Mendes R, Raaijmakers JM. Cross-kingdom similarities in microbiome functions. ISME J. 2015;9:1905–7.
Google Scholar
Berg G, Rybakova D, Fischer D, Cernava T, Vergès M-CC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8:103.
Google Scholar
Hall AB, Tolonen AC, Xavier RJ. Human genetic variation and the gut microbiome in disease. Nat Rev Genet. 2017;18:690–9.
Google Scholar
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant-microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.
Google Scholar
Ramírez-Puebla ST, Servín-Garcidueñas LE, Jiménez-Marín B, Bolaños LM, Rosenblueth M, Martínez J, et al. Gut and root microbiota commonalities. Appl Environ Microbiol. 2013;79:2–9.
Google Scholar
Lu T, Ke M, Lavoie M, Jin Y, Fan X, Zhang Z, et al. Rhizosphere microorganisms can influence the timing of plant flowering. Microbiome. 2018;6:231.
Google Scholar
Zhang J, Liu Y-X, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84.
Google Scholar
Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat Biotechnol. 2018;36:1100–9.
Google Scholar
Li H, La S, Zhang X, Gao L, Tian Y. Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress. ISME J. 2021;15:2865–82.
Google Scholar
Xu L, Dong Z, Chiniquy D, Pierroz G, Deng S, Gao C, et al. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nat Commun. 2021;12:3209.
Google Scholar
Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17:219–32.
Google Scholar
Lee SM, Kong HG, Song GC, Ryu CM. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J. 2021;15:330–47.
Google Scholar
Stacy A, Andrade-Oliveira V, McCulloch JA, Hild B, Oh JH, Perez-Chaparro PJ, et al. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell. 2021;184:615–.e17.
Google Scholar
Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat Rev Gastroenterol Hepatol. 2019;16:605–16.
Google Scholar
Bhattacharyya PN, Jha DK. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol. 2012;28:1327–50.
Google Scholar
Bashan Y, de-Bashan LE, Prabhu SR, Hernandez J-P. Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil. 2014;378:1–33.
Google Scholar
Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174:1388–.e21.
Google Scholar
Kaakoush NO. Fecal transplants as a microbiome-based therapeutic. Curr Opin Microbiol. 2020;56:16–23.
Google Scholar
Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108:500–8.
Google Scholar
Baruch EN, Youngster I, Ben-Betzalel G, Ortenberg R, Lahat A, Katz L, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science. 2021;371:602–9.
Google Scholar
Weller DM, Raaijmakers JM, Gardener BBM, Thomashow LS. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol. 2002;40:309–48.
Google Scholar
Gopal M, Gupta A, Thomas GV. Bespoke microbiome therapy to manage plant diseases. Front Microbiol. 2013;4:355.
Google Scholar
Raaijmakers JM, Bonsall RF, Weller DM. Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat. Phytopathology. 1999;89:470–5.
Google Scholar
Mazurier S, Corberand T, Lemanceau P, Raaijmakers JM. Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt. ISME J. 2009;3:977–91.
Google Scholar
Siddiqui ZA, Shakeel U. Screening of Bacillus isolates for potential biocontrol of the wilt disease complex of pigeon pea (Cajanus cajan) under greenhouse and small-scale field conditions. J Plant Pathol. 2007;89:179–83.
Yadav K, Damodaran T, Dutt K, Singh A, Muthukumar M, Rajan S, et al. Effective biocontrol of banana fusarium wilt tropical race 4 by a bacillus rhizobacteria strain with antagonistic secondary metabolites. Rhizosphere. 2021;18:100341.
Meng Q, Yin J, Rosenzweig N, Douches D, Hao JJ. Culture-based assessment of microbial communities in soil suppressive to potato common scab. Plant Dis. 2012;96:712–7.
Google Scholar
Carrión VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, et al. Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. ISME J. 2018;12:2307–21.
Google Scholar
Gómez Expósito R, de Bruijn I, Postma J, Raaijmakers JM. Current insights into the role of rhizosphere bacteria in disease suppressive soils. Front Microbiol. 2017;8:2529.
