Lab publications



Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut 2019;:gutjnl-2019-319045. doi:10.1136/gutjnl-2019-319045

Gossmann TI, Shanmugasundram A, Börno S, et al. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019;29:1712-1720.e7. doi:10.1016/j.cub.2019.04.020

Hildebrand, F., Moitinho-Silva, L., Blasche, S., Jahn, M. T., Gossmann, T. I., Huerta-Cepas, J., … Bork, P. (2019). Antibiotics-induced monodominance of a novel gut bacterial order. Gut, gutjnl-2018-317715.

Wally, N., Schneider, M., Thannesberger, J., Kastner, M. T., Bakonyi, T., Indik, S., … Steininger, C. (2019). Plasmid DNA contaminant in molecular reagents. Scientific Reports, 9(1), 1–11.


*Bahram, M., *Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., … Bork, P. (2018). Structure and function of the global topsoil microbiome. Nature, 560(7717), 233–237.

*Costea, P. I., *Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, M. J., Bushman, F. D., … Bork, P. (2018). Enterotypes in the landscape of gut microbial community composition. Nature Microbiology, 3(1), 8–16.

Pedersen, H. K., Forslund, S. K., Gudmundsdottir, V., Petersen, A. Ø., Hildebrand, F., Hyötyläinen, T., … Nielsen, H. B. (2018). A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links. Nature Protocols, 13(12), 2781–2800.

Bedarf, J. R., Hildebrand, F., Goeser, F., Bork, P., & Wüllner, U. (2018). Das Darmmikrobiom bei der Parkinson-Krankheit. Der Nervenarzt.

Tito, R. Y., Chaffron, S., Caenepeel, C., Lima-Mendez, G., Wang, J., Vieira-Silva, S., … Raes, J. (2018). Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut, gutjnl-2018-316106.

Jones, J. C. C., Fruciano, C., Marchant, J., Hildebrand, F., Forslund, S., Bork, P., … Hughes, W. O. H. O. H. (2018). The gut microbiome is associated with behavioural task in honey bees. Insectes Sociaux, 0(0), 0.

Kleinteich, J., Puddick, J., Wood, S., Hildebrand, F., Laughinghouse IV, H., Pearce, D., … Wilmotte, A. (2018). Toxic Cyanobacteria in Svalbard: Chemical Diversity of Microcystins Detected Using a Liquid Chromatography Mass Spectrometry Precursor Ion Screening Method. Toxins, 10(4), 147.

Pent, M., Hiltunen, M., Põldmaa, K., Furneaux, B., Hildebrand, F., Johannesson, H., … Bahram, M. (2018). Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environmental Microbiology.

Bahram, M., Anslan, S., Hildebrand, F., Bork, P., & Tedersoo, L. (2018). Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environmental Microbiology Reports, 5.


Costea, P. I., Coelho, L. P., Sunagawa, S., Munch, R., Huerta‐Cepas, J., Forslund, K., … Bork, P. (2017). Subspecies in the global human gut microbiome. Molecular Systems Biology, 13(12), 960.

Jones, J. C., Fruciano, C., Hildebrand, F., Al Toufalilia, H., J Balfour, N., Bork, P., … Hughes, W. O. (2017). Gut microbiota composition is associated with environmental landscape in honey bees. Ecology and Evolution, (October), 1–11.

*Bedarf, J. R., *Hildebrand, F., Coelho, L. P., Sunagawa, S., Bahram, M., Goeser, F., … Wüllner, U. (2017). Erratum: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients. [Genome Medicine. 9, (2017) (39)] DOI: 10.1186/s13073-017-0428-y. Genome Medicine, 9(1).

*Kleinteich, J., *Hildebrand, F., Bahram, M., Voigt, A. Y., Wood, S. A., Jungblut, A. D., … Dietrich, D. R. (2017). Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change. Frontiers in Ecology and Evolution, 5(November), 1–11.

Bedarf, J. R. R., Hildebrand, F., Coelho, L. P. P., Sunagawa, S., Bahram, M., Goeser, F., … Wüllner, U. (2017). Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients. Genome Medicine, 9(1), 39.

Saary, P., Forslund, K., Bork, P., & Hildebrand, F. (2017). RTK: efficient rarefaction analysis of large datasets. Bioinformatics, (April), 1–2.


Vieira-Silva, S., Falony, G., Darzi, Y., Lima-Mendez, G., Garcia Yunta, R., Okuda, S., … Raes, J. (2016). Species–function relationships shape ecological properties of the human gut microbiome. Nature Microbiology, 1(8), 16088.

Li, S. S., Zhu, A., Benes, V., Costea, P. I., Hercog, R., Hildebrand, F., … Bork, P. (2016). Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science, 352(6285), 586–589.

Noguera-Julian, M., Rocafort, M., Guillén, Y., Rivera, J., Casadellà, M., Nowak, P., … Paredes, R. (2016). Gut Microbiota Linked to Sexual Preference and HIV Infection. EBioMedicine, 5, 135–146.

Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., … Pedersen, O. (2016). Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535(7612), 376–381.


Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., … Velayoudon, D. (2015). Structure and function of the global ocean microbiome. Science, 348(6237), 1261359–1261359.

