Food Microbiology, Gut Health, and Fermentation

Research output

Research output per year 1994 2013 2014 2015 2018 2019 2020 2021 2022 2023 2024 2025

• 529 Journal article
• 34 Ph.D. thesis
• 28 Review
• 15 Book chapter
• 61 More
  • 15 Poster
  • 11 Conference abstract for conference
  • 7 Comment/debate
  • 6 Conference abstract in journal
  • 5 Article in proceedings
  • 5 Letter
  • 4 Editorial
  • 2 Conference abstract in proceedings
  • 2 Contribution to newspaper - Comment/debate
  • 1 Book
  • 1 Paper
  • 1 Conference article
  • 1 Preprint

Research output per year

Research output per year

Search results

• 2025

  Gut microbiota in rainbow trout Oncorhynchus mykiss with different susceptibility to Flavobacterium psychrophilum infection

  Karami, A. M., Kania, P. W., Al-Jubury, A., Stefanova, D., Krych, L., Madsen, L., Nielsen, T. & Buchmann, K., 2025, In: Aquaculture. 596, 9 p., 741841.

  Research output: Contribution to journal › Journal article › Research

  Open Access

  File
• 2024

  16S rRNA gene sequencing of non-lactic acid bacteria cultures from lait caillé in Burkina Faso

  Bayili, G. R., Compaoré, C. S., Diawara, B., Jespersen, L. & Sawadogo-Lingani, H., 2024, In: All Life. 17, 1, 8 p., 2309346.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  14 Downloads (Pure)

• A Chemical Structure and Machine Learning Approach to Assess the Potential Bioactivity of Endogenous Metabolites and Their Association with Early Childhood Systemic Inflammation

  Lovrić, M., Wang, T., Staffe, M. R., Šunić, I., Časni, K., Lasky-Su, J., Chawes, B. & Rasmussen, M. A., 2024, In: Metabolites. 14, 5, 16 p., 278.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  8 Downloads (Pure)

• Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis

  Loivamaa, I., Sillanpää, A., Deptula, P., Chamlagain, B., Edelmann, M., Auvinen, P., Nyman, T. A., Savijoki, K., Piironen, V. & Varmanen, P., 2024, In: mSystems. 9, 10, 26 p., e00615-24.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• A Gently Processed Skim Milk-Derived Whey Protein Concentrate for Infant Formula: Effects on Gut Development and Immunity in Preterm Pigs

  Aasmul-Olsen, K., Akıllıoğlu, H. G., Christiansen, L. I., Engholm-Keller, K., Brunse, A., Stefanova, D. V., Bjørnshave, A., Bechshøft, M. R., Skovgaard, K., Thymann, T., Sangild, P. T., Lund, M. N. & Bering, S. B., 2024, In: Molecular Nutrition and Food Research. 68, 6, 2300458.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  24 Downloads (Pure)

• Amino acid preference and fermentation performance of Pichia kluyveri strains in a synthetic wort

  Miguel, G. A., Carlsen, S., Almeida-Faria, R., Saerens, S. & Arneborg, N., 2024, In: LWT -Food Science and Technology. 199, 8 p., 116059.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  6 Downloads (Pure)

• Analyzing postprandial metabolomics data using multiway models: a simulation study

  Li, L., Yan, S., Bakker, B. M., Hoefsloot, H., Chawes, B., Horner, D., Rasmussen, M. A., Smilde, A. K. & Acar, E., 2024, In: BMC Bioinformatics. 25, 22 p., 94.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  3 Citations (Scopus)

  8 Downloads (Pure)

• A single-stranded based library preparation method for virome characterization

  Zhai, X., Gobbi, A., Kot, W., Krych, L., Nielsen, D. S. & Deng, L., 2024, In: Microbiome. 12, 15 p., 219.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Asthma development is associated with low mucosal IL-10 during viral infections in early life

  Melgaard, M. E., Jensen, S. K., Eliasen, A., Pedersen, C. E. T., Thorsen, J., Mikkelsen, M., Vahman, N., Schoos, A. M. M., Gern, J., Brix, S., Stokholm, J., Chawes, B. L. & Bønnelykke, K., 2024, In: Allergy: European Journal of Allergy and Clinical Immunology. 79, 11, p. 2981-2992 12 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  1 Citation (Scopus)

