19,557
Views
41
CrossRef citations to date
0
Altmetric
Research Paper/Report

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

, , ORCID Icon, , , ORCID Icon, ORCID Icon, ORCID Icon, , , & show all
Pages 721-734 | Received 25 Jul 2019, Accepted 30 Nov 2019, Published online: 13 Jan 2020

References

  • Turnbaugh PJ, Gordon JI. 2009. The core gut microbiome, energy balance and obesity. J Physiol. 587:4153–4158. doi:10.1113/jphysiol.2009.174136.
  • Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, et al. 2014. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 5:1–11. doi:10.1038/ncomms5498.
  • Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. 2011. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21:1616–1625. doi:10.1101/gr.122705.111.
  • Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 466:334–338. doi:10.1038/nature09199.
  • Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Paul Ross R. 2013. Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes. 4:4–16. doi:10.4161/gmic.22371.
  • Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI. 2013. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc Natl Acad Sci. 110:20236–20241. doi:10.1073/pnas.1319470110.
  • Jang S, Sun J, Chen P, Lakshman S, Molokin A, Harnly JM, Vinyard BT, Urban JF, Davis CD, Solano-Aguilar G, et al. 2016. Flavanol-enriched cocoa powder alters the intestinal microbiota, tissue and fluid metabolite profiles, and intestinal gene expression in pigs. J Nutr. 146:673–680. doi:10.3945/jn.115.222968.
  • Etxeberria U, Fernández-Quintela A, Milagro FI, Aguirre L, Martínez JA, Portillo MP. 2013. Impact of polyphenols and polyphenol-rich dietary sources on gut microbiota composition. J Agric Food Chem. 61:9517–9533. doi:10.1021/jf402506c.
  • Louis P, Scott KP, Duncan SH, Flint HJ. 2007. Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol. 102:1197–1208. doi:10.1111/jam.2007.102.issue-5.
  • Roberfroid MB. 2005. Introducing inulin-type fructans. Br J Nutr. 93(Suppl 1):S13–5. doi:10.1079/BJN20041350.
  • Wu, M., McNulty, N.P., Rodionov, D.A., Khoroshkin, M.S., Griffin, N.W., Cheng, J., Latreille, P., Kerstetter, R.A., Terrapon, N., Henrissat, B, et al. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Sci. 3502015; 350.
  • Cobián Güemes AG, Youle M, Cantú VA, Felts B, Nulton J, Rohwer F. 2016. Viruses as winners in the game of life. Annu Rev Virol. 3:197–214. doi:10.1146/annurev-virology-100114-054952.
  • Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, et al. 2013. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 110:10771–10776. doi:10.1073/pnas.1305923110.
  • Carda-Diéguez M, Mizuno CM, Ghai R, Rodriguez-Valera F, Amaro C. 2015. Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla). Front Microbiol. 6:3.
  • Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP, Rohwer F, et al. 2011. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci. 108:4547–4553. doi:10.1073/pnas.1000089107.
  • Pavlova SI, Tao L. 2000. Induction of vaginal Lactobacillus phages by the cigarette smoke chemical benzo[a]pyrene diol epoxide. Mutat Res - Genet Toxicol Environ Mutagen. 466:57–62. doi:10.1016/S1383-5718(00)00003-6.
  • Danovaro R, Corinaldesi C. 2003. Sunscreen products increase virus production through prophage induction in marine bacterioplankton. Microb Ecol. 45:109–118. doi:10.1007/s00248-002-1033-0.
  • Chen Q, Tang S, Jin X, Zou J, Chen K, Zhang T, Xiao X. 2009. Investigation of the genotoxicity of quinocetone, carbadox and olaquindox in vitro using Vero cells. Food Chem Toxicol. 47:328–334. doi:10.1016/j.fct.2008.11.020.
  • O’Brien AD, Newland JW, Miller SF, Holmes RK, Smith HW, Formal SB Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Sci 1984; 226: 694–696. doi: 10.1126/science.6387911
  • Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R. 2013. Meta-analyses of studies of the human microbiota. Genome Res. 23:1704–1714. doi:10.1101/gr.151803.112.
  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. 2009. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 1:6ra14. doi:10.1126/scitranslmed.3000322.
  • Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, Coleman ML, Meyer F, Chang EB. 2016. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. Isme J. 10:1217–1227. doi:10.1038/ismej.2015.183.
  • Gonzalez R, Dunkel R, Koletzko B, Schusdziarra V, Allescher HD. 1998. Effect of capsaicin-containing red pepper sauce suspension on upper gastrointestinal motility in healthy volunteers. Dig Dis Sci. 43:1165–1171. doi:10.1023/A:1018831018566.
  • Kurita S, Kitagawa E, Kim C-H, Momose Y, Iwahashi H. 2002. Studies on the antimicrobial mechanisms of capsaicin using yeast DNA microarray. Biosci Biotechnol Biochem. 66:532–536. doi:10.1271/bbb.66.532.
  • Henke MO, Ratjen F. 2007. Mucolytics in cystic fibrosis. Paediatr Respir Rev. 8:24–29. doi:10.1016/j.prrv.2007.02.009.
  • Huynh HQ, Couper RTL, Tran CD, Moore L, Kelso R, Butler RN. 2004. N-acetylcysteine, a novel treatment for Helicobacter pylori infection. Dig Dis Sci. 49:1853–1861. doi:10.1007/s10620-004-9583-2.
  • Zhang, T., Breitbart, M., Lee, W.H., Run, J.Q., Wei, C.L., Soh, S.W.L., Hibberd, M.L., Liu, E.T., Rohwer, F. and Ruan, Y. 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4:0108–0118.
  • Lauterburg BH, Corcoran GB, Mitchell JR. 1983. Mechanism of action of N-acetylcysteine in the protection against the hepatotoxicity of acetaminophen in rats in vivo. J Clin Invest. 71:980–991. doi:10.1172/JCI110853.
  • Holmay MJ, Terpstra M, Coles LD, Mishra U, Ahlskog M, Öz G, Cloyd JC, Tuite PJ. 2013. N-acetylcysteine boosts brain and blood glutathione in gaucher and Parkinson diseases. Clin Neuropharmacol. 36:103–106. doi:10.1097/WNF.0b013e31829ae713.
  • Geiler J, Michaelis M, Naczk P, Leutz A, Langer K, Doerr H-W, Cinatl J. 2010. N-acetyl-L-cysteine (NAC) inhibits virus replication and expression of pro-inflammatory molecules in A549 cells infected with highly pathogenic H5N1 influenza A virus. Biochem Pharmacol. 79:413–420. doi:10.1016/j.bcp.2009.08.025.
  • Parry MF, Neu HC. 1977. Effect of N-acetylcysteine on antibiotic activity and bacterial growth in vitro. J Clin Microbiol. 5:58–61.
  • Quah SY, Wu S, Lui JN, Sum CP, Tan KS. 2012. N-acetylcysteine inhibits growth and eradicates biofilm of Enterococcus faecalis. J Endod. 38:81–85. doi:10.1016/j.joen.2011.10.004.
  • Sevier CS, Kaiser CA. 2002. Formation and transfer of disulphide bonds in living cells. Nat Rev Mol Cell Biol. 3:836–847. doi:10.1038/nrm954.
  • Tadhani MB, Subhash R. 2007. In vitro antimicrobial activity of Stevia rebaudiana Bertoni leaves. Trop J Pharm Res. 5:557–560. doi:10.4314/tjpr.v5i1.14633.
  • Fazal H, Ahmad N, Ullah I, Inayat H, Khan L, Abbasi BH. 2011. Antibacterial potential in Parthenium. In Vitro. 43:1307–1313.
  • Tomita T, Sato N, Arai T, Shiraishi H, Sato M, Takeuchi M. 1997. Bactericidal activity of a fermented hot-water extract from Stevia rebaudiana Bertoni towards enterohemorrhagic Escherichia coli O157: h7and other food-borne pathogenic bacteria. Microbiol Immunol. 41:1005–1009. doi:10.1111/j.1348-0421.1997.tb01961.x.
  • Paduch R, Kandefer-Szerszeń M, Trytek M, Terpenes: FJ. 2007. Substances useful in human healthcare. Arch Immunol Ther Exp (Warsz). 55:315–327. doi:10.1007/s00005-007-0039-1.
  • Geuns J. Stevioside. Phytochemistry. 2003;64:913–921.
