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Metagenomics in Deciphering Microbial Communities Associated with Medicinal Plants

Part of the Environmental and Microbial Biotechnology book series (EMB)

Abstract

Medicinal plants hold a very important place in therapeutics. Plant growth is affected by a number of abiotic and biotic factors. Among these factors, microorganisms associated with these plants play an important role in the plant health and thus indirectly influence humans as well. Many of these microbes are known to be involved in the production of compounds that are not only useful for the host plant, but also have commercial importance. For in-depth analysis of these plant-associated microbiomes, metagenomic approaches provide the necessary platform of robust, high-throughput techniques. This chapter discusses the microbial communities associated with different medicinal plants, and how metagenomics can be helpful in studying their diversity and versatility.

Keywords

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References

  • Abbey JA, Percival D, Abbey L, Asiedu SK, Prithiviraj B, Schilder A (2019) Biofungicides as alternative to synthetic fungicide control of grey mould (Botrytis cinerea)—prospects and challenges. Biocontrol Sci Tech 29:207–228

    Article  Google Scholar 

  • Abdel-Aziz H, Fawzy N, Ismail AI, El-Askary H (2011) Toxicological studies on a standardized extract of Solanum indicum ssp. distichum. Food Chem Toxicol 49:903–909

    Article  CAS  PubMed  Google Scholar 

  • Aboellil A, Aboellil A (2012) Colonization abilities of microflora to attach aquatic plants. Global J Sci Front Res Biol Sci 12:21–27

    Google Scholar 

  • Aggarwal BB, Sung B (2009) Pharmacological basis for the role of curcumin in chronic diseases: an age-old spice with modern targets. Trends Pharmacol Sci 30:85–94

    Article  CAS  PubMed  Google Scholar 

  • Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G (2016) Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis. Evol Bioinform 12:5–16

    Google Scholar 

  • Ahn K (2017) The worldwide trend of using botanical drugs and strategies for developing global drugs. BMB Rep 50:111–116. https://doi.org/10.5483/bmbrep.2017.50.3.221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Akinsanya MA, Goh JK, Lim SP, Ting ASY (2015) Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genom Data 6:159–163

    Article  PubMed  PubMed Central  Google Scholar 

  • Ambardar S, Sangwan N, Manjula A, Rajendhran J, Gunasekaran P, Lal R et al (2014) Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach. World J Microb Biotechnol 30:2701–2709

    Article  CAS  Google Scholar 

  • Aswathy AJ, Jasim B, Jyothis M, Radhakrishnan E (2013) Identification of two strains of Paenibacillus sp. as indole 3 acetic acid-producing rhizome-associated endophytic bacteria from Curcuma longa. 3 Biotech 3:219–224

    Article  PubMed  Google Scholar 

  • Baldan E, Nigris S, Populin F, Zottini M, Squartini A, Baldan B (2014) Identification of culturable bacterial endophyte community isolated from tissues of Vitis vinifera “Glera”. Plant Biosyst 148:508–516

    Article  Google Scholar 

  • Beiranvand M, Amin M, Hashemi-Shahraki A, Romani B, Yaghoubi S, Sadeghi P (2017) Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran. Iran J Microbiol 9:11

    PubMed  PubMed Central  Google Scholar 

  • Béjà O, Koonin EV, Aravind L, Taylor LT, Seitz H, Stein JL et al (2002) Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 68:335–345

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP et al (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2:516–529

    Article  PubMed  Google Scholar 

  • Bell PJ, Sunna A, Gibbs MD, Curach NC, Nevalainen H, Bergquist PL (2002) Prospecting for novel lipase genes using PCR. Microbiology 148:2283–2291

    Article  CAS  PubMed  Google Scholar 

  • Berendsen RL, Pieterse CM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–48610

    Article  CAS  PubMed  Google Scholar 

  • Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486

    Article  CAS  PubMed  Google Scholar 

  • Berg G (2009) Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, Hallmann J (2005) Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51:215–229

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Zachow C, Cardinale M, Müller H (2011) Ecology and human pathogenicity of plant-associated bacteria. In: Ehlers RU (ed) Regulation of biological control agents. Springer, Dordrecht, pp 175–189. https://doi.org/10.1007/978-90-481-3664-3

    Chapter  Google Scholar 

  • Boumehira AZ, El-Enshasy HA, Hacène H, Elsayed EA, Aziz R, Park EY (2016) Recent progress on the development of antibiotics from the genus Micromonospora. Biotechnol Bioproc Eng E21:199–223

    Article  CAS  Google Scholar 

  • Brady SF, Chao CJ, Clardy J (2002) New natural product families from an environmental DNA (eDNA) gene cluster. J Am Chem Soc 124:9968–9969

    Article  CAS  PubMed  Google Scholar 

  • Brady SF, Clardy J (2003) Synthesis of long-chain fatty acid enol esters isolated from an environmental DNA clone. Org Lett 5:121–124

    Article  CAS  PubMed  Google Scholar 

  • Bragina A, Berg C, Cardinale M, Shcherbakov A, Chebotar V, Berg G (2012) Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle. ISME J 6:802–813

    Article  CAS  PubMed  Google Scholar 

  • Bragina A, Berg C, Müller H, Moser D, Berg G (2013) Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning. Sci Rep 3:1–8

    Article  Google Scholar 

  • Brand C, Ferrante A, Prager R, Riley T, Carson C, Finlay-Jones J et al (2001) The water-soluble components of the essential oil of Melaleuca alternifolia (tea tree oil) suppress the production of superoxide by human monocytes, but not neutrophils, activated in vitro. Inflamm Res 50:213–219

