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Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum.

Lindenberg F, Krych L, Fielden J, Kot W, Frøkiær H, van Galen G, Nielsen DS, Hansen AK.

Sci Rep. 2019 Sep 3;9(1):12674. doi: 10.1038/s41598-019-49081-5.


Genomic and Ecogenomic Characterization of Proteus mirabilis Bacteriophages.

Alves DR, Nzakizwanayo J, Dedi C, Olympiou C, Hanin A, Kot W, Hansen L, Lametsch R, Gahan CGM, Schellenberger P, Ogilvie LA, Jones BV.

Front Microbiol. 2019 Aug 6;10:1783. doi: 10.3389/fmicb.2019.01783. eCollection 2019.


A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples.

Deng L, Silins R, Castro-Mejía JL, Kot W, Jessen L, Thorsen J, Shah S, Stokholm J, Bisgaard H, Moineau S, Nielsen DS.

Viruses. 2019 Jul 20;11(7). pii: E667. doi: 10.3390/v11070667.


Prebiotic Effect of Lycopene and Dark Chocolate on Gut Microbiome with Systemic Changes in Liver Metabolism, Skeletal Muscles and Skin in Moderately Obese Persons.

Wiese M, Bashmakov Y, Chalyk N, Nielsen DS, Krych Ł, Kot W, Klochkov V, Pristensky D, Bandaletova T, Chernyshova M, Kyle N, Petyaev I.

Biomed Res Int. 2019 Jun 2;2019:4625279. doi: 10.1155/2019/4625279. eCollection 2019.


Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum-A Novel Lineage of Lactobacillus Phages Comprising Five New Members.

Kyrkou I, Byth Carstens A, Ellegaard-Jensen L, Kot W, Zervas A, Djurhuus AM, Neve H, Hansen M, Hestbjerg Hansen L.

Viruses. 2019 Jul 4;11(7). pii: E611. doi: 10.3390/v11070611.


Targeting gut microbiota and barrier function with prebiotics to alleviate autoimmune manifestations in NOD mice.

Hansen CHF, Larsen CS, Petersson HO, Zachariassen LF, Vegge A, Lauridsen C, Kot W, Krych Ł, Nielsen DS, Hansen AK.

Diabetologia. 2019 Sep;62(9):1689-1700. doi: 10.1007/s00125-019-4910-5. Epub 2019 May 28.


A novel six-phage cocktail reduces Pectobacterium atrosepticum soft rot infection in potato tubers under simulated storage conditions.

Carstens AB, Djurhuus AM, Kot W, Hansen LH.

FEMS Microbiol Lett. 2019 May 1;366(9). pii: fnz101. doi: 10.1093/femsle/fnz101.


Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation.

Ren S, Hui Y, Goericke-Pesch S, Pankratova S, Kot W, Pan X, Thymann T, Sangild PT, Nguyen DN.

Am J Physiol Gastrointest Liver Physiol. 2019 Jul 1;317(1):G67-G77. doi: 10.1152/ajpgi.00042.2019. Epub 2019 May 15.


Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet.

Rasmussen TS, de Vries L, Kot W, Hansen LH, Castro-Mejía JL, Vogensen FK, Hansen AK, Nielsen DS.

Viruses. 2019 May 13;11(5). pii: E435. doi: 10.3390/v11050435.


The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health.

Li Z, Rasmussen TS, Rasmussen ML, Li J, Henríquez Olguín C, Kot W, Nielsen DS, Jensen TE.

Front Microbiol. 2019 Apr 4;10:709. doi: 10.3389/fmicb.2019.00709. eCollection 2019.


Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties.

Larsen N, Bussolo de Souza C, Krych L, Barbosa Cahú T, Wiese M, Kot W, Hansen KM, Blennow A, Venema K, Jespersen L.

Front Microbiol. 2019 Feb 15;10:223. doi: 10.3389/fmicb.2019.00223. eCollection 2019.


Cesarean Section Induces Microbiota-Regulated Immune Disturbances in C57BL/6 Mice.

Zachariassen LF, Krych L, Rasmussen SH, Nielsen DS, Kot W, Holm TL, Hansen AK, Hansen CHF.

J Immunol. 2019 Jan 1;202(1):142-150. doi: 10.4049/jimmunol.1800666. Epub 2018 Nov 28.


Isolation and characterization of bacteriophages active against methicillin-resistant Staphylococcus pseudintermedius.

Moodley A, Kot W, Nälgård S, Jakociune D, Neve H, Hansen LH, Guardabassi L, Vogensen FK.

Res Vet Sci. 2019 Feb;122:81-85. doi: 10.1016/j.rvsc.2018.11.008. Epub 2018 Nov 12.


Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani.

Carstens AB, Djurhuus AM, Kot W, Jacobs-Sera D, Hatfull GF, Hansen LH.

Viruses. 2018 Nov 10;10(11). pii: E621. doi: 10.3390/v10110621.


Cheese brines from Danish dairies reveal a complex microbiota comprising several halotolerant bacteria and yeasts.

Haastrup MK, Johansen P, Malskær AH, Castro-Mejía JL, Kot W, Krych L, Arneborg N, Jespersen L.

Int J Food Microbiol. 2018 Nov 20;285:173-187. doi: 10.1016/j.ijfoodmicro.2018.08.015. Epub 2018 Aug 23.


Modulation of gut microbiota from obese individuals by in vitro fermentation of citrus pectin in combination with