  • Yasukawa K, Kitanaka S, Seo S. 2002. Inhibitory Effect of Stevioside on Tumor Promotion by 12-O-Tetradecanoylphorbol-13-acetate in Two-Stage Carcinogenesis in Mouse Skin. Biol Pharm Bull. 25:1488–1490. doi:10.1248/bpb.25.1488.
  • Abou-Donia MB, El-Masry EM, Abdel-Rahman AA, McLendon RE, Schiffman SS. 2008. Splenda alters gut microflora and increases intestinal P-glycoprotein and cytochrome P-450 in male rats. J Toxicol Environ Heal - Part A Curr Issues. 71:1415–1429. doi:10.1080/15287390802328630.
  • Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger A, et al. 2014. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 514:181–186. doi:10.1038/nature13793.
  • Frankenfeld CL, Sikaroodi M, Lamb E, Shoemaker S, Gillevet PM. 2015. High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States. Ann Epidemiol. 25:736–742. doi:10.1016/j.annepidem.2015.06.083.
  • Brudzynski K, Abubaker K, Miotto D. 2012. Unraveling a mechanism of honey antibacterial action : polyphenol/H2O2 -induced oxidative effect on bacterial cell growth and on DNA degradation. Food Chem. 133:329–336. doi:10.1016/j.foodchem.2012.01.035.
  • Roquetto, A.R., Monteiro, N.E.S., Moura, C.S., Toreti, V.C., de Pace, F., dos Santos, A., Park, Y.K. and Amaya-Farfan, J. 2015. Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet. Food Res Int. 76:796–803. doi:10.1016/j.foodres.2015.07.026.
  • Xiao P, He L, Wang L. 1984. Ethnopharmacologic study of chinese rhubarb. J Ethnopharmacol. 10:275–293. doi:10.1016/0378-8741(84)90016-3.
  • Allahverdiyev AM, Bagirova M, Yaman S, Koc RC, Abamor ES, Ates SC, Baydar, S.Y., Elcicek, S. and Oztel, O.N. 2013. Development of new antiherpetic drugs based on plant compounds. In: Rai MK, Kon KV, editors. Fighting multidrug resistance with herbal extracts, essential oils and their components. Elsevier; p. 245–259.
  • Xiong HR, Shen YY, Lu L, Hou W, Luo F, Xiao H and Yang, Z.Q. 2012. The inhibitory effect of Rheum palmatum against coxsackievirus B3 in vitro and in vivo. Am J Chin Med. 40:801–812. doi:10.1142/S0192415X12500607.
  • Utsunomiya H, Ichinose M, Uozaki M, Tsujimoto K, Yamasaki H, Koyama AH. 2008. Antiviral activities of coffee extracts in vitro. Food Chem Toxicol. 46:1919–1924. doi:10.1016/j.fct.2008.01.031.
  • Wang G-F, Shi L-P, Ren Y-D, Liu Q-F, Liu H-F, Zhang R-J, Li Z, Zhu F-H, He P-L, Tang W, et al. 2009. Anti-hepatitis B virus activity of chlorogenic acid, quinic acid and caffeic acid in vivo and in vitro. Antiviral Res. 83:186–190. doi:10.1016/j.antiviral.2009.05.002.
  • Namba T, Kurokawa M, Kadota S, Shiraki K. 1998. Development of antiviral therapeutic agents from traditional medicines. Yakugaku Zasshi. 118:383–400. doi:10.1248/yakushi1947.118.9_383.
  • DH G, Kitajima M, JR T, Bright KR. 2014. Antiviral efficacy and mechanisms of action of oregano essential oil and its primary component carvacrol against murine norovirus. J Appl Microbiol. 116:1149–1163. doi:10.1111/jam.12453.
  • Pilau MR, Alves SH, Weiblen R, Arenhart S, Cueto AP, Lovato LT. 2011. Antiviral activity of the Lippia graveolens (Mexican oregano) essential oil and its main compound carvacrol against human and animal viruses. Braz J Microbiol. 42:1616–1624. doi:10.1590/S1517-83822011000400049.
  • Reddy BU, Mullick R, Kumar A, Sudha G, Srinivasan N, Das S. 2015. Small molecule inhibitors of HCV replication from Pomegranate. Sci Rep. 4:5411. doi:10.1038/srep05411.