    Article  CAS  PubMed  Google Scholar 

  • Brannock J (2004) Characterization of root endophytic bacteria. University of Cincinnati. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1100806990

  • Bromberg JS, Fricke WF, Brinkman CC, Simon T, Mongodin EF (2015) Microbiota—implications for immunity and transplantation. Nat Rev Nephrol 11:342–353. https://doi.org/10.1038/nrneph.2015.70

    Article  CAS  PubMed  Google Scholar 

  • Brown D (2008) RHS encyclopedia of herbs and their uses. Dorling Kindersley, London

    Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carro L, Razmilic V, Nouioui I, Richardson L, Pan C, Golinska P et al (2018) Hunting for cultivable Micromonospora strains in soils of the Atacama Desert. Antonievan Leeuwenhoek 111:1375–1387

    Article  CAS  Google Scholar 

  • Carvalho CR, Wedge DE, Cantrell CL, Silva-Hughes AF, Pan Z, Moraes RM et al (2016) Molecular phylogeny, diversity, and bioprospecting of endophytic fungi associated with wild ethnomedicinal North American plant Echinacea purpurea (Asteraceae). Chem Biodivers 13:918–930

    Article  CAS  PubMed  Google Scholar 

  • Chakravorty S, Helb D, Burday M, Connell N, Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69:330–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandra S (2012) Endophytic fungi: novel sources of anticancer lead molecules. Appl Microbiol Biotechnol 95:47–59

    Article  CAS  PubMed  Google Scholar 

  • Chen Q, Liu B, Guan X, Tang J (2014) Analysis of Anoectochilus roxburghii root microbial diversity by metagenomic technology. J Agric Biotechnol 22:1441–1446

    CAS  Google Scholar 

  • Chiellini C, Maida I, Emiliani G, Mengoni A, Mocali S, Fabiani A et al (2014) Endophytic and rhizospheric bacterial communities isolated from the medicinal plants Echinacea purpurea and Echinacea angustifolia. Int Microbiol 17:165–174

    CAS  PubMed  Google Scholar 

  • Chong CW, Pearce DA, Convey P, Yew WC, Tan IKP (2012) Patterns in the distribution of soil bacterial 16S rRNA gene sequences from different regions of Antarctica. Geoderma 181–182:45–55. https://doi.org/10.1016/j.geoderma.2012.02.017

    Article  Google Scholar 

  • Christenhusz MJ, Byng JW (2016) The number of known plants species in the world and its annual increase. Phytotaxa 261:201–217

    Article  Google Scholar 

  • Compant S, Kaplan H, Sessitsch A, Nowak J, Ait Barka E, Clément C (2008) Endophytic colonization of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN: from the rhizosphere to inflorescence tissues. FEMS Microbiol Ecol 63:84–93

    Article  CAS  PubMed  Google Scholar 

  • Compant S, Reiter B, Sessitsch A, Nowak J, Clément C, Barka EA (2005) Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl Environ Microbiol 71:1685–1693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coque TM, Oliver A, Pérez-Díaz JC, Baquero F, Cantón R (2002) Genes encoding TEM-4, SHV-2, and CTX-M-10 extended-spectrum β-lactamases are carried by multiple Klebsiella pneumoniae clones in a single hospital (Madrid, 1989 to 2000). Antimicrob Agents Chemother 46:500–510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Courtois S, Cappellano CM, Ball M, Francou F-X, Normand P, Helynck G et al (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69:49–55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cunnane SC, Ganguli S, Menard C, Liede AC, Hamadeh MJ, Chen Z-Y et al (1993) High α-linolenic acid flaxseed (Linum usitatissimum): some nutritional properties in humans. Br J Nutr 69:443–453

    Article  CAS  PubMed  Google Scholar 

  • Da Silva G, Serrano R, Silva O (2011) Maytenus heterophylla and Maytenus senegalensis, two traditional herbal medicines. J Nat Sci Biol Med 2:59

    Article  PubMed  PubMed Central  Google Scholar 

  • Dante G, Facchinetti F (2011) Herbal treatments for alleviating premenstrual symptoms: a systematic review. J Psychosom Obstet Gynecol 32:42–51

    Article  Google Scholar 

  • DeSantis G, Zhu Z, Greenberg WA, Wong K, Chaplin J, Hanson SR et al (2002) An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives. J Am Chem Soc 124:9024–9025

    Article  CAS  PubMed  Google Scholar 

  • Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280. https://doi.org/10.1371/journal.pbio.0060280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:629–632. https://doi.org/10.1038/nature06810

    Article  CAS  PubMed  Google Scholar 

  • Dubey RK, Tripathi V, Prabha R, Chaurasia R, Singh DP, Rao CS et al (2020) Unravelling the soil microbiome: perspectives for environmental sustainability. Springer, Cham

    Book  Google Scholar 

  • Egamberdieva D, Wirth S, Behrendt U, Ahmad P, Berg G (2017) Antimicrobial activity of medicinal plants correlates with the proportion of antagonistic endophytes. Front Microbiol 8:199

    Article  PubMed  PubMed Central  Google Scholar 

  • El-Badry M (2016) Bacterial community metagenomic and variation of some medicinal plant rhizosphere collected form Sinai. SCIREA J Agric 1:16

