Lab publications

 

2019

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. https://doi.org/10.1136/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. https://doi.org/10.1038/s41598-019-38733-1


2018

*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. https://doi.org/10.1038/s41586-018-0386-6

*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. https://doi.org/10.1038/s41564-017-0072-8

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. https://doi.org/10.1038/s41596-018-0064-z

Bedarf, J. R., Hildebrand, F., Goeser, F., Bork, P., & Wüllner, U. (2018). Das Darmmikrobiom bei der Parkinson-Krankheit. Der Nervenarzt. https://doi.org/10.1007/s00115-018-0601-6

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. https://doi.org/10.1136/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. https://doi.org/10.1007/s00040-018-0624-9

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. https://doi.org/10.3390/toxins10040147

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. https://doi.org/10.1111/1462-2920.14069

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. https://doi.org/10.1111/1758-2229.12684


2017

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. https://doi.org/10.15252/msb.20177589

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. https://doi.org/10.1002/ece3.3597

*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). https://doi.org/10.1186/s13073-017-0451-z

*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. https://doi.org/10.3389/fevo.2017.00137

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. https://doi.org/10.1186/s13073-017-0428-y

Saary, P., Forslund, K., Bork, P., & Hildebrand, F. (2017). RTK: efficient rarefaction analysis of large datasets. Bioinformatics, (April), 1–2. https://doi.org/10.1093/bioinformatics/btx206


2016

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. https://doi.org/10.1038/nmicrobiol.2016.88

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. https://doi.org/10.1126/science.aad8852

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. https://doi.org/10.1016/j.ebiom.2016.01.032

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. https://doi.org/10.1038/nature18646


2015

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. https://doi.org/10.1126/science.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. https://doi.org/10.1128/genomeA.00376-15

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. https://doi.org/10.1126/science.aaa5594

*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. https://doi.org/10.1016/j.jff.2015.04.039

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. https://doi.org/10.3897/mycokeys.10.4852

*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. https://doi.org/10.1038/nature15766


2014

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. https://doi.org/10.1371/journal.pone.0110038

Hildebrand, F., Tadeo, R., Voigt, A., Bork, P., & Raes, J. (2014). LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome, 2(1), 30. https://doi.org/10.1186/2049-2618-2-30

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. https://doi.org/10.1111/exd.12458

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. https://doi.org/10.1017/S0954102014000145

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. https://doi.org/10.1007/s10534-014-9734-7

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. https://doi.org/10.1111/2049-632X.12170

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. https://doi.org/10.1038/nbt.2939


2009-2013

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. https://doi.org/10.1038/nature12506

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. https://doi.org/10.1097/MIB.0b013e3182a8759a

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. https://doi.org/10.1007/s10534-013-9653-z

*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. https://doi.org/10.1186/gb-2013-14-1-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. https://doi.org/10.1038/ismej.2012.141

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. https://doi.org/10.1186/1471-2164-13-514

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. https://doi.org/10.1093/nar/gks017

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. https://doi.org/10.1186/1471-2164-12-325

*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. https://doi.org/10.1038/cddis.2011.101

Hildebrand, F., Meyer, A., & Eyre-Walker, A. (2010). Evidence of Selection upon Genomic GC-Content in Bacteria. PLoS Genetics, 6(9), e1001107. https://doi.org/10.1371/journal.pgen.1001107

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. https://doi.org/10.1371/journal.ppat.1000160