• A Stress Reduction Intervention for Lactating Mothers Alters Maternal Gut, Breast Milk, and Infant Gut Microbiomes: Data from a Randomized Controlled Trial

  Yu, J., Zhang, Y., Wells, J. C. K., Wei, Z., Bajaj-Elliott, M., Nielsen, D. S. & Fewtrell, M. S., 2024, In: Nutrients. 16, 7, 15 p., 1074.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  6 Downloads (Pure)

• Bacterial colonisation of the airway in neonates and risk of asthma and allergy until age 18 years

  Sunde, R. B., Thorsen, J., Kim, M., Schoos, A. M. M., Stokholm, J., Bønnelykke, K., Bisgaard, H. & Chawes, B., 2024, In: The European respiratory journal. 63, 1, 15 p., 2300471.

  Research output: Contribution to journal › Journal article › Research › peer-review
  2 Citations (Scopus)

• Bilirubin metabolism in early life and respiratory health during preschool age: A combined analysis of two independent birth cohorts

  Kim, M., Brustad, N., Eliasen, A. U., Ali, M., Wang, T., Rasmussen, M. A., Ernst, M., Hougaard, D., Litonjua, A. A., Wheelock, C. E., Kelly, R. S., Chen, Y., Prince, N., Townsend, P. A., Stokholm, J., Weiss, S. T., Bønnelykke, K., Lasky-Su, J. & Chawes, B., 2024, (Accepted/In press) In: Med.

  Research output: Contribution to journal › Journal article › Research › peer-review

• Bovine colostrum prevents formula-induced gut microbiota dysbiosis in preterm pigs

  Yang, L., Hui, Y., Thymann, T., Nielsen, D. S., Jiang, P-P. & Sangild, P. T., 2024, (E-pub ahead of print) In: Pediatric Research.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

• Burden and Subtypes of Early Life Infections Increase the Risk of Asthma

  Kyvsgaard, J. N., Hesselberg, L. M., Sunde, R. B., Brustad, N., Vahman, N., Schoos, A-M. M., Bønnelykke, K., Stokholm, J. & Chawes, B. L., 2024, In: Journal of Allergy and Clinical Immunology: In Practice. 12, 8, p. 2056-2065.e10 20 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  1 Citation (Scopus)

• Cereal-based fermented foods as microbiota-directed products for improved child nutrition and health in sub-Saharan Africa

  Houngbédji, M., Jespersen, J. S., Wilfrid Padonou, S. & Jespersen, L., 2024, (E-pub ahead of print) In: Critical Reviews in Food Science and Nutrition.

  Research output: Contribution to journal › Review › Research › peer-review
  1 Citation (Scopus)

• Characterization and diversity of spoilage yeasts in dairy production with focus on their inhibitory potential

  Geronikou, A., 2024, Department of Food Science, Faculty of Science, University of Copenhagen. 166 p.

  Research output: Book/Report › Ph.D. thesis › Research

  File

• Characterizing human postprandial metabolic response using multiway data analysis

  Yan, S., Li, L., Horner, D., Ebrahimi, P., Chawes, B., Dragsted, L. O., Rasmussen, M. A., Smilde, A. K. & Acar, E., 2024, In: Metabolomics. 20, 3, 14 p., 50.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Citation (Scopus)

  13 Downloads (Pure)

• Danish consumers’ knowledge about and willingness to buy dairy products close to the best-before-date

  Melgaard, C. V., Voss, E., Hansen, M. F., Lassen, M., Hvidtfeldt, M., Pandey, S., Rasmussen, M. A. & Thomsen, M., 2024, In: Food Frontiers. 5, 2, p. 494-507

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Citation (Scopus)

  9 Downloads (Pure)

• Delayed Gut Colonization Changes Future Insulin Resistance and Hepatic Gene Expression but Not Adiposity in Obese Mice

  Ebert, M. B. B., Mentzel, C. M. J., Brunse, A., Krych, L. & Hansen, C. H. F., 2024, In: Journal of Obesity. 2024, 1, 11 p., 5846674.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Development and application of methodology in the study of the gastrointestinal virome

  Zhai, X., 2024, Department of Food Science, Faculty of Science, University of Copenhagen. 208 p.

