Hardoim, P. R. et al. The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).
Google Scholar
Zhang, H. W., Song, Y. C. & Tan, R. X. Biology and chemistry of endophytes. Nat. Prod. Rep. 23, 753–771 (2006).
Google Scholar
Köberl, M., Schmidt, R., Ramadan, E. M., Bauer, R. & Berg, G. The microbiome of medicinal plants: Diversity and importance for plant growth, quality and health. Front. Microbiol. 4, 400 (2013).
Google Scholar
Soto, M. J., Domínguez-Ferreras, A., Pérez-Mendoza, D., Sanjuán, J. & Olivares, J. Mutualism versus pathogenesis: The give-and-take in plant–bacteria interactions. Cell. Microbiol. 11, 381–388 (2009).
Google Scholar
Leff, J. W., Del Tredici, P., Friedman, W. E. & Fierer, N. Spatial structuring of bacterial communities within individual Ginkgo biloba trees. Environ. Microbiol. 17, 2352–2361. https://doi.org/10.1111/1462-2920.12695 (2015).
Google Scholar
Berg, G., Rybakova, D., Grube, M. & Köberl, M. The plant microbiome explored: Implications for experimental botany. J. Exp. Bot. 67, 995–1002. https://doi.org/10.1093/jxb/erv466 (2016).
Google Scholar
Cregger, M. A. et al. The Populus holobiont: Dissecting the effects of plant niches and genotype on the microbiome. Microbiome 6, 31. https://doi.org/10.1186/s40168-018-0413-8 (2018).
Google Scholar
Wang, Y., Liu, Y., Wu, Q., Yao, X. & Cheng, Z. Rapid and sensitive determination of major active ingredients and toxic components in Ginkgo biloba leaves extract (EGb 761) by a validated UPLC–MS-MS method. J. Chromatogr. Sci. 55, 459–464. https://doi.org/10.1093/chromsci/bmw206 (2017).
Google Scholar
Mesquita, T. R. R. et al. Cardioprotective action of Ginkgo biloba extract against sustained β-adrenergic stimulation occurs via activation of M2/NO pathway. Front. Pharmacol. 8, 220. https://doi.org/10.3389/fphar.2017.00220 (2017).
Google Scholar
Woelk, H., Arnoldt, K. H., Kieser, M. & Hoerr, R. Ginkgo biloba special extract EGb 761® in generalized anxiety disorder and adjustment disorder with anxious mood: A randomized, double-blind, placebo-controlled trial. J. Psychiatr. Res. 41, 472–480. https://doi.org/10.1016/j.jpsychires.2006.05.004 (2007).
Google Scholar
Rojas, P., Montes, P., Rojas, C., Serrano-Garcia, N. & Rojas-Castaneda, J. C. Effect of a phytopharmaceutical medicine, Ginko biloba extract 761, in an animal model of Parkinson’s disease: Therapeutic perspectives. Nutrition 28, 1081–1088. https://doi.org/10.1016/j.nut.2012.03.007 (2012).
Google Scholar
Tan, M.-S. et al. Efficacy and adverse effects of Ginkgo biloba for cognitive impairment and dementia: A systematic review and meta-analysis. J. Alzheimer’s Dis. 43, 589–603 (2015).
Google Scholar
Kennedy, D. O., Jackson, P. A., Haskell, C. F. & Scholey, A. B. Modulation of cognitive performance following single doses of 120 mg Ginkgo biloba extract administered to healthy young volunteers. Hum. Psychopharm. Clin. 22, 559–566. https://doi.org/10.1002/hup.885 (2007).
Google Scholar
Yao, Z.-X., Han, Z., Drieu, K. & Papadopoulos, V. Ginkgo biloba extract (Egb 761) inhibits β-amyloid production by lowering free cholesterol levels. J. Nutr. Biochem. 15, 749–756. https://doi.org/10.1016/j.jnutbio.2004.06.008 (2004).
Google Scholar
Chen, D., Sun, S., Cai, D. & Kong, G. Induction of mitochondrial-dependent apoptosis in T24 cells by a selenium (Se)-containing polysaccharide from Ginkgo biloba L. leaves. Int. J. Biol. Macromol. 101, 126–130 (2017).
