Our research ranks among the top 1% most cited works across several different fields


Getzke F#, Wang L#, Chesneau G, Böhringer N, Mesny F, Denissen N, Wesseler H, Adisa PT, Marner M, Schulze-Lefert P, Schäberle TF*, Hacquard S*. (2024)  Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease. Nature Communications. 15,4438. #joint first authors, *co-corresponding authors.


Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S. (2023) Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota . Nature Communications 14,8274.

Basak AK, Piasecka A, Hucklenbroich J, Türksoy GM, Guan R, Zhang P, Getzke F, Garrido-Oter R, Hacquard S, Strzałka K, Bednarek P, Yamada K, Nakano RT. (2023) ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly. New Phytol. doi: 10.1111/nph.19289.

Mesny F, Hacquard S, Thomma BPHJ. (2023) Co‐evolution within the plant holobiont drives host performance. EMBO reports 24 (9), e57455.

Getzke F, Hassani MA, Crüsemann M, Malisic M, Zhang P, Ishigaki Y, Böhringer N, Jiménez Fernández A, Wang L, Ordon J, Ma K-W, Thiergart T, Harbort CJ, Wesseler H, Miyauchi S, Garrido-Oter R, Shirasu K, Schäberle TF, Hacquard S*, Schulze-Lefert P*. (2023) Co-functioning of bacterial exometabolites drives root microbiota establishment. . Proceedings of the National Academy of Sciences USA 120 (15), e2221508120. *co-corresponding authors.


Mataigne V, Vannier N, Vandenkoornhuyse P*, Hacquard S*. (2022) Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. Microbiome 10, 217. *co-corresponding authors

Durán P, Ellis TJ, Thiergart T, Ågren J*, Hacquard S*. (2022) Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations. New phytologist 236, 608-621. *co-corresponding authors

Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. (2022) Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods 19, 429-440.                  

Hacquard S, Wang E, Slater H, Martin F. (2022) Impact of global change on the plant microbiome. New Phytologist 234, 1907-1909.

Getzke F, Hacquard S. (2022) High-Throughput Profiling of Root-Associated Microbial Communities. Environmental Responses in Plants 2494, 325-337.


Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R. (2021) Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Communications 1, 73.

Mataigne V, Vannier N, Vandenkoornhuyse P*, Hacquard S*. (2021) Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes. Frontiers in Microbiology 12, 780469. *co-corresponding authors.

Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM*, Hacquard S*. (2021). Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nature Communications 12, 7227. *co-corresponding authors

Wolinska KW, Vannier N, Thiergart T, Pickel B, Gremmen S, Piasecka A, Piślewska-Bednarek M, Nakano RT, Belkhadir Y, Bednarek P, Hacquard S. (2021). Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots. Proceedings of the National Academy of Sciences USA, 118, 49: e2111521118.

Hou S, Thiergart T, Vannier N, Mesny F, Ziegler J, Pickel B, Hacquard S (2021) A microbiota–root–shoot circuit favours Arabidopsis growth over defence under suboptimal light. Nature Plants 7, 1078–1092.

Schütz,.V., Frindte, K., Cui, J., Zhang, P., Hacquard, S., Schulze-Lefert, P., Knief ,C, Schulz, M, Dörmann, P. (2021) Differential impact of plant secondary metabolites on the soil microbiota. Frontiers in microbiology 12, 1267.

Mayer T, Mari A, Almario J, Murillo-Roos M, Abdullah M, Dombrowski N, Hacquard S, Kemen EM, Agler MT. Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing. Molecular Ecology Resources 21, 1952-1965.

Hou S#, Wolinska KW#, Hacquard S (2021) Microbiota-root-shoot-environment axis and stress tolerance in plants. Current Opinion in Plant Biology 62, 102028. # joint first authors


Thiergart T#, Durán P#, Ellis T, Vannier N, Garrido-Oter R, Roux F, Alonso-Blanco C, Ågren J*, Schulze-Lefert P*, Hacquard S* (2019) Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology & Evolution 4, 122-131. # joint first authors, *co-corresponding authors

Guo X, Zhang X, Qin Y, Liu Y-X, Zhang J, Zhang N, Wu K, Qu B, He Z, Wang X, Zhang X, Hacquard S, Fu X*, Bai Y*. (2020) Host-associated quantitative abundance profiling reveals the microbial load variation of root microbiome. Plant Communications 100003. *co-corresponding authors


Getzke F#, Thiergart T#, Hacquard S. Contribution of bacterial-fungal balance to plant and animal health. (2019) Current Opinion in Microbiology 49, 66-72. # joint first authors

Hacquard S*. Stéphane Hacquard. (2019) New Phytologist 224, 1442-1443.