  Research output: Book/Report › Ph.D. thesis › Research

  File

• Development of a novel, cost effective diagnostic tool for detection of genetic disorders in humans using nanopore sequencing technology

  Schack, A. K., 2024, Department of Food Science, Faculty of Science, University of Copenhagen. 145 p.

  Research output: Book/Report › Ph.D. thesis › Research

  File

• Dimensional profiling of psychopathology in children and adolescents based on the K-SADS-PL and an analysis of the construct validity of two ADHD symptom dimensions

  Hagstrøm, J., Nielsen, T., Sørensen, M. E., Aagaard, K., Rasmussen, M. A., Rosenberg, J. B., Mohammadzadeh, P., Sevelsted, A., Hernández-lorca, M., Fagerlund, B., Rydkjær, J., Pagsberg, A. K., Kaufman, J., Ebdrup, B. H., Bilenberg, N. & Jepsen, J. R. M., 2024, In: Nordic Journal of Psychiatry. 78, 1, p. 71-78 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

• Draft genome sequences of 53 Lactococcus and Leuconostoc strains isolated from two undefined DL-starter cultures

  Li, W., Soto-Serrano, A., Panah, F. M., Arik, G., Deptula, P., Lucena, D., Vogensen, F. K. & Krych, L., 2024, In: Microbiology resource announcements. 13, 6, 7 p., e00228-24.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Editorial: Preparation, function and application of postbiotics

  Li, Z., Peng, C., Sun, Z., Deng, L. & Lukasz, K., 2024, In: Frontiers in Microbiology. 15, 3 p., 1491550.

  Research output: Contribution to journal › Editorial › Research › peer-review

  Open Access

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• Effects of Wholegrain Compared to Refined Grain Intake on Cardiometabolic Risk Markers, Gut Microbiota, and Gastrointestinal Symptoms in Children: A Randomized Crossover Trial

  Madsen, M. T. B., Landberg, R., Nielsen, D. S., Zhang, Y., Anneberg, O. M. R., Lauritzen, L. & Damsgaard, C. T., 2024, In: American Journal of Clinical Nutrition. 119, 1, p. 18-28

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  5 Citations (Scopus)

  31 Downloads (Pure)

• Enhancement of pyranoanthocyanin formation in blueberry wine with non-Saccharomyces yeasts

  Zhou, J., Tang, C., Zou, S., Lei, L., Wu, Y., Yang, W., Harindintwali, J. D., Zhang, J., Zeng, W., Deng, D., Zhao, M., Yu, X., Liu, X., Qiu, S. & Arneborg, N., 2024, In: Food Chemistry. 438, 10 p., 137956.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  4 Citations (Scopus)

  11 Downloads (Pure)

• Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages

  Dion, M. B., Shah, S. A., Deng, L., Thorsen, J., Stokholm, J., Krogfelt, K. A., Schjørring, S., Horvath, P., Allard, A., Nielsen, D. S., Petit, M. A. & Moineau, S., 2024, In: The ISME Journal. 18, 1, 9 p., wrae005.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Citation (Scopus)

  21 Downloads (Pure)

• Exploring the capacity of Bacillus species for production of kokumi γ-glutamyl peptides: A comparative study

  Li, Q., Zhang, L., Nielsen, D. S., Jespersen, L. & Lametsch, R., 2024, In: LWT - Food Science and Technology. 206, 9 p., 116542.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  5 Downloads (Pure)

• Exploring the Gut Microbiota-Obesity Link in Children and Adolescents

  Poulsen, C. E., 2024, Department of Food Science, Faculty of Science, University of Copenhagen. 149 p.

  Research output: Book/Report › Ph.D. thesis › Research

  File

• Fecal virus-like particles are sufficient to reduce necrotizing enterocolitis

  Offersen, S. M., Mao, X., Spiegelhauer, M. R., Larsen, F., Li, V. R., Sandris Nielsen, D., Aunsholt, L., Thymann, T. & Brunse, A., 2024, In: Gut Microbes. 16, 1, 22 p., 2392876.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Citation (Scopus)

  6 Downloads (Pure)

• Feeding cessation and antibiotics improve clinical symptoms and alleviate gut and systemic inflammation in preterm pigs sensitive to necrotizing enterocolitis