Google Scholar
Hamdoun, S. & Efferth, T. Ginkgolic acids inhibit migration in breast cancer cells by inhibition of NEMO sumoylation and NF-κB activity. Oncotarget 8, 35103 (2017).
Google Scholar
Fei, R. et al. Purified polysaccharide from Ginkgo biloba leaves inhibits P-selectin-mediated leucocyte adhesion and inflammation. Acta Pharmacol. Sin. 29, 499–506 (2008).
Google Scholar
Mahadevan, S. & Park, Y. Multifaceted therapeutic benefits of Ginkgo biloba L.: Chemistry, efficacy, safety, and uses. J. Food Sci. 73, R14–R19 (2008).
Google Scholar
Zimmermann, M., Colciaghi, F., Cattabeni, F. & Di Luca, M. Ginkgo biloba extract: From molecular mechanisms to the treatment of Alzheimer’s disease. Cell. Mol. Biol. 48, 613–623 (2002).
Google Scholar
van Beek, T. A. & Montoro, P. Chemical analysis and quality control of Ginkgo biloba leaves, extracts, and phytopharmaceuticals. J. Chromatogr. A 1216, 2002–2032 (2009).
Google Scholar
Lu, X. et al. Combining metabolic profiling and gene expression analysis to reveal the biosynthesis site and transport of ginkgolides in Ginkgo biloba L.. Front. Plant Sci. 8, 872. https://doi.org/10.3389/fpls.2017.00872 (2017).
Google Scholar
Mancuso, C. & Santangelo, R. Panax ginseng and Panax quinquefolius: From pharmacology to toxicology. Food Chem. Toxicol. 107, 362–372 (2017).
Google Scholar
Karmazyn, M., Moey, M. & Gan, X. T. Therapeutic potential of Ginseng in the management of cardiovascular disorders. Drugs 71, 1989–2008. https://doi.org/10.2165/11594300-000000000-00000 (2011).
Google Scholar
Predy, G. N. et al. Efficacy of an extract of North American ginseng containing poly-furanosyl-pyranosyl-saccharides for preventing upper respiratory tract infections: A randomized controlled trial. Can. Med. Assoc. J. 173, 1043–1048. https://doi.org/10.1503/cmaj.1041470 (2005).
Google Scholar
Yuan, C.-S., Wang, C.-Z., Wicks, S. M. & Qi, L.-W. Chemical and pharmacological studies of saponins with a focus on American ginseng. J. Ginseng Res. 34, 160 (2010).
Google Scholar
Yang, W.-Z., Hu, Y., Wu, W.-Y., Ye, M. & Guo, D.-A. Saponins in the genus Panax L. (Araliaceae): A systematic review of their chemical diversity. Phytochemistry 106, 7–24. https://doi.org/10.1016/j.phytochem.2014.07.012 (2014).
Google Scholar
Solieri, L., Dakal, T. C. & Giudici, P. Next-generation sequencing and its potential impact on food microbial genomics. Ann. Microbiol. 63, 21–37 (2013).
Google Scholar
Ercolini, D. High-throughput sequencing and metagenomics: Moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 79, 3148–3155 (2013).
Google Scholar
Metzker, M. L. Sequencing technologies—the next generation. Nat. Rev. Genet. 11, 31 (2010).
Google Scholar
Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: Genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).
Google Scholar
Robinson, R. J. et al. Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant Soil 405, 381–396. https://doi.org/10.1007/s11104-015-2495-4 (2016).
Google Scholar
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol 10, 828–840. https://doi.org/10.1038/nrmicro2910 (2012).
Google Scholar
Dasgupta, M. G. et al. Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance. Microbiol. Res. 241, 126579. https://doi.org/10.1016/j.micres.2020.126579 (2020).
Google Scholar
Knief, C. et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6, 1378–1390. https://doi.org/10.1038/ismej.2011.192 (2012).