Google Scholar
Raaijmakers JM, Mazzola M. Soil immune responses. Science. 2016;352:1392–3.
Google Scholar
Bakker PAHM, Pieterse CMJ, de Jonge R, Berendsen RL. The soil-borne legacy. Cell. 2018;172:1178–80.
Google Scholar
Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T. Disease suppressive soils: new insights from the soil microbiome. Phytopathology. 2017;107:1284–97.
Google Scholar
Kyselková M, Kopecký J, Frapolli M, Défago G, Ságová-Marecková M, Grundmann GL, et al. Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J. 2009;3:1127–38.
Google Scholar
Rosenzweig N, Tiedje JM, Quensen JF, Meng Q, Hao JJ. Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis. 2012;96:718–25.
Google Scholar
Cha JY, Han S, Hong H-J, Cho H, Kim D, Kwon Y, et al. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 2016;10:119–29.
Google Scholar
Liu X, Zhang S, Jiang Q, Bai Y, Shen G, Li S, et al. Using community analysis to explore bacterial indicators for disease suppression of tobacco bacterial wilt. Sci Rep. 2016;6:36773.
Google Scholar
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science. 2011;332:1097–100.
Google Scholar
Wei Z, Gu Y, Friman VP, Kowalchuk GA, Xu Y, Shen Q, et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv. 2019;5:eaaw0759.
Google Scholar
Rillig MC, Antonovics J, Caruso T, Lehmann A, Powell JR, Veresoglou SD, et al. Interchange of entire communities: microbial community coalescence. Trends Ecol Evol. 2015;30:470–6.
Google Scholar
Deng S, Caddell DF, Xu G, Dahlen L, Washington L, Yang J, et al. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. ISME J. 2021;15:3181–94.
Google Scholar
Mendes LW, Mendes R, Raaijmakers JM, Tsai SM. Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME J. 2018;12:3038–42.
Google Scholar
Hu J, Wei Z, Kowalchuk GA, Xu Y, Shen Q, Jousset A. Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development. Environ Microbiol. 2020;22:5005–18.
Google Scholar
Schreiter S, Ding G-C, Heuer H, Neumann G, Sandmann M, Grosch R, et al. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. Front Microbiol. 2014;5:144.
Google Scholar
Wei Z, Hu J, Gu Y, Yin S, Xu Y, Jousset A, et al. Ralstonia solanacearum pathogen disrupts bacterial rhizosphere microbiome during an invasion. Soil Biol Biochem. 2018;118:8–17.
Google Scholar
Jiang G, Wei Z, Xu J, Chen H, Zhang Y, She X, et al. Bacterial wilt in China: History, current status, and future perspectives. Front Plant Sci. 2017;8:1549.
Google Scholar
Manda RR, Addanki VA, Srivastava S. Bacterial wilt of solanaceous crops. Int J Chem Stud. 2020;8:1048–57.
Google Scholar
Barik S, Reddy AC, Ponnam N, Kumari M, C AG, Reddy DCL, et al. Breeding for bacterial wilt resistance in eggplant (Solanum melongena L.): progress and prospects. Crop Prot. 2020;137:105270.
Google Scholar
Wei Z, Yang X, Yin S, Shen Q, Ran W, Xu Y. Efficacy of Bacillus-fortified organic fertiliser in controlling bacterial wilt of tomato in the field. Appl Soil Ecol. 2011;48:152–9.
Park E-J, Lee S-D, Chung E-J, Lee M-H, Um H-Y, Murugaiyan S, et al. MicroTom – A model plant system to study bacterial wilt by Ralstonia solanacearum. Plant Pathol J. 2007;23:239–44.
Schandry N. A practical guide to visualization and statistical analysis of R. solanacearum infection data using R. Front Plant Sci. 2017;8:623.
Google Scholar
Gu S, Wei Z, Shao Z, Friman VP, Cao K, Yang T, et al. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat Microbiol. 2020;5:1002–10.
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–642.
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.
Shenhav L, Thompson M, Joseph TA, Briscoe L, Furman O, Bogumil D, et al. FEAST: fast expectation-maximization for microbial source tracking. Nat Methods. 2019;16:627–32.