  Wu, Z., Bæk, O., Muk, T., Yang, L., Shen, R. L., Gangadharan, B., Bilic, I., Nielsen, D. S., Sangild, P. T. & Nguyen, D. N., 2024, In: Biomedicine and Pharmacotherapy. 179, 13 p., 117391.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Downloads (Pure)

• Fermentation Analytical Technology (FAT): Monitoring industrial E. coli fermentations using absolute quantitative ¹H NMR spectroscopy

  Forsberg, J., Rasmussen, C. T., van den Berg, F. W. J., Engelsen, S. B. & Aru, V., 2024, In: Analytica Chimica Acta. 1311, 10 p., 342722.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  9 Downloads (Pure)

• Fermented Rapeseed and Soybean Alone and in Combination with Macro Algae Inhibit Human and Pig Pathogenic Bacteria In Vitro

  Beck, F., Pedersen, N. R. & Nielsen, D. S., 2024, In: Microorganisms. 12, 5, 13 p., 891.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  1 Citation (Scopus)

  9 Downloads (Pure)

• Fish oil supplementation during pregnancy, anthropometrics, and metabolic health at age ten: A randomized clinical trial

  Vinding, R. K., Sevelsted, A., Horner, D., Vahman, N., Lauritzen, L., Hagen, C. P., Chawes, B., Stokholm, J. & Bønnelykke, K., 2024, In: American Journal of Clinical Nutrition. 119, 4, p. 960-968

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  4 Citations (Scopus)

  9 Downloads (Pure)

• Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study

  Røder, H. L., Christidi, E., Amador, C. I., Music, S., Olesen, A. K., Svensson, B., Madsen, J. S., Herschend, J., Kreft, J-U. & Burmølle, M., 2024, In: Applied and Environmental Microbiology. 90, 1, 15 p., e01510-23.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

• Genetic predisposition to high BMI increases risk of early life respiratory infections and episodes of severe wheeze and asthma

  Jensen, S. K., Pedersen, C. E. T., Fischer-Rasmussen, K., Melgaard, M. E., Brustad, N., Kyvsgaard, J. N., Vahman, N., Schoos, A. M. M., Stokholm, J., Chawes, B., Eliasen, A. & Bønnelykke, K., 2024, In: European Respiratory Journal. 64, 3, 16 p., 2400169.

  Research output: Contribution to journal › Journal article › Research › peer-review
  2 Citations (Scopus)

• Gut heavy metal and antibiotic resistome of humans living in the high Arctic

  Hauptmann, A. L., Johansen, J., Stæger, F. F., Nielsen, D. S., Mulvad, G., Hanghøj, K., Rasmussen, S., Hansen, T. & Albrechtsen, A., 2024, In: Frontiers in Microbiology. 15, 15 p., 1493803.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Gut microbiota-mediated polyphenol metabolism is restrained by parasitic whipworm infection and associated with altered immune function in mice

  Schytz Andersen-Civil, A. I., Arora, P., Zhu, L., Myhill, L. J., Büdeyri Gökgöz, N., Castro-Mejia, J. L., Leppä, M. M., Hansen, L. H., Lessard-Lord, J., Salminen, J. P., Thamsborg, S. M., Sandris Nielsen, D., Desjardins, Y. & Williams, A. R., 2024, In: Gut Microbes. 16, 1, 23 p., 2370917.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  11 Downloads (Pure)

• Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia

  Tesfaw, G., Siraj, D. S., Abdissa, A., Jakobsen, R. R., Johansen, Ø. H., Zangenberg, M., Hanevik, K., Mekonnen, Z., Langeland, N., Bjørang, O., Safdar, N., Mapes, A. C., Kates, A., Krych, L., Castro-Mejía, J. L. & Nielsen, D. S., 2024, In: Nature Communications. 15, 1, 15 p., 7532.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• High-dose vitamin D3 supplementation in pregnancy and risk of neurodevelopmental disorders in the children at age 10: A randomized clinical trial

  Aagaard, K., Jepsen, J. R. M., Sevelsted, A., Horner, D., Vinding, R., Rosenberg, J. B., Brustad, N., Eliasen, A., Mohammadzadeh, P., Følsgaard, N., Hernández-lorca, M., Fagerlund, B., Glenthøj, B. Y., Rasmussen, M. A., Bilenberg, N., Stokholm, J., Bønnelykke, K., Ebdrup, B. H. & Chawes, B., 2024, In: The American Journal of Clinical Nutrition. 119, 2, p. 362-370 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  4 Citations (Scopus)