    Google Scholar 

  • Emiliani G, Mengoni A, Maida I, Perrin E, Chiellini C, Fondi M et al (2014) Linking bacterial endophytic communities to essential oils: clues from Lavandula angustifolia Mill. Evid Based Complement Alternat Med 2014:650905. https://doi.org/10.1155/2014/650905

    Article  PubMed  PubMed Central  Google Scholar 

  • Entcheva P, Liebl W, Johann A, Hartsch T, Streit WR (2001) Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol 67:89–99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ernawati M, Solihin DD, Lestari Y (2016) Community structures of endophytic actinobacteria from medicinal plant Centella asiatica L. urban-based on metagenomic approach. Int J Pharm Pharm Sci 8:292–297

    CAS  Google Scholar 

  • Eschenfeldt WH, Stols L, Rosenbaum H, Khambatta ZS, Quaite-Randall E, Wu S et al (2001) DNA from uncultured organisms as a source of 2, 5-diketo-D-gluconic acid reductases. Appl Environ Microbiol 67:4206–4214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Evans WC (2009) Trease and Evans Pharmacognosy, International Edition E-Book. Elsevier Health Sciences, Saunders Ltd., London

    Google Scholar 

  • Fürnkranz M, Lukesch B, Müller H, Huss H, Grube M, Berg G (2012) Microbial diversity inside pumpkins: microhabitat-specific communities display a high antagonistic potential against phytopathogens. Microb Ecol 63:418–428

    Article  PubMed  CAS  Google Scholar 

  • Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F (2010, 2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harbor Protocols:pdb.prot5368

    Google Scholar 

  • González V, Tello ML (2011) The endophytic mycota associated with Vitis vinifera in central Spain. Fungal Divers 47:29–42

    Article  Google Scholar 

  • Goodfellow M, Fiedler H-P (2010) A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie Van Leeuwenhoek 98:119–142

    Article  PubMed  Google Scholar 

  • Gordon-Bradley N, Lymperopoulou DS, Williams HN (2014) Differences in bacterial community structure on Hydrilla verticillata and Vallisneria americana in a freshwater spring. Microbes Environ 29(1):67–73

    Article  PubMed  PubMed Central  Google Scholar 

  • Goryluk-Salmonowicz A, Piorek M, Rekosz-Burlaga H, Studnicki M, Błaszczyk M (2016) Endophytic detection in selected European herbal plants. Pol J Microbiol 65:369–375

    Article  PubMed  Google Scholar 

  • Gualandi Jr RJ (2010) Fungal endophytes enhance growth and production of natural products in Echinacea purpurea (Moench.) Master’s Thesis, University of Tennessee. https://trace.tennessee.edu/utk_gradthes/713

  • Gupta R, Saikia SK, Pandey R (2017) Bioconsortia augments antioxidant and yield in Matricaria recutita L. against Meloidogyne incognita (Kofoid and White) Chitwood infestation. Proc Natl Acad Sci India Sect B Biol Sci 87:335–342

    Article  Google Scholar 

  • Gupta S, Kaul S, Singh B, Vishwakarma RA, Dhar MK (2016) Production of gentisyl alcohol from Phoma herbarum endophytic in Curcuma longa L. and its antagonistic activity towards leaf spot pathogen Colletotrichum gloeosporioides. Appl Biochem Biotechnol 180:1093–1109

    Article  CAS  PubMed  Google Scholar 

  • Hammer KA, Carson CF, Riley TV (1999) Antimicrobial activity of essential oils and other plant extracts. J Appl Microbiol 86:985–990

    Article  CAS  PubMed  Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249

    Article  CAS  PubMed  Google Scholar 

  • Hao D-c, Xiao P-g (2017) Rhizosphere microbiota and microbiome of medicinal plants: from molecular biology to omics approaches. Chin Herb Med 9:199–217

    Article  Google Scholar 

  • Hardoim PR, Hardoim CC, Van Overbeek LS, Van Elsas JD (2012) Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One 7(2):e30438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hart P, Brand C, Carson C, Riley T, Prager R, Finlay-Jones J (2000) Terpinen-4-ol, the main component of the essential oil of Melaleuca alternifolia (tea tree oil), suppresses inflammatory mediator production by activated human monocytes. Inflamm Res 49:619–626

    Article  CAS  PubMed  Google Scholar 

  • Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312:7–14

    Article  CAS  Google Scholar 

  • Healy F, Ray R, Aldrich H, Wilkie A, Ingram L, Shanmugam K (1995) Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl Microbiol Biotechnol 43:667–674

    Article  CAS  PubMed  Google Scholar 

  • Henne A, Daniel R, Schmitz RA, Gottschalk G (1999) Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-Hydroxybutyrate. Appl Environ Microbiol 65:3901–3907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henne A, Schmitz RA, Bömeke M, Gottschalk G, Daniel R (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66:3113–3116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP et al (2016) Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology. Front Microbiol 7:484

    Article  PubMed  PubMed Central  Google Scholar 

  • Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961

    Article  CAS  PubMed  Google Scholar 

  • Huang W, Long C, Lam E (2018) Roles of plant-associated microbiota in traditional herbal medicine. Trends Plant Sci 23:559–562

    Article  CAS  PubMed  Google Scholar 

  • Hugenholtz P, Tyson GW (2008) Metagenomics. Nature 455:481–483

    Article  CAS  PubMed  Google Scholar 

  • Hummel W (1999) Large-scale applications of NAD (P)-dependent oxidoreductases: recent developments. Trends Biotechnol 17:487–492

