Ouameur A A, Déraspe M, et al. The initial state of the human gut microbiome determines its reshaping by antibiotics[J]. The ISME Journal, 2015, 10:707-720

    Google Scholar Pub Med

    Li J, Rettedal E A, van der Helm E, et al. Antibiotic treatment drives the diversification of the human gut resistome[J]. Genomics, Proteomics & Bioinformatics, 2019, 17(1):39-51

    Google Scholar Pub Med

    Forslund K, Sunagawa S, Roat Kultima J, et al. Country-specific antibiotic use practices impact the human gut resistome[J]. Genome Research, 2013, 23(7):1163-1169

    Google Scholar Pub Med

    Maier L, Pruteanu M, Kuhn M, et al. Extensive impact of non-antibiotic drugs on human gut bacteria[J]. Nature, 2018, 555(7698):623

    Google Scholar Pub Med

    Wang Y, Lu J, Mao L, et al. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera[J]. The ISME Journal, 2019, 13(2):509-522

    Google Scholar Pub Med

    Lu J, Jin M, Nguyen S H, et al. Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation[J]. Environment International, 2018, 118:257-265

    Google Scholar Pub Med

    Häsler R, Kautz C, Rehman A, et al. The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany[J]. Microbiome, 2018, 6(1):37

    Google Scholar Pub Med

    Smits S A, Leach J, Sonnenburg E D, et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania[J]. Science, 2017, 357(6353):802-806

    Google Scholar Pub Med

    Pehrsson E C, Tsukayama P, Patel S, et al. Interconnected microbiomes and resistomes in low-income human habitats[J]. Nature, 2016, 533(7602):212

    Google Scholar Pub Med

    Pal C, Bengtsson-Palme J, Kristiansson E, et al. The structure and diversity of human, animal and environmental resistomes[J]. Microbiome, 2016, 4(1):54

    Google Scholar Pub Med

    Xie J, Jin L, Luo X, et al. Seasonal disparities in airborne bacteria and associated antibiotic resistance genes in PM2.5 between urban and rural sites[J]. Environmental Science & Technology Letters, 2018, 5(2):74-79

    Google Scholar Pub Med

    Liu Y Y, Wang Y, Walsh T R, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China:A microbiological and molecular biological study[J]. The Lancet Infectious Diseases, 2016, 16(2):161-168

    Google Scholar Pub Med

    Ma L, Li B, Jiang X T, et al. Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey[J]. Microbiome, 2017, 5(1):154

    Google Scholar Pub Med

    李林云, 谭璐, 崔玉晓, 等. 饮用水中细菌耐药及其健康风险研究进展[J]. 生态毒理学报, 2018, 13(2):2-12 Li L Y, Tan L, Cui Y X, et al. Bacterial resistance and human health risk in drinking water[J]. Asian Journal of Ecotoxicology, 2018, 13(2):2-12(in Chinese)

    Google Scholar Pub Med

    盛嫣然, 朱晓勇. 母-胎肠道内微生物群落以及母-胎微生物传输的研究进展[J]. 中华生殖与避孕杂志, 2017, 37(9):773-778 Sheng Y R, Zhu X Y. Research progress on the maternal-fetal intestinal microbiome and maternal-fetal microbial transmission[J]. Chinese Journal of Reproduction and Contraception, 2017, 37(9):773-778(in Chinese)

    Google Scholar Pub Med

    Jiménez E, Marín M L, Martín R, et al. Is meconium from healthy newborns actually sterile?[J]. Research in Microbiology, 2008, 159(3):187-193

    Google Scholar Pub Med

    Aagaard K, Ma J, Antony K M, et al. The placenta harbors a unique microbiome[J]. Science Translational Medicine, 2014, 6(237):237ra65

    Google Scholar Pub Med

    Gosalbes M J, Vallès Y, Jiménez-Hernández N, et al. High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples[J]. Journal of Developmental Origins of Health and Disease, 2015, 7(1):35-44