Vannier N, Agler M*, Hacquard S*. (2019) Microbiota-mediated disease resistance in plants. Plos Pathogens 15: e1007740. *co-corresponding authors



Durán P#, Thiergart T#, Garrido-Oter R, Agler M, Kemen E, Schulze-lefert P*, Hacquard S* (2018) Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973-983. # joint first authors, *co-corresponding authors

Deveau A, Bonito G, Uehling J, Paoletti M, Becker S, Binschedler S, Hacquard S, Herve V, Labbe J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, Van Elsas JD, Wick LY (2018) Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews.

Hassani MA#, Durán P#, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6, 58. # joint first authors

Robbins C, Thiergart T, Hacquard S, Garrido-Oter R, Gans W, Peiter E, Schulze-lefert P*, Spaepen S* (2018) Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels. Phytobiomes 2, 24-34. *co-corresponding authors

Lorrain C, Marchal C, Hacquard S, Delaruelle C, Petrowski J, Petre B, Hecker A, Frey P, Duplessis S (2018) The rust fungus Melampsora larici-populina expresses a conserved genetic program and distinct sets of secreted protein genes during infection of its two host plants, larch and poplar. Molecular Plant-microbe Interactions 31, 695-706.



Hacquard S, Spaepen S, Garrido-Oter R, Schulze-lefert P (2017) Interplay between innate immunity and the plant microbiota. Annual Review of Phytopathology 55, 565-589.

Hacquard S (2017) Commentary: Microbial small talk: volatiles in fungal-bacterial interactions. Frontiers in Microbiology 8, 1.

Dombrowski N, Schlaeppi K, Agler MT, Hacquard S, Kemen E, Wunder J, Coupland G, Schulze-lefert P (2017) Root microbiota dynamics of perennial Arabis alpina is dependent on soil residence time but independent of flowering time. The ISME Journal 11, 43-55.



Agler MT, Mari A, Dombrowski N, Hacquard S, Kemen EM (2016) New insights in host-associated microbial diversity with broad and accurate taxonomic resolution. Biorxiv

Takahara H#, Hacquard S#, Kombrink A, Hugues HB, Halder V, Robin GP, Hiruma K, Neumann U, Shinya T, Kombrink E, Shibuya N, Thomma BPHJ, O’connell RJ (2016) Colletotrichum higginsianum extracellular LysM proteins play dual roles in appressorial function and suppression of chitin-triggered plant immunity. New Phytologist. # joint first authors

Hacquard S#, Kracher B#, Hiruma K, Münch PC, Garrido-Oter R, Weimann A, Thon MR, Damm U, Dallery J-F, Hainaut M, Henrissat B, Lespinet O, Sacristán S, Ver Loren Van Themaat E, Kemen E, Mchardy AC, Schulze-lefert P*, O’connell RJ* (2016) Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nature Communications 7, 11362. # joint first authors, *co-corresponding authors

Hiruma K, Gerlach N, Sacristán S, Nakano RT, Hacquard S, Kracher B, Neumann U, Ramirez D, Bucher M, O’connell RJ*, Schulze-lefert P* (2016) Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status-dependent. Cell 165, 464-74. *co-corresponding authors

Hacquard S (2016). Disentangling the factors shaping microbiota composition across the plant holobiont. New Phytologist 209, 454-457.



Hacquard S#, Garrido-Oter R#, Gonzáles A#, Spaepen S#, Ackermann G, Lebeis S, McHardy AC*, Dangl Jl*, Knight R*, Ley R*, Schulze-lefert P* (2015) Microbiota and host nutrition across plant and animal kingdoms. Cell Host & Microbe 17, 603-616. # joint first authors, *co-corresponding authors

Hacquard S*, Schadt CW* (2015) Towards a holistic understanding of the beneficial interactions across the Populus microbiome. New Phytologist 205, 1424-1430. *co-corresponding authors



Hacquard S (2014) The genomics of powdery mildew fungi: past achievements, present status and future prospects. Advances in Botanical Research 70, 109-142.