    Article  CAS  PubMed  Google Scholar 

  • Igai K, Itakura M, Nishijima S, Tsurumaru H, Suda W, Tsutaya T et al (2016) Nitrogen fixation and nifH diversity in human gut microbiota. Sci Rep 6:1–11

    Article  CAS  Google Scholar 

  • Jalgaonwala R, Mohite B, Mahajan R (2010) Evaluation of endophytes for their antimicrobial activity from indigenous medicinal plants belonging to North Maharashtra region India. Int J Pharm Biomed Res 1:136–141

    Google Scholar 

  • Jalgaonwala RE, Mahajan RT (2014) Production of anticancer enzyme asparaginase from endophytic Eurotium sp. isolated from rhizomes of Curcuma longa. Eur J Exp Biol 4:36–43

    Google Scholar 

  • Janatiningrum I, Solihin D, Meryandini A, Lestari Y (2018) Comparative study on the diversity of endophytic actinobacteria communities from Ficus deltoidea using metagenomic and culture-dependent approaches. Biodiversitas 19:1514–1520

    Article  Google Scholar 

  • Jiang M, Zhang Y, Hu X, Huang Q (2004) Endophytic fungus producing gamma-linolenic acid from evening primrose (Oenothera biennis L.). Chinese J Oil Crop Sci 26:78–81

    Google Scholar 

  • Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5:46–56

    CAS  PubMed  Google Scholar 

  • Köberl M, Ramadan EM, Adam M, Cardinale M, Hallmann J, Heuer H et al (2013b) Bacillus and Streptomyces were selected as broad-spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiol Lett 342:168–178

    Article  PubMed  CAS  Google Scholar 

  • Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G (2013a) The microbiome of medicinal plants and its potential for biocontrol and promotion of plant growth and quality. Front Microbiol 4:400

    Article  PubMed  PubMed Central  Google Scholar 

  • Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G (2013c) The microbiome of medicinal plants: diversity and importance for plant growth, quality and health. Front Microbiol 4:400

    Article  PubMed  PubMed Central  Google Scholar 

  • Köberl M, White RA, Erschen S, El-Arabi TF, Jansson JK, Berg G (2015) Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla. Genome Announc 3:e00861–e00815

    Article  PubMed  PubMed Central  Google Scholar 

  • Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U et al (2005) UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol 166:1063–1068

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Singh R, Yadav A, Giri D, Singh P, Pandey KD (2016) Isolation and characterization of bacterial endophytes of Curcuma longa L. 3 Biotech 6:60

    Article  PubMed  PubMed Central  Google Scholar 

  • Kusari P, Kusari S, Spiteller M, Kayser O (2013) Endophytic fungi harbored in Cannabis sativa L.: diversity and potential as biocontrol agents against host plant-specific phytopathogens. Fungal Divers 60:137–151

    Article  Google Scholar 

  • Lata H, Li X, Silva B, Moraes R, Halda-Alija L (2006) Identification of IAA-producing endophytic bacteria from micropropagated Echinacea plants using 16S rRNA sequencing. Plant Cell Tissue Organ Cult 85:353–359

    Article  CAS  Google Scholar 

  • Leff JW, Del Tredici P, Friedman WE, Fierer N (2015) Spatial structuring of bacterial communities within individual Ginkgo biloba trees. Environ Microbiol 17:2352–2361

    Article  PubMed  Google Scholar 

  • Lefor MW (1999) Hydrophyte. In: Knödel, Klaus, Lange, Gerhard, Voigt, Hans-Jürgen Environmental Geology. Springer, Dordrecht, pp 338–338. https://doi.org/10.1007/1-4020-4494-1_184

    Chapter  Google Scholar 

  • Li H, Xiao J, Gao Y-Q, Tang JJ, Zhang A-L, Gao J-M (2014) Chaetoglobosins from Chaetomium globosum, an endophytic fungus in Ginkgo biloba, and their phytotoxic and cytotoxic activities. J Agric Food Chem 62:3734–3741

    Article  CAS  PubMed  Google Scholar 

  • Li J, Zhao GZ, Chen HH, Wang HB, Qin S, Zhu WY et al (2008) Antitumour and antimicrobial activities of endophytic streptomycetes from pharmaceutical plants in rainforest. Lett Appl Microbiol 47:574–580

    Article  CAS  PubMed  Google Scholar 

  • Li RW, Myers SP, Leach DN, Lin GD, Leach G (2003) A cross-cultural study: anti-inflammatory activity of Australian and Chinese plants. J Ethnopharmacol 85:25–32

    Article  PubMed  Google Scholar 

  • Liu W, Zhou Z, Liu Y, Hu X, Guo Y, Li J (2017) Application of high-throughput internal transcribed spacer rRNA metagenomics analysis in deciphering endophytic fungi diversity of Dendrobium Officinale. J Biobaased Mater Bioenergy 11:106–118. https://doi.org/10.1166/jbmb.2017.1647

    Article  CAS  Google Scholar 

  • Liu X, Dong M, Chen X, Jiang M, Lv X, Yan G (2007) Antioxidant activity and phenolics of an endophytic Xylaria sp. from Ginkgo biloba. Food Chem 105:548–554

    Article  CAS  Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Ann Rev Microbiol 63:541–556

    Article  CAS  Google Scholar 

  • Machavariani NG, Ivankova TD, Sineva ON, Terekhova LP (2014) Isolation of endophytic actinomycetes from medicinal plants of the Moscow region, Russia. World Appl Sci J 30:1599–1604