  20 Downloads (Pure)

• High fat diet is associated with gut microbiota dysbiosis and decreased gut microbial derived metabolites related to metabolic health in young Göttingen Minipigs

  Lützhøft, D. O., Bækgård, C., Wimborne, E., Straarup, E. M., Pedersen, K. M., Swann, J. R., Pedersen, H. D., Kristensen, K., Morgills, L., Nielsen, D. S., Hansen, A. K., Bracken, M. K., Cirera, S. & Christoffersen, B. Ø., 2024, In: PLoS ONE. 19, 3, 27 p., e0298602.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  2 Citations (Scopus)

  19 Downloads (Pure)

• Infantile colic is associated with development of later constipation and atopic disorders

  Stokholm, J., Thorsen, J., Schoos, A-M. M., Rasmussen, M. A., Brandt, S., Sørensen, S. J., Vahman, N., Chawes, B. & Bønnelykke, K., 2024, (Accepted/In press) In: Allergy: European Journal of Allergy and Clinical Immunology.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

• Influence of dairy matrix on the prebiotic effects of inulin related to gut metabolic activity and bone health

  Zhao, X., He, W., Jakobsen, L. M. A., Panah, F. M., Correia, B. S. B., Nielsen, D. S., Hansen, A. K. & Bertram, H. C., 2024, In: Food and Function. 15, 22, p. 11129-11140 12 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

• Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth

  Yang, N., Røder, H. L., Wicaksono, W. A., Wassermann, B., Russel, J., Li, X., Nesme, J., Berg, G., Sørensen, S. J. & Burmølle, M., 2024, In: The ISME Journal. 18, 1, 15 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Key risk factors of asthma-like symptoms are mediated through infection burden in early childhood

  Kyvsgaard, J. N., Brustad, N., Hesselberg, L. M., Vahman, N., Thorsen, J., Schoos, A. M. M., Bønnelykke, K., Stokholm, J. & Chawes, B. L., 2024, In: Journal of Allergy and Clinical Immunology. 153, 3, p. 684-694 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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  2 Citations (Scopus)

  2 Downloads (Pure)

• Levels of total IgE versus specific IgE during childhood for defining and predicting T2-high asthma

  Sultan, T., Skov, F., Brustad, N., Vahman, N., Stokholm, J., Bønnelykke, K., Schoos, A. M. M. & Chawes, B., 2024, In: World Allergy Organization Journal. 17, 12, 12 p., 100994.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

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• Liraglutide and Colesevelam Changes Serum and Fecal Bile Acid Levels in a Randomized Trial with Patients with Bile Acid Diarrhea

  Ellegaard, A. M., Kårhus, M. L., Krych, L., Sonne, D. P., Forman, J. L., Hansen, S. H., Dragsted, L. O., Nielsen, D. S. & Knop, F. K., 2024, In: Clinical and Translational Gastroenterology. 15, 11, 14 p., e00772.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• Longitudinal Sensitization Patterns in Childhood and Adolescence

  Thorsen, J., Rasmussen, M. A., Chawes, B., Stokholm, J., Bønnelykke, K. & Schoos, A-M. M., 2024, (E-pub ahead of print) In: Allergy.

  Research output: Contribution to journal › Letter › Research › peer-review

• Low-gainer diet-induced obese microbiota transplanted mice exhibit increased fighting

  Junker Mentzel, C. M., Hui, Y., Hammerich, T. M. S., Klug-Dambmann, M., Liu, Y., Zachariassen, L. F., Hansen, L. H., Aslampaloglou, A., Kiersgaard, M., Nielsen, D. S., Hansen, A. K. & Krych, L., 2024, In: Clinical and Translational Science. 17, 9, 12 p., e13906.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies

  Zachariasen, T., Russel, J., Petersen, C., Vestergaard, G. A., Shah, S., Atienza Lopez, P., Passali, M., Turvey, S. E., Sørensen, S. J., Lund, O., Stokholm, J., Brejnrod, A. & Thorsen, J., 2024, In: Nature Communications. 15, 1, 10 p., 5734.

  Research output: Contribution to journal › Journal article › Research › peer-review

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