  • Su X, Sangster MY, D’Souza DH. 2011. Time-dependent effects of pomegranate juice and pomegranate polyphenols on foodborne viral reduction. Foodborne Pathog Dis. 8:1177–1183. doi:10.1089/fpd.2011.0873.
  • Haidari M, Ali M, Ward Casscells S, Pomegranate MM. 2009. (Punica granatum) purified polyphenol extract inhibits influenza virus and has a synergistic effect with oseltamivir. Phytomedicine. 16:1127–1136. doi:10.1016/j.phymed.2009.06.002.
  • Molly K, Vande WM, De SI, Verstraete W. 1994. Validation of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) reactor using microorganism-associated activities. Microb Ecol Health Dis. 7:191–200. doi:10.3109/08910609409141354.
  • Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: A Fast Phage Search Tool. Nucleic Acids Res. 39:347–352. doi:10.1093/nar/gkr485.
  • Akhter S, Aziz RK, Edwards RA. 2012. PhiSpy: A novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies. Nucleic Acids Res. 40:1–13. doi:10.1093/nar/gks406.
  • Kohler B, Karch H, Schmidt H. 2000. Antibacterials that are used as growth promoters in animal husbandry can affect the bacteriophages and Shiga toxins 2 from Escherichia coli strains. Microbiol. 146:1085–1090. doi:10.1099/00221287-146-5-1085.
  • Cuevas DA, Edwards RA. 2017. PMAnalyzer: a new web interface for bacterial growth curve analysis. Bioinf. 33:1905–1906. doi:10.1093/bioinformatics/btx084.
  • Sanchez SE, Cuevas DA, Rostron JE, Liang TY, Pivaroff CG, Haynes MR, Nulton, J., Felts, B., Bailey, B.A., Salamon, P, et al. 2015. Phage Phenomics: physiological Approaches to Characterize Novel Viral Proteins. J Vis Exp. 100:e52854.
  • Jones E, Oliphant T, Peterson P SciPy: open Source Scientific Tools for Python. 2001.
  • Zwietering MH, Jongenburger I, Rombouts FM, van ’t Riet K. 1990. Modeling of the bacterial growth curve. Appl Environ Microbiol. 56:1875–1881.
  • Wickham H. 2016 ggplot2.
  • Firsov AA, Vostrov SN, Shevchenko AA, Cornaglia G. 1997. Parameters of bacterial killing and regrowth kinetics and antimicrobial effect examined in terms of area under the concentration-time curve relationships: action of ciprofloxacin against Escherichia coli in an in vitro dynamic model. Antimicrob Agents Chemother. 41:1281–1287. doi:10.1128/AAC.41.6.1281.
  • R Core Team. R: a language and environment for statistical computing | GBIF.ORG. R: A language and environment for statistical computing.
  • Warnes G, Bolker B, Bonebakker L. 2009. gplots: various R programming tools for plotting data. R Packag Version.
  • Molan PC. 2006. The antibacterial activity of honey: 1. The Nature of the Antibacterial Activity. 73:5–28.
  • Imlay JA, Linn S. 1987. Mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide. J Bacteriol. 169:2967–2976. doi:10.1128/jb.169.7.2967-2976.1987.
  • Selva L, Viana D, Regev-Yochay G, Trzcinski K, JM C, Lasa Í, Novick RP, Penades JR. 2009. Killing niche competitors by remote-control bacteriophage induction. Proc Natl Acad Sci. 106:1234–1238. doi:10.1073/pnas.0809600106.
  • Sekulović O, Fortier LC. Characterization of functional prophages in Clostridium difficile. In: Roberts A, Mullany P, editors. Methods in Molecular Biology. New York (NY): Humana Press; 2016. p. 143–165.
  • Brussaard CPD, Payet JP, Winter C, Weinbauer MG. Quantification of aquatic viruses by flow cytometry. Man Aquat Viral Ecol. 2010;102–109.
  • Torres PJ, Edwards RA, McNair KAPARTIE. 2017. A partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive. Bioinf. 33:2389–2391. doi:10.1093/bioinformatics/btx184.
  • Edwards R linsalrob/SearchSRA: Alpha Release. 2017.