    Google Scholar 

  • MacNeil I, Tiong C, Minor C, August P, Grossman T, Loiacono K et al (2001) Expression and isolation of antimicrobial small molecules from soil DNA libraries. J Mol Microbiol Biotechnol 3:301–308

    CAS  PubMed  Google Scholar 

  • Madhavan A, Sindhu R, Parameswaran B, Sukumaran RK, Pandey A (2017) Metagenome analysis: a powerful tool for enzyme bioprospecting. Appl Biochem Biotechnol 183:636–651

    Article  CAS  PubMed  Google Scholar 

  • Maggi F (2019) Dandelion. In: Nabavi SM, Silva AS (eds) Nonvitamin and nonmineral nutritional supplements. Elsevier, San Diego, pp 203–204. https://doi.org/10.1016/C2016-0-03546-5

    Chapter  Google Scholar 

  • Majernı́k A, Gottschalk G, Daniel R (2001) Screening of environmental DNA libraries for the presence of genes conferring Na+ (Li+)/H+ antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183:6645–6653

    Article  PubMed  PubMed Central  Google Scholar 

  • Marchesi JR, Weightman AJ (2003) Comparing the dehalogenase gene pool in cultivated α-halocarboxylic acid-degrading bacteria with the environmental metagene pool. Appl Environ Microbiol 69:4375–4382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marco D (2010) Metagenomics. Theory, methods and applications. Caister Academic Press, Norfolk

    Google Scholar 

  • Martinez M, Poirrier P, Chamy R, Prüfer D, Schulze-Gronover C, Jorquera L et al (2015) Taraxacum officinale and related species—an ethnopharmacological review and its potential as a commercial medicinal plant. J Ethnopharmacol 169:244–262

    Article  CAS  PubMed  Google Scholar 

  • McKernan K, Spangler J, Helbert Y, Lynch RC, Devitt-Lee A, Zhang L et al (2016) Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests. F1000Res 5:2471–2471. https://doi.org/10.12688/f1000research.9662.1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mehmood Z, Khan MS, Qais FA, Ahmad I (2019) Herb and modern drug interactions: efficacy, quality, and safety aspects. In: New look to phytomedicine. Elsevier, London, pp 503–520

    Google Scholar 

  • Melcher U, Verma R, Schneider WL (2014) Metagenomic search strategies for interactions among plants and multiple microbes. Front Plant Sci 5:268

    Article  PubMed  PubMed Central  Google Scholar 

  • Mengoni A, Maida I, Chiellini C, Emiliani G, Mocali S, Fabiani A et al (2014) Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs. Res Microbiol 165:686–694

    Article  CAS  PubMed  Google Scholar 

  • Mielnik M, Olsen E, Vogt G, Adeline D, Skrede G (2006) Grape seed extract as antioxidant in cooked, cold stored Turkey meat. LWT-Food Sci Technol 39:191–198

    Article  CAS  Google Scholar 

  • Miller KI, Ingrey SD, Alvin A, Sze MYD, Roufogalis BD, Neilan BA (2010) Endophytes and the microbial genetics of traditional medicines. Microbiol Aust 31:60–63

    Article  Google Scholar 

  • Miller KI, Qing C, Sze DMY, Neilan BA (2012b) Investigation of the biosynthetic potential of endophytes in traditional Chinese anticancer herbs. PLoS One 7(5):e35953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller KI, Qing C, Sze DM-Y, Roufogalis BD, Neilan BA (2012a) Culturable endophytes of medicinal plants and the genetic basis for their bioactivity. Microb Ecol 64:431–449

    Article  PubMed  Google Scholar 

  • Mohamad OAA, Ma J-B, Liu Y-H, Li L, Hatab S, Li W-J (2019) Medicinal plant-associated microbes as a source of protection and production of crops. In: Egamberdieva D, Tiezzi A (eds) Medically important plant biomes: source of secondary metabolites. Springer, Singapore, pp 239–263. https://doi.org/10.1007/978-981-13-9566-6

    Chapter  Google Scholar 

  • Moreno DA, Ilic N, Poulev A, Brasaemle DL, Fried SK, Raskin I (2003) Inhibitory effects of grape seed extract on lipases. Nutrition 19:876–879

    Article  CAS  PubMed  Google Scholar 

  • Morgan XC, Huttenhower C (2012) Chapter 12: Human microbiome analysis. PLoS Comput Biol 8:e1002808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muir AD, Westcott ND (2003) Flax: the genus Linum. CRC Press, Boca Raton, FL

    Book  Google Scholar 

  • Munir R, Semmar N, Farman M, Ahmad NS (2017) An updated review on pharmacological activities and phytochemical constituents of evening primrose (genus Oenothera). Asian Pac J Trop Biomed 7:1046–1054

    Article  Google Scholar 

  • Murugappan R, Begum SB, Roobia RR (2013) Symbiotic influence of endophytic Bacillus pumilus on growth promotion and probiotic potential of the medicinal plant Ocimum sanctum. Symbiosis 60:91–99

    Article  Google Scholar 

  • Nalini M, Prakash H (2017) Diversity and bioprospecting of actinomycete endophytes from the medicinal plants. Lett Appl Microbiol 64:261–270

    Article  CAS  PubMed  Google Scholar 

  • Newman DJ, Cragg GM (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 75:311–335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ni J, Dong L, Jiang Z, Yang X, Chen Z, Wu Y et al (2018a) Comprehensive transcriptome analysis and flavonoid profiling of ginkgo leaves reveals flavonoid content alterations in day–night cycles. PLoS One 13(3):e0193897