Google Scholar
Idris, R., Trifonova, R., Puschenreiter, M., Wenzel, W. W. & Sessitsch, A. Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense. Appl. Environ. Microbiol. 70, 2667–2677. https://doi.org/10.1128/aem.70.5.2667-2677.2004 (2004).
Google Scholar
Rastogi, G. et al. Leaf microbiota in an agroecosystem: Spatiotemporal variation in bacterial community composition on field-grown lettuce. Isme J. 6, 1812–1822. https://doi.org/10.1038/ismej.2012.32 (2012).
Google Scholar
Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95. https://doi.org/10.1038/nature11336 (2012).
Google Scholar
Kielak, A. M., Cipriano, M. A. P. & Kuramae, E. E. Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Arch. Microbiol. 198, 987–993. https://doi.org/10.1007/s00203-016-1260-2 (2016).
Google Scholar
Fuerst, J. A. & Sagulenko, E. Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function. Nat. Rev. Microbiol 9, 403–413. https://doi.org/10.1038/nrmicro2578 (2011).
Google Scholar
Wiegand, S., Jogler, M. & Jogler, C. On the maverick planctomycetes. FEMS Microbiol. Rev. 42, 739–760. https://doi.org/10.1093/femsre/fuy029 (2018).
Google Scholar
Kim, H. et al. High population of Sphingomonas species on plant surface. J. Appl. Microbiol. 85, 731–736. https://doi.org/10.1111/j.1365-2672.1998.00586.x (1998).
Google Scholar
Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. 106, 16428–16433. https://doi.org/10.1073/pnas.0905240106 (2009).
Google Scholar
Kampfer, P., Busse, H. J., McInroy, J. A. & Glaeser, S. P. Sphingomonas zeae sp nov., isolated from the stem of Zea mays. Int. J. Syst. Evol. Microbiol. 65, 2542–2548. https://doi.org/10.1099/ijs.0.000298 (2015).
Google Scholar
Xie, C.-H. & Yokota, A. Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa. Int. J. Syst. Evol. Microbiol. 56, 889–893. https://doi.org/10.1099/ijs.0.64056-0 (2006).
Google Scholar
Videira, S. S., De Araujo, J. L. S., Da Silva Rodrigues, L., Baldani, V. L. D. & Baldani, J. I. Occurrence and diversity of nitrogen-fixing Sphingomonas bacteria associated with rice plants grown in Brazil. FEMS Microbiol. Lett. 293, 11–19. https://doi.org/10.1111/j.1574-6968.2008.01475.x (2009).
Google Scholar
Innerebner, G., Knief, C. & Vorholt, J. A. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77, 3202–3210. https://doi.org/10.1128/aem.00133-11 (2011).
Google Scholar
Khan, A. L. et al. Bacterial endophyte Sphingomonas sp LK11 produces gibberellins and IAA and promotes tomato plant growth. J. Microbiol. 52, 689–695. https://doi.org/10.1007/s12275-014-4002-7 (2014).
Google Scholar
Asaf, S., Numan, M., Khan, A. L. & Al-Harrasi, A. Sphingomonas: From diversity and genomics to functional role in environmental remediation and plant growth. Crit. Rev. Biotechnol. 40, 138–152. https://doi.org/10.1080/07388551.2019.1709793 (2020).
Google Scholar
Ali, A. et al. Biotransformation of benzoin by Sphingomonas sp. LK11 and ameliorative effects on growth of Cucumis sativus. Arch. Microbiol. 201, 591–601. https://doi.org/10.1007/s00203-019-01623-1 (2019).
Google Scholar
Chhetri, G., Kim, J., Kim, I., Kim, H. & Seo, T. Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int. J. Syst. Evol. Microbiol. 70, 3724–3730. https://doi.org/10.1099/ijsem.0.004226 (2020).
Google Scholar
Dai, Y. et al. Wheat-associated microbiota and their correlation with stripe rust reaction. J. Appl. Microbiol. 128, 544–555. https://doi.org/10.1111/jam.14486 (2020).
Google Scholar
Buczolits, S. et al. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp nov. Int. J. Syst. Evol. Microbiol. 52, 445–456. https://doi.org/10.1099/00207713-52-2-445 (2002).