Google Scholar
Mendiburu F de. agricolae: Statistical procedures for agricultural research. R package version 1.3–5. 2021.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
Google Scholar
Deng Y, Jiang Y-H, Yang Y, He Z, Luo F, Zhou J. Molecular ecological network analyses. BMC Bioinformatics. 2012;13:113.
Google Scholar
Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X. Functional molecular ecological networks. mBio. 2010;1:e00169–10.
Google Scholar
Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, et al. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome. 2020;8:82.
Google Scholar
Kuntal BK, Chandrakar P, Sadhu S, Mande SS. ‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets. ISME J. 2019;13:442–54.
Google Scholar
Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38:685–8.
Google Scholar
Choi K, Choi J, Lee PA, Roy N, Khan R, Lee HJ, et al. Alteration of bacterial wilt resistance in tomato plant by microbiota transplant. Front Plant Sci. 2020;11:1186.
Google Scholar
Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin J-M, Morrison RM, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science. 2021;371:595–602.
Google Scholar
D’Haens GR, Jobin C. Fecal microbial transplantation for diseases beyond recurrent Clostridium difficile infection. Gastroenterology. 2019;157:624–36.
Google Scholar
Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis. 2011;53:994–1002.
Google Scholar
Durack J, Lynch SV. The gut microbiome: relationships with disease and opportunities for therapy. J Exp Med. 2019;216:20–40.
Google Scholar
Danne C, Rolhion N, Sokol H. Recipient factors in faecal microbiota transplantation: one stool does not fit all. Nat Rev Gastroenterol Hepatol. 2021;18:503–13.
Google Scholar
Jiang G, Wang N, Zhang Y, Zhang Y, Yu J, Zhang Y, et al. The relative importance of soil moisture in predicting bacterial wilt disease occurrence. Soil Ecol Lett. 2021;3:356–66.
Wei Z, Friman VP, Pommier T, Geisen S, Jousset A, Shen Q. Rhizosphere immunity: targeting the underground for sustainable plant health management. Front Agric Sci Eng. 2020;7:317–28.
Hu J, Wei Z, Friman VP, Gu SH, Wang X-F, Eisenhauer N, et al. Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. mBio. 2016;7:e01790–16.
Google Scholar
Bakker PAHM, Doornbos RF, Zamioudis C, Berendsen RL, Pieterse CMJ. Induced systemic resistance and the rhizosphere microbiome. Plant Pathol J. 2013;29:136–43.
Google Scholar
Wei Z, Yang T, Friman VP, Xu Y, Shen Q, Jousset A. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat Commun. 2015;6:8413.
Google Scholar
Li M, Wei Z, Wang J, Jousset A, Friman V-P, Xu Y, et al. Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett. 2019;22:149–58.
Google Scholar
Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME J. 2018;12:212–24.
Google Scholar
Rosales PF, Bordin GS, Gower AE, Moura S. Indole alkaloids: 2012 until now, highlighting the new chemical structures and biological activities. Fitoterapia. 2020;143:104558.
Google Scholar
Sarbu LG, Bahrin LG, Babii C, Stefan M, Birsa ML. Synthetic flavonoids with antimicrobial activity: a review. J Appl Microbiol. 2019;127:1282–90.
Google Scholar
Madadi E, Mazloum-Ravasan S, Yu JS, Ha JW, Hamishehkar H, Kim KH. Therapeutic application of betalains: a review. Plants. 2020;9:E1219.
Google Scholar
Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, et al. The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat Rev Microbiol. 2009;7:514–25.
Google Scholar
Kolton M, Erlacher A, Berg G, Cytryn E. The Flavobacterium genus in the plant holobiont: ecological, physiological, and applicative insights. In: Castro-Sowinski S, editor. Microbial models: from environmental to industrial sustainability. Singapore: Springer; 2016. p. 189–207.
Haas D, Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 2005;3:307–19.
Google Scholar
Fira D, Dimkić I, Berić T, Lozo J, Stanković S. Biological control of plant pathogens by Bacillus species. J Biotechnol. 2018;285:44–55.
Google Scholar
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