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ni J, Dong L, Jiang Z, Yang X, Sun Z, Li J et al (2018b) Salicylic acid-induced flavonoid accumulation in Ginkgo biloba leaves is dependent on red and far-red light. Ind Crop Prod 118:102–110

    Article  CAS  Google Scholar 

  • Ni J, Hao J, Jiang Z, Zhan X, Dong L, Yang X et al (2017) NaCl induces flavonoid biosynthesis through a putative novel pathway in post-harvest Ginkgo leaves. Front Plant Sci 8:920

    Article  PubMed  PubMed Central  Google Scholar 

  • Nikfarjam M, Bahmani M, Heidari-Soureshjani S (2016) Phytotherapy for depression: a review of the most important medicinal plants of flora of Iran effective on depression. J Chem Pharm Sci 9:1242–1247

    Google Scholar 

  • Nikolouli K, Mossialos D (2012) Bioactive compounds synthesized by non-ribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics. Biotechnol Lett 34:1393–1403

    Article  CAS  PubMed  Google Scholar 

  • Nuttall S, Kendall M, Bombardelli E, Morazzoni P (1998) An evaluation of the antioxidant activity of a standardized grape seed extract, Leucoselect®. J Clin Pharm Ther 23:385–389

    Article  CAS  PubMed  Google Scholar 

  • Opelt K, Berg G (2004) Diversity and antagonistic potential of bacteria associated with bryophytes from nutrient-poor habitats of the Baltic Sea Coast. Appl Environ Microbiol 70:6569–6579

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pandey G, Dorrian SJ, Russell RJ, Oakeshott JG (2009) Biotransformation of the neonicotinoid insecticides imidacloprid and thiamethoxam by Pseudomonas sp. 1G. Bioch Biophys Res Commun 380:710–714

    Article  CAS  Google Scholar 

  • Park CM, Park JY, Noh KH, Shin JH, Song YS (2011) Taraxacum officinale Weber extracts inhibit LPS-induced oxidative stress and nitric oxide production via the NF-κB modulation in RAW 264.7 cells. J Ethnopharmacol 133:834–842

    Article  PubMed  Google Scholar 

  • Paul NC, Kim WK, Woo SK, Park MS, Yu SH (2006) Diversity of endophytic fungi associated with Taraxacum coreanum and their antifungal activity. Mycobiology 34:185–190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pawlik M, Cania B, Thijs S, Vangronsveld J, Piotrowska-Seget Z (2017) Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site. Environ Sci Pollut Res Int 24:19640–19652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pereira P, Ibáñez F, Rosenblueth M, Etcheverry M, Martínez-Romero E (2011) Analysis of the bacterial diversity associated with the roots of maize (Zea mays L.) through culture-dependent and culture-independent methods. ISRN Ecol 2011:938546

    Google Scholar 

  • Piccolo S, Alfonzo A, Burruano S, Moschetti G (2016) Detection of bacterial endophytes in Vitis vinifera L. and antibiotic activity against grapevine fungal pathogens. In: Biocontrol of major grapevine diseases: leading research. CABI, Boston, pp 182–190

    Chapter  Google Scholar 

  • Porras-Alfaro A, Raghavan S, Garcia M, Sinsabaugh RL, Natvig DO, Lowrey TK (2014) Endophytic fungal symbionts associated with gypsophilous plants. Botany 92:295–301

    Article  CAS  Google Scholar 

  • Prakash O, Sharma R, Rahi P, Karthikeyan N (2015) Role of microorganisms in plant nutrition and health. In: Nutrient use efficiency: from basics to advances. Springer, New Delhi, pp 125–161

    Chapter  Google Scholar 

  • Primanita M, Wahyudi A, Lestari Y (2015) 16S rRNA-based metagenomic analysis of endophytic Actinomycetes diversity from Tinospora crispa L. Miers. Microbiol Indones 9:4

    Article  Google Scholar 

  • Qi X, Wang E, Xing M, Zhao W, Chen X (2012) Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia. World J Microbiol Biotechnol 28:2257–2265

    Article  PubMed  Google Scholar 

  • Qin J-C, Zhang Y-M, Gao J-M, Bai M-S, Yang S-X, Laatsch H et al (2009) Bioactive metabolites produced by Chaetomium globosum, an endophytic fungus isolated from Ginkgo biloba. Bioorg Med Chem Lett 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Qin S, Chen HH, Zhao GZ, Li J, Zhu WY, Xu LH et al (2012) Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austro yunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods. Environ Microbiol Rep 4:522–531

    Article  PubMed  Google Scholar 

  • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR et al (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raaijmakers JM, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol 50:403–424

    Article  CAS  PubMed  Google Scholar 

  • Rachman F, Septiana E, Lekatompessy SJ, Widowati T, Sukiman HI, Simanjuntak P (2015) Screening for endophytic fungi from turmeric plant (Curcuma longa L.) of Sukabumi and Cibinong with potency as antioxidant compounds producer. Pak J Biol Sci 18:42

    PubMed  CAS  Google Scholar 

  • Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL (2016) Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun 469:967–977

    Article  CAS  PubMed  Google Scholar 

  • Raynaud X, Nunan N (2014) Spatial ecology of bacteria at the microscale in soil. PLoS One 9:e87217

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14:435–443

    Article  PubMed  Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    Article  CAS  PubMed  Google Scholar 