Google Scholar
Su, S. Y. et al. Hymenobacter kanuolensis sp nov., a novel radiation-resistant bacterium. Int. J. Syst. Evol. Microbiol. 64, 2108–2112. https://doi.org/10.1099/ijs.0.051680-0 (2014).
Google Scholar
Dimitrijevic, S. et al. Plant growth-promoting bacteria elevate the nutritional and functional properties of black cumin and flaxseed fixed oil. J. Sci. Food Agric. 98, 1584–1590. https://doi.org/10.1002/jsfa.8631 (2018).
Google Scholar
Yang, R. X., Fan, X. J., Cai, X. Q. & Hu, F. P. The inhibitory mechanisms by mixtures of two endophytic bacterial strains isolated from Ginkgo biloba against pepper phytophthora blight. Biol. Control 85, 59–67. https://doi.org/10.1016/j.biocontrol.2014.09.013 (2015).
Google Scholar
Islam, M. N., Choi, J. & Baek, K. H. Control of foodborne pathogenic bacteria by endophytic bacteria isolated from Ginkgo biloba L. Foodborne Pathog. Dis. 16, 661–670. https://doi.org/10.1089/fpd.2018.2496 (2019).
Google Scholar
Datta, S. et al. Endophytic bacteria in xenobiotic degradation In Microbial endophytes (eds. Kumar, A. & Singh, V. K.) 125–156 (Woodhead Publishing, 2020).
Newmaster, S. G., Grguric, M., Shanmughanandhan, D., Ramalingam, S. & Ragupathy, S. DNA barcoding detects contamination and substitution in North American herbal products. BMC Med. 11, 222 (2013).
Google Scholar
Gao, Z. et al. Derivative technology of DNA barcoding (Nucleotide Signature and SNP Double Peak methods) detects adulterants and substitution in Chinese patent medicines. Sci. Rep. 7, 5858. https://doi.org/10.1038/s41598-017-05892-y (2017).
Google Scholar
Ichim, M. C. & de Boer, H. J. A review of authenticity and authentication of commercial ginseng herbal medicines and food supplements. Front. Pharmacol. https://doi.org/10.3389/fphar.2020.612071 (2021).
Google Scholar
Dhivya, S. et al. Validated identity test method for Ginkgo biloba NHPs using DNA-based species-specific hydrolysis PCR probe. J. AOAC Int. 102, 1779–1786. https://doi.org/10.5740/jaoacint.18-0319 (2019).
Google Scholar
Singh, A., Bajpai, V., Srivastava, M., Arya, K. R. & Kumar, B. Rapid screening and distribution of bioactive compounds in different parts of Berberis petiolaris using direct analysis in real time mass spectrometry. J. Pharm. Anal. 5, 332–335 (2015).
Google Scholar
Kim, H. K., Choi, Y. H. & Verpoorte, R. NMR-based metabolomic analysis of plants. Nat. Protoc. 5, 536 (2010).
Google Scholar
Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).
Google Scholar
Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. & Dangl, J. L. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10, 999–1002 (2013).
Google Scholar
Illumina. 16S Metagenomic Sequencing Library Preparation. Preparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System (Part 15044223 Rev. B). (2013), Accessed 07-2017, available at https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf.
Chong, J., Liu, P., Zhou, G. & Xia, J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat. Protoc. 15, 799–821. https://doi.org/10.1038/s41596-019-0264-1 (2020).
Google Scholar
Dhariwal, A. et al. MicrobiomeAnalyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 45, W180–W188. https://doi.org/10.1093/nar/gkx295 (2017).
Google Scholar
Hulsen, T., de Vlieg, J. & Alkema, W. BioVenn—A web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genom. 9, 488. https://doi.org/10.1186/1471-2164-9-488 (2008).
Google Scholar
vegan: Community Ecology Package v. 2.5-6 (2019), available at https://cran.r-project.org/web/packages/vegan/index.html
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30. https://doi.org/10.1093/nar/28.1.27 (2000).
Google Scholar
Source: Ecology - nature.com