Petre B, Hacquard S, Duplessis S, Rouhier N (2013) Genome analysis of poplar LRR-RLP gene clusters reveals RISP, a defense-related gene coding a candidate endogenous peptide elicitor. Frontiers in Plant Science 5, 111.

Hacquard S, Delaruelle C, Frey P, Tisserant E, Kohler A, Duplessis S (2013) Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes. Frontiers in Plant Science 4, 456.

Hacquard S#, Kracher B#, Maekawa T, Vernaldi S, Schulze-lefert P*, Ver Loren Van Themaat E* (2013) Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proceedings of the National Academy of Sciences USA 110, E2219-28. # joint first authors, *co-corresponding authors

Hacquard S#, Tisserant E#, Brun a, Legue V, Martin F, Kohler A (2013) Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments. Environmental Microbiology 15, 1853-1859. # joint first authors



Petre B, Morin E, Tisserant E, Hacquard S, Da Silva C, Poulain J, Delaruelle C, Rouhier N, Martin F, Kohler A, Duplessis S (2012) RNA-seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers Ptsultr3;5, a fungal-induced host sulfate transporter. Plos One 7, E44408.

O’connel RJ#, Thon MR#, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CL, Becker C, Birren BW, Chen Z, Choi Y, Crouch JA, Duvick J, Farman ML, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun M-H, Lee Y-H, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, Van Der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-lefert P, Ver Loren Van Themaat E, Ma L-J, Vaillancourt LJ (2012) Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics 44,1060-1065. # joint first authors

Kleemann J, Rincon LJ, Takahara H, Neumann U, Ver Loren Van Themaat E, Van Der Does HC, Hacquard S, Stüber K, Will I, Schmalenbach W, Schmelzer E, O’connell RJ (2012) Sequential delivery of host-induced virulence effectors by appressoria and intracellular hyphae of the phytopathogen Colletotrichum higginsianum. Plos Pathogens 8, E1002643.

Hacquard S#, Joly DL#, Lin Y-C, Tisserant E, Feau N, Delaruelle C, Legue V, Kohler A, Tanguay P, Petre B, Frey P, Van De Peer Y, Rouze P, Martin F, Hamelin RC, Duplessis S (2012) A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust). Molecular Plant-microbe Interactions 25, 279-293. # joint first authors



Hacquard S#, Petre B#, Frey P, Hecker A, Rouhier N, Duplessis S (2011) the Poplar- Poplar Rust Interaction: Insights From Genomics and Transcriptomics. Journal of Pathogens 2011, 716041. # joint first authors

Duplessis S#, Hacquard S#, Delaruelle C, Tisserant E, Frey P, Martin F, Kohler A (2011) Melampsora larici-populina transcript profiling during germination and time-course infection of poplar leaves reveals dynamic expression patterns associated with virulence and biotrophy. Molecular Plant-microbe Interactions 24, 808-818. # joint first authors

Duplessis S#*, Cuomo CA#*, Lin Y-C, Aerts A, Tisserant E, Veneault-fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel B, Chiu R, Couthinho P, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr M, Kodira C, Kohler A, Kues U, Lindquist EA, Lucas S, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Schmutz J, Selles B, Shapiro H, Tangay P, Tuskan GA, Van De Peer Y, Henrissat B, Rouze P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ*, Martin F* (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences USA 108, 9166-9171. # joint first authors, *co-corresponding authors

Hacquard S, Veneault-fourrey C, Delaruelle C, Frey P, Martin F, Duplessis S (2011) Validation of Melampsora larici-populina reference genes for in planta RT-quantitative PCR expression profiling during time-course infection of poplar leaves. Physiological and Molecular Plant Pathology 75, 106-112.



Hacquard S, Delaruelle C, Legue V, Tisserant E, Kohler A, Frey P, Martin F, Duplessis S (2010) Laser capture microdissection of uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation. Molecular Plant-microbe Interactions 23, 1275-1286.

Joly DL, Hacquard S, Feau N, Tanguay P, Martin F, Hamelin R, Duplessis S (2010) Chasing effectors in the secretome of Melampsora larici-populina. Paper 77 in biology of plant-microbe Interactions, Vol. 7, H. Antoun, T. Avis, L. Brisson, D. Prévost, and M. Trepanier, Eds. International Society for Molecular Plant-microbe Interactions, St. Paul, Mn.



Go to Editor View