Wang, D., Hildebrand, F., Ye, L., Wei, Q., & Ma, L. Z. (2015). Genome Sequence of Mucoid Pseudomonas aeruginosa Strain FRD1. Genome Announcements, 3(2), 2–3.

Tedersoo, L., Bahram, M., Polme, S., Anslan, S., Riit, T., Koljalg, U., … Abarenkov, K. (2015). Response to Comment on “Global diversity and geography of soil fungi.” Science, 349(6251), 936–936.

*Marzorati, M., *Qin, B., *Hildebrand, F., Klosterbuer, A., Roughead, Z., Roessle, C., … Possemiers, S. (2015). Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Journal of Functional Foods, 16, 211–222.

Tedersoo, L., Anslan, S., Bahram, M., Põlme, S., Riit, T., Liiv, I., … Abarenkov, K. (2015). Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys, 10, 1–43.

*Forslund, K., *Hildebrand, F., *Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., … Pedersen, O. (2015). Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature, 528(7581), 262–266.


Ye, L., Hildebrand, F., Dingemans, J., Ballet, S., Laus, G., Matthijs, S., … Cornelis, P. (2014). Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens. PLoS ONE, 9(11), e110038.

Hildebrand, F., Tadeo, R., Voigt, A., Bork, P., & Raes, J. (2014). LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome, 2(1), 30.

Kubica, M., Hildebrand, F., Brinkman, B. M., Goossens, D., Del Favero, J., Vercammen, K., … Declercq, W. (2014). The skin microbiome of caspase-14-deficient mice shows mild dysbiosis. Experimental Dermatology, 23(8), 561–567.

Kleinteich, J., Hildebrand, F., Wood, S. A., Ciŕs, S., Agha, R., Quesada, A., … Dietrich, D. R. (2014). Diversity of toxin and non-toxin containing cyanobacterial mats of meltwater ponds on the Antarctic Peninsula: a pyrosequencing approach. Antarctic Science, 26(05), 521–532.

Ye, L., Matthijs, S., Bodilis, J., Hildebrand, F., Raes, J., & Cornelis, P. (2014). Analysis of the draft genome of Pseudomonas fluorescens ATCC17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines. BioMetals, 27(4), 633–644.

Dingemans, J., Ye, L., Hildebrand, F., Tontodonati, F., Craggs, M., Bilocq, F., … Cornelis, P. (2014). The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung. Pathogens and Disease, 71(1), 26–38.

Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., … Ehrlich, S. D. (2014). Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology, 32(8), 822–828.


Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., … Yamada, T. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500(7464), 541–546.

Brinkman, B. M., Becker, A., Ayiseh, R. B., Hildebrand, F., Raes, J., Huys, G., & Vandenabeele, P. (2013). Gut Microbiota Affects Sensitivity to Acute DSS-induced Colitis Independently of Host Genotype. Inflammatory Bowel Diseases, 19(12), 2560–2567.

Ye, L., Ballet, S., Hildebrand, F., Laus, G., Guillemyn, K., Raes, J., … Cornelis, P. (2013). A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies. BioMetals, 26(4), 561–575.

*Hildebrand, F., *Nguyen, T. L. A., Brinkman, B., Yunta, R., Cauwe, B., Vandenabeele, P., … Raes, J. (2013). Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biology, 14(1), R4.

Jacobsen, U. P., Nielsen, H. B., Hildebrand, F., Raes, J., Sicheritz-Ponten, T., Kouskoumvekaki, I., & Panagiotou, G. (2013). The chemical interactome space between the human host and the genetically defined gut metabotypes. The ISME Journal, 7(4), 730–742.

Vermeire, S., Joossens, M., Verbeke, K., Hildebrand, F., Machiels, K., Van den Broeck, K., … Raes, J. (2012). Pilot Study on the Safety and Efficacy of Faecal Microbiota Transplantation in Refractory Crohn’s Disease. Gastroenterology, 142(5), S360–S360.

*Hildebrand, F., *Ebersbach, T., Nielsen, H., Li, X., Sonne, S., Bertalan, M., … Licht, T. (2012). A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). BMC Genomics, 13(1), 514.

Wei, Q., Le Minh, P. N., Dotsch, A., Hildebrand, F., Panmanee, W., Elfarash, A., … Cornelis, P. (2012). Global regulation of gene expression by OxyR in an important human opportunistic pathogen. Nucleic Acids Research, 40(10), 4320–4333.

Qiu, H., Hildebrand, F., Kuraku, S., & Meyer, A. (2011). Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. BMC Genomics, 12(1), 325.

*Brinkman, B. M., *Hildebrand, F., Kubica, M., Goosens, D., Del Favero, J., Declercq, W., … Vandenabeele, P. (2011). Caspase deficiency alters the murine gut microbiome. Cell Death and Disease, 2(10), e220.

Hildebrand, F., Meyer, A., & Eyre-Walker, A. (2010). Evidence of Selection upon Genomic GC-Content in Bacteria. PLoS Genetics, 6(9), e1001107.

Wirth, T., Hildebrand, F., Allix-Béguec, C., Wölbeling, F., Kubica, T., Kremer, K., … Niemann, S. (2008). Origin, Spread and Demography of the Mycobacterium tuberculosis Complex. PLoS Pathogens, 4(9), e1000160.