Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

Cell - Tập 152 - Trang 39-50 - 2013
Corinne Ferrier Maurice1, Henry Joseph Haiser1, Peter James Turnbaugh1
1FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA

Tài liệu tham khảo

Baselt, 2008 Ben-Amor, 2005, Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis, Appl. Environ. Microbiol., 71, 4679, 10.1128/AEM.71.8.4679-4689.2005 Blaut, 2011, Ecology and physiology of the intestinal tract, Curr. Top. Microbiol. Immunol. Bouvier, 2011, A single-cell analysis of virioplankton adsorption, infection, and intracellular abundance in different bacterioplankton physiologic categories, Microb. Ecol., 62, 669, 10.1007/s00248-011-9862-3 Bouvier, 2007, A comparative study of the cytometric characteristics of high and low nucleic-acid bacterioplankton cells from different aquatic ecosystems, Environ. Microbiol., 9, 2050, 10.1111/j.1462-2920.2007.01321.x Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Caporaso, 2011, Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc. Natl. Acad. Sci. USA, 108, 4516, 10.1073/pnas.1000080107 Caporaso, 2012, Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J., 6, 1621, 10.1038/ismej.2012.8 Davey, 2003, Using flow cytometry to quantify microbial heterogeneity, Curr. Issues Mol. Biol., 5, 9 Del Giorgio, 2008, Physiological structure and single-cell activity in marine bacterioplankton, 243 Dethlefsen, 2011, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proc. Natl. Acad. Sci. USA, 108, 4554, 10.1073/pnas.1000087107 Gasol, 1999, Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria, Appl. Environ. Microbiol., 65, 4475, 10.1128/AEM.65.10.4475-4483.1999 Gosalbes, 2011, Metatranscriptomic approach to analyze the functional human gut microbiota, PLoS ONE, 6, e17447, 10.1371/journal.pone.0017447 Guillebault, 2010, Improved method for bacterial cell capture after flow cytometry cell sorting, Appl. Environ. Microbiol., 76, 7352, 10.1128/AEM.00621-10 Haiser, 2012, Is it time for a metagenomic basis of therapeutics?, Science, 336, 1253, 10.1126/science.1224396 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234 Jellett, 1996, Metabolic activity of bacterioplankton communities assessed by flow cytometry and single carbon substrate utilization, Mar. Ecol. Prog. Ser., 136, 213, 10.3354/meps136213 Jernberg, 2010, Long-term impacts of antibiotic exposure on the human intestinal microbiota, Microbiology, 156, 3216, 10.1099/mic.0.040618-0 Jochem, 2004, Growth and grazing rates of bacteria groups with different apparent DNA content in the Gulf of Mexico, Mar. Biol., 145, 1213, 10.1007/s00227-004-1406-7 Joux, 2000, Use of fluorescent probes to assess physiological functions of bacteria at single-cell level, Microbes Infect., 2, 1523, 10.1016/S1286-4579(00)01307-1 Kohanski, 2007, A common mechanism of cellular death induced by bactericidal antibiotics, Cell, 130, 797, 10.1016/j.cell.2007.06.049 Kristiansson, 2009, ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes, Bioinformatics, 25, 2737, 10.1093/bioinformatics/btp508 Le Blay, 2007, In vitro inhibition activity of nisin A, nisin Z, pediocin PA-1 and antibiotics against common intestinal bacteria, Lett. Appl. Microbiol., 45, 252, 10.1111/j.1472-765X.2007.02178.x Lee, 2012, Microbial environments confound antibiotic efficacy, Nat. Chem. Biol., 8, 6, 10.1038/nchembio.740 Levin, 2006, Non-inherited antibiotic resistance, Nat. Rev. Microbiol., 4, 556, 10.1038/nrmicro1445 Lindenbaum, 1981, Inactivation of digoxin by the gut flora: reversal by antibiotic therapy, N. Engl. J. Med., 305, 789, 10.1056/NEJM198110013051403 Magnusson, 1982, Metabolism of digoxin and absorption site, Br. J. Clin. Pharmacol., 14, 284, 10.1111/j.1365-2125.1982.tb01976.x Martínez, 2011, Metabolic regulation of antibiotic resistance, FEMS Microbiol. Rev., 35, 768, 10.1111/j.1574-6976.2011.00282.x McNulty, 2011, The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins, Sci. Transl. Med., 3, ra106, 10.1126/scitranslmed.3002701 Mortimer, 2000, Flow cytometric monitoring of antibiotic-induced injury in Escherichia coli using cell-impermeant fluorescent probes, Antimicrob. Agents Chemother., 44, 676, 10.1128/AAC.44.3.676-681.2000 Novo, 2000, Multiparameter flow cytometric analysis of antibiotic effects on membrane potential, membrane permeability, and bacterial counts of Staphylococcus aureus and Micrococcus luteus, Antimicrob. Agents Chemother., 44, 827, 10.1128/AAC.44.4.827-834.2000 Peris-Bondia, 2011, The active human gut microbiota differs from the total microbiota, PLoS ONE, 6, e22448, 10.1371/journal.pone.0022448 Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821 Raaflaub, 1975, On the pharmacokinetics of phenacetin in man, Eur. J. Clin. Pharmacol., 8, 261, 10.1007/BF00567125 Reshef, 2011, Detecting novel associations in large data sets, Science, 334, 1518, 10.1126/science.1205438 Rey, 2010, Dissecting the in vivo metabolic potential of two human gut acetogens, J. Biol. Chem., 285, 22082, 10.1074/jbc.M110.117713 Segata, 2011, Metagenomic biomarker discovery and explanation, Genome Biol., 12, R60, 10.1186/gb-2011-12-6-r60 Shapiro, 2000, Microbial analysis at the single-cell level: tasks and techniques, J. Microbiol. Methods, 42, 3, 10.1016/S0167-7012(00)00167-6 Smith, 1974, Metabolism of N-acylated and O-alkylated drugs by the intestinal microflora during anaerobic incubation in vitro, Xenobiotica, 4, 477, 10.3109/00498257409052100 Somogyi, 1995, Evaluation of the intestinal absorption of erythromycin in man: absolute bioavailability and comparison with enteric coated erythromycin, Pharm. Res., 12, 149, 10.1023/A:1016215510223 Sousa, 2008, The gastrointestinal microbiota as a site for the biotransformation of drugs, Int. J. Pharm., 363, 1, 10.1016/j.ijpharm.2008.07.009 Tatusov, 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33, 10.1093/nar/28.1.33 Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540 Turnbaugh, 2009, The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice, Sci. Transl. Med., 1, 6ra14, 10.1126/scitranslmed.3000322 Turnbaugh, 2010, Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins, Proc. Natl. Acad. Sci. USA, 107, 7503, 10.1073/pnas.1002355107 Walter, 2011, The human gut microbiome: ecology and recent evolutionary changes, Annu. Rev. Microbiol., 65, 411, 10.1146/annurev-micro-090110-102830 Wang, 2009, Isolation and characterization of low nucleic acid (LNA)-content bacteria, ISME J., 3, 889, 10.1038/ismej.2009.46 Wickens, 2000, Flow cytometric investigation of filamentation, membrane patency, and membrane potential in Escherichia coli following ciprofloxacin exposure, Antimicrob. Agents Chemother., 44, 682, 10.1128/AAC.44.3.682-687.2000 Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053 Zubkov, 2004, Coexistence of dominant groups in marine bacterioplankton community - a combination of experimental and modelling approaches, J. Mar. Biol. Assoc. UK., 84, 519, 10.1017/S002531540400952Xh Abubucker, S., Segata, N., Goll, J., Schubert, A.M., Izard, J., Cantarel, B.L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012). Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358. Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P. (2004). Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 573, 83–92. Edgar, R.C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461. Faith, J.J., McNulty, N.P., Rey, F.E., and Gordon, J.I. (2011). Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 333, 101–104. Haugland, R.P. (2005). The Handbook: A Guide to Fluorescent Probes and Labeling Technologies, Tenth Edition (Carlsbad, CA: Invitrogen Corp). Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Res. 32(Database issue), D277–D280. Lebaron, P., Servais, P., Agogué, H., Courties, C., and Joux, F. (2001). Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl. Environ. Microbiol. 67, 1775–1782. Li, W., and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659. Martens-Habbena, W., and Sass, H. (2006). Sensitive determination of microbial growth by nucleic acid staining in aqueous suspension. Appl. Environ. Microbiol. 72, 87–95. Maurice, C.F., Mouillot, D., Bettarel, Y., De Wit, R., Sarmento, H., and Bouvier, T. (2011). Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons. ISME J. 5, 831–842. Müller, S., Harms, H., and Bley, T. (2010). Origin and analysis of microbial population heterogeneity in bioprocesses. Curr. Opin. Biotechnol. 21, 100–113. Ning, Z., Cox, A.J., and Mullikin, J.C. (2001). SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729. Quince, C., Lanzen, A., Davenport, R.J., and Turnbaugh, P.J. (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38. Sträuber, H., and Müller, S. (2010). Viability states of bacteria—specific mechanisms of selected probes. Cytometry A 77, 623–634. Strnad, H., Ridl, J., Paces, J., Kolar, M., Vlcek, C., and Paces, V. (2011). Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. J. Bacteriol. 193, 791–792. Suller, M.T.E., and Lloyd, D. (1999). Fluorescence monitoring of antibiotic-induced bacterial damage using flow cytometry. Cytometry 35, 235–241. Zipper, H., Brunner, H., Bernhagen, J., and Vitzthum, F. (2004). Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 32, e103.