  • Riess K, Oberwinkler F, Bauer R, Garnica S (2014) Communities of endophytic sebacinales associated with roots of herbaceous plants in agricultural and grassland ecosystems are dominated by Serendipita herbamans sp. nov. PLoS One 9:e94676–e94676

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rimbach G, Gohil K, Matsugo S, Moini H, Saliou C, Virgili F et al (2001) Induction of glutathione synthesis in human keratinocytes by Ginkgo biloba extract (EGb761). Biofactors 15:39–52

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118

    Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rondot Y, Reineke A (2018) Endophytic Beauveria bassiana in grapevine Vitis vinifera (L.) reduces infestation with piercing-sucking insects. Biol Control 116:82–89

    Article  Google Scholar 

  • Rosa LH, Tabanca N, Techen N, Wedge DE, Pan Z, Bernier UR et al (2012) Diversity and biological activities of endophytic fungi associated with micropropagated medicinal plant Echinacea purpurea (L.) Moench. Am J Plant Sci 3:1105–1114

    Article  Google Scholar 

  • Rybakova D, Cernava T, Köberl M, Liebminger S, Etemadi M, Berg G (2016) Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus. Plant Soil 405:125–140

    Article  CAS  Google Scholar 

  • Saito M, Hosoyama H, Ariga T, Kataoka S, Yamaji N (1998) Antiulcer activity of grape seed extract and procyanidins. J Agric Food Chem 46:1460–1464

    Article  CAS  Google Scholar 

  • Santosa DA (2001) Rapid extraction and purification of environmental DNA for molecular cloning applications and molecular diversity studies. Mol Biotechnol 17:59–64

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmeisser C, Stöckigt C, Raasch C, Wingender J, Timmis K, Wenderoth D et al (2003) Metagenome survey of biofilms in drinking-water networks. Appl Environ Microbiol 69:7298–7309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 69:4927–4934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shah N, Tang H, Doak TG, Ye Y (2011) Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. In: Altman RS (ed) Biocomputing 2011. World Scientific, Kohala Coast, HI, pp 165–176. https://doi.org/10.1142/8021

    Chapter  Google Scholar 

  • Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front Plant Sci 5:209

    Article  PubMed  PubMed Central  Google Scholar 

  • Shi Y, Lou K, Li C (2010) Growth and photosynthetic efficiency promotion of sugar beet (Beta vulgaris L.) by endophytic bacteria. Photosynth Res 105:5–13

    Article  CAS  PubMed  Google Scholar 

  • Shidoji Y, Ogawa H (2004) Natural occurrence of cancer-preventive geranylgeranoic acid in medicinal herbs. J Lipid Res 45:1092–1103

    Article  CAS  PubMed  Google Scholar 

  • Singh D, Rathod V, Ninganagouda S, Hiremath J, Singh AK, Mathew J (2014) Optimization and characterization of silver nanoparticle by endophytic fungi Penicillium sp. isolated from Curcuma longa (turmeric) and application studies against MDRE. coli and S. aureus. Bioinorg Chem Appl 2014:408021

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh G, Mukerji KG (2006) Root exudates as determinant of rhizospheric microbial biodiversity. In: Mukerji KG, Manoharachary C, Singh J (eds) Microbial activity in the rhizosphere. Springer, Berlin, Heidelberg, pp 39–53. https://doi.org/10.1007/3-540-29420-1

    Chapter  Google Scholar 

  • Singh O, Khanam Z, Misra N, Srivastava MK (2011) Chamomile (Matricaria chamomilla L.): an overview. Pharmacogn Rev 5:82–95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stanford QH, Moran W (1978) Geography: a study of its physical elements. Oxford University Press, Toronto

    Google Scholar 

  • Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178:591–599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Streit W, Entcheva P (2003) Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production. Appl Microbiol Biotechnol 61:21–31

    Article  CAS  PubMed  Google Scholar 

  • Streit WR, Schmitz RA (2004) Metagenomics—the key to the uncultured microbes. Curr Opin Microbiol 7:492–498

    Article  CAS  PubMed  Google Scholar 

  • Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268

    Article  CAS  PubMed  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis. Microb Inform Exp 2(1):3

    Article  PubMed  PubMed Central  Google Scholar 

  • Todd DA, Gulledge TV, Britton ER, Oberhofer M, Leyte-Lugo M, Moody AN et al (2015) Ethanolic Echinacea purpurea extracts contain a mixture of cytokine-suppressive and cytokine-inducing compounds, including some that originate from endophytic bacteria. PLoS One 10(5):e0124276

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Triantafyllidi A, Xanthos T, Papalois A, Triantafillidis JK (2015) Herbal and plant therapy in patients with inflammatory bowel disease. Ann Gastroenterol 28(2):210–220

    PubMed  PubMed Central  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al (2005) Comparative metagenomics of microbial communities. Science 308:554

    Article  CAS  PubMed  Google Scholar 

  • Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep 7:40–50

    Article  Google Scholar 

  • Tsai Y-L, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58:2292–2295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  CAS  PubMed  Google Scholar 

  • Vasar M, Andreson R, Davison J, Jairus T, Moora M, Remm M et al (2017) Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza 27:761–773

    Article  CAS  PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  CAS  PubMed  Google Scholar 

  • Vieites JM, Guazzaroni M-E, Beloqui A, Golyshin PN, Ferrer M (2008) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33:236–255

    Article  PubMed  CAS  Google Scholar 

  • Wang G-Y-S, Graziani E, Waters B, Pan W, Li X, McDermott J et al (2000) Novel natural products from soil DNA libraries in a streptomycete host. Org Lett 2:2401–2404