    Google Scholar Pub Med

    关怀, 齐宸, 武晓旭, 等. 胎儿肠道菌群定植的研究进展[J]. 人民军医, 2019, 62(8):764-767

    Google Scholar Pub Med

    Kelsall B. Recent progress in understanding the phenotype and function of intestinal dendritic cells and macrophages[J]. Mucosal Immunology, 2008, 1(6):460-469

    Google Scholar Pub Med

    Pärnänen K, Karkman A, Hultman J, et al. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements[J]. Nature Communications, 2018, 9(1):3891

    Google Scholar Pub Med

    Dominguez-Bello M G, Costello E K, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns[J]. Proceedings of the National Academy of Sciences, 2010, 107(26):11971-11975

    Google Scholar Pub Med

    Martín R, Langa S, Reviriego C, et al. Human milk is a source of lactic acid bacteria for the infant gut[J]. The Journal of Pediatrics, 2003, 143(6):754-758

    Google Scholar Pub Med

    Rizzo L, Manaia C, Merlin C, et al. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment:A review[J]. Science of the Total Environment, 2013, 447:345-360

    Google Scholar Pub Med

    Karkman A, Pärnänen K, Larsson D G J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments[J]. Nature Communications, 2019, 10(1):80

    Google Scholar Pub Med

    马筱玲, 鲁怀伟, 张艳. 认识细菌的天然耐药和获得性耐药[J]. 中华检验医学杂志, 2012, 35(8):762-763

    Google Scholar Pub Med

    Cox G, Wright G D. Intrinsic antibiotic resistance:Mechanisms, origins, challenges and solutions[J]. International Journal of Medical Microbiology, 2013, 303(6-7):287-292

    Google Scholar Pub Med

    Dodd M C. Potential impacts of disinfection processes on elimination and deactivation of antibiotic resistance genes during water and wastewater treatment[J]. Journal of Environmental Monitoring, 2012, 14(7):1754-1771

    Google Scholar Pub Med

    Nordgård L, Brusetti L, Raddadi N, et al. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats[J]. BMC Research Notes, 2012, 5(1):170

    Google Scholar Pub Med

    Stinear T P, Olden D C, Johnson P D R, et al. Enterococcal van B resistance locus in anaerobic bacteria in human faeces[J]. The Lancet, 2001, 357(9259):855-856

    Google Scholar Pub Med

    Graham M, Ballard S A, Grabsch E A, et al. High rates of fecal carriage of nonenterococcal van B in both children and adults[J]. Antimicrobial Agents and Chemotherapy, 2008, 52(3):1195-1197

    Google Scholar Pub Med

    Waters J L, Salyers A A. Regulation of CTnDOT conjugative transfer is a complex and highly coordinated series of events[J]. mBio, 2013, 4(6):e00569-13

    Google Scholar Pub Med

    Manrique P, Dills M, Young J M. The human gut phage community and its implications for health and disease[J]. Viruses, 2017, 9(6):141

    Google Scholar Pub Med

    Quirós P, Colomer-Lluch M, Martínez-Castillo A, et al. Antibiotic resistance genes in the bacteriophage DNA fraction of human fecal samples[J]. Antimicrobial Agents and Chemotherapy, 2014, 58(1):606-609

    Google Scholar Pub Med

    Modi S R, Lee H H, Spina C S, et al. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome[J]. Nature, 2013, 499(7457):219-222

    Google Scholar Pub Med

    D'costa V M, King C E, Kalan L, et al. Antibiotic resistance is ancient[J]. Nature, 2011, 477(7365):457-461

    Google Scholar Pub Med

    Bhullar K, Waglechner N, Pawlowski A, et al. Antibiotic resistance is prevalent in an isolated cave microbiome[J]. PLoS One, 2012, 7(4):e34953

    Google Scholar Pub Med

    Santiago-Rodriguez T M, Fornaciari G, Luciani S, et al. Gut microbiome of an 11th century A.D. pre-Columbian Andean mummy[J]. PLoS One, 2015, 10(9):e0138135

    Google Scholar Pub Med

    Miteva V I, Sheridan P P, Brenchley J E. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core[J]. Applied and Environmental Microbiology, 2004, 70(1):202-213

    Google Scholar Pub Med

    Davies J, Davies D. Origins and evolution of antibiotic resistance[J]. Microbiology and Molecular Biology Reviews, 2010, 74(3):417-433

    Google Scholar Pub Med

    Zhang G, Leclercq S O, Tian J, et al. A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3'')-Ⅱ, is horizontally transferred among Acinetobacter spp. by homologous recombination[J]. PLoS Genetics, 2017, 13(2):e1006602

    Google Scholar Pub Med

    Datta N P, Kontomichalou. Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae[J]. Nature, 1965, 208:239-241

    Google Scholar Pub Med

    厉文辉, 史亚利, 高立红, 等. 加速溶剂萃取-高效液相色谱-串联质谱法同时检测鱼肉中喹诺酮、磺胺与大环内酯类抗生素[J]. 分析测试学报, 2010, 29(10):987-992 Li W H, Shi Y L, Gao L H, et al. Simultaneous determination of quinolones, sulfonamides and macrolides in fish samples using accelerated solvent extraction followed by high performance liquid chromatography-electrospray ionization tandem mass spectrometry[J]. Journal of Instrumental Analysis, 2010, 29(10):987-992(in Chinese)

    Google Scholar Pub Med

    Bush K. Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae[J]. Current Opinion in Microbiology, 2010, 13(5):558-564

    Google Scholar Pub Med

    Bradford P A. Extended-spectrum β-lactamases in the 21st Century:Characterization, epidemiology, and detection of this important resistance threat[J]. Clinical Microbiology Reviews, 2001, 14(4):933-951

    Google Scholar Pub Med

    Bronzwaer S L A M, Cars O, Buchholz U, et al. The relationship between antimicrobial use and antimicrobial resistance in Europe[J]. Emerging Infectious Diseases, 2002, 8(3):278-282

    Google Scholar Pub Med

    Tadesse D A, Zhao S, Tong E, et al. Antimicrobial drug resistance in Escherichia coli from humans and food animals, United States, 1950-2002[J]. Emerging Infectious Diseases, 2012, 18(5):741-749

    Google Scholar Pub Med

    Kahn L H. Perspective:The one-health way[J]. Nature, 2017, 543(7647):S47

    Google Scholar Pub Med

    李鹏媛, 原丽红, 陆家海. 应对新发传染病, One Health策略势在必行[J]. 传染病信息, 2018, 31(1):11-14 , 54 Li P Y, Yuan L H, Lu J H. Imperative One Health strategy for the emerging infectious diseases[J]. Infectious Disease Information, 2018, 31(1):11-14, 54(in Chinese)

    Google Scholar Pub Med

    刘羽. 国家自然科学基金环境地球科学学科布局优化战略研究[J]. 科学通报, 2020, doi:10.1360/TB-2020 -0424 Liu Y. Research on the strategy of optimizing the discipline layout of environmental geosciences under the National Natural Science Foundation of China[J]. Chinese Science Bulletin, 2020, doi:10.1360/TB-2020-0424(in Chinese)

    Google Scholar Pub Med

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Advances in Human Gut Resistome

  • Received Date: 25/03/2020
Fund Project:

Abstract: Human gut microbiota is the reservoir of antibiotic resistance genes (ARGs) and it plays an important role to human health. The abuse of antibiotics is still severe at present, which further aggravates the spread of ARGs. Bacterial resistance seriously affects human health, food safety and ecological safety, and pathogens carrying ARGs pose a great threat to clinical treatment. In combination with the research progress in China and abroad, this paper discussed in detail about gut resistome from the aspects including the composition, origin, propagation and evolution. In addition, the research methods of human gut resistome and the future prospect were summarized. This study could promote the public’s understanding of gut resistome and provide theoretical support for rational use of antibiotics.

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