    Google Scholar 

  • Wei-nan L (2008) Primary studies on isolation and detection of three strains endophytic fungi from Dandelion (Taraxacum mongolicum Hand-Mazz) and its antimicrobial activity of poultry pathogenic. J Anhui Agric Sci 22:9540–9542

    Google Scholar 

  • Weinstock GM (2012) Genomic approaches to studying the human microbiota. Nature 489:250–256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weizman Z, Alkrinawi S, Goldfarb D, Bitran C (1993) Efficacy of herbal tea preparation in infantile colic. J Pediatr 122:650–652

    Article  CAS  PubMed  Google Scholar 

  • Wijesinghe M, Germida J, Walley F (2015) Root-associated bacterial communities in flax (Linum usitatissimum) and their response to arbuscular mycorrhizal (AM) inoculation. In: Soils and crops workshop. https://harvest.usask.ca/bitstream/handle/10388/8902/M.%20Wijesingh%20et%20al.,%202015.pdf?sequence=1

  • Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA et al (2014) Understanding cultivar-specificity and soil determinants of the Cannabis microbiome. PLoS One 9(6):e99641

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yan X, Tang X-X, Chen L, Yi Z-W, Fang M-J, Wu Z et al (2014) Two new cytotoxic indole alkaloids from a deep-sea sediment derived metagenomic clone. Mar Drugs 12:2156–2163

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang J, Kloepper JW, Ryu C-M (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1–4

    Article  CAS  PubMed  Google Scholar 

  • Yang M-Z, Ma M-D, Yuan M-Q, Huang Z-Y, Yang W-X, Zhang H-B et al (2016) Fungal endophytes as a metabolic fine-tuning regulator for wine grape. PLoS One 11(9):e0163186

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ye Y, Xiao Y, Ma L, Li H, Xie Z, Wang M et al (2013) Flavipin in Chaetomium globosum CDW7, an endophytic fungus from Ginkgo biloba, contributes to antioxidant activity. Appl Microbiol Biotechnol 97:7131–7139

    Article  CAS  PubMed  Google Scholar 

  • Yuan Y, Tian J-M, Xiao J, Shao Q, Gao J-M (2014) Bioactive metabolites isolated from Penicillium sp. YY-20, the endophytic fungus from Ginkgo biloba. Nat Prod Res 28:278–281

    Article  CAS  PubMed  Google Scholar 

  • Yuan Z, Druzhinina IS, Labbé J, Redman R, Qin Y, Rodriguez R et al (2016) Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity. Sci Rep 6:1–13

    CAS  Google Scholar 

  • Zarraonaindia I, Smith DP, Gilbert JA (2013) Beyond the genome: community-level analysis of the microbial world. Biol Philos 28:261–282

    Article  PubMed  Google Scholar 

  • Zhang H, Xiong Y, Zhao H, Yi Y, Zhang C, Yu C et al (2013) An antimicrobial compound from the endophytic fungus Phoma sp. isolated from the medicinal plant Taraxacum mongolicum. J Taiwan Inst Chem E 44:177–181

    Article  CAS  Google Scholar 

  • Zhang W, Wei W, Shi J, Chen C, Zhao G, Jiao R et al (2015) Natural phenolic metabolites from endophytic Aspergillus sp. IFB-YXS with antimicrobial activity. Bioorg Med Chem Lett 25:2698–2701

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Guo L, He H, Liu C, Zhang Y, Li C et al (2014a) Micromonospora taraxaci sp. nov., a novel endophytic actinomycete isolated from dandelion root (Taraxacum mongolicum Hand.-Mazz.). Antonievan Leeuwenhoek 106:667–674

    Article  CAS  Google Scholar 

  • Zhao K, Penttinen P, Chen Q, Guan T, Lindström K, Ao X et al (2012) The rhizospheres of traditional medicinal plants in Panxi, China, host a diverse selection of actinobacteria with antimicrobial properties. Appl Microbiol Biotechnol 94:1321–1335

    Article  CAS  PubMed  Google Scholar 

  • Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J et al (2011) The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi plateau, China. Curr Microbiol 62:182–190

    Article  CAS  PubMed  Google Scholar 

  • Zhao X, Song P, Feng L, Hong W, WuC YR et al (2014b) Isolation and identification of a growth-promoting and aluminum-resistant endophytic bacterium from tea tree. Acta Agric Univ Jiangxiensis 36:407–412

    CAS  Google Scholar 

  • Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6:e02288–e02214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Z-Y (2009) An overview of fossil Ginkgoales. Palaeoworld 18:1–22

    Google Scholar 

  • Zubek S, Błaszkowski J (2009) Medicinal plants as hosts of arbuscular mycorrhizal fungi and dark septate endophytes. Phytochem Rev 8:571

    Article  CAS  Google Scholar 

  • Zubek S, Stefanowicz AM, Błaszkowski J, Niklińska M, Seidler-Łożykowska K (2012) Arbuscular mycorrhizal fungi and soil microbial communities under contrasting fertilization of three medicinal plants. Appl Soil Ecol 59:106–115

    Article  Google Scholar 

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Saleem, H., Mohsin, H., Asif, A., Tanvir, R., Rehman, Y. (2021). Metagenomics in Deciphering Microbial Communities Associated with Medicinal Plants. In: Yadav, A.N., Singh, J., Singh, C., Yadav, N. (eds) Current Trends in Microbial Biotechnology for Sustainable Agriculture . Environmental and Microbial Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-15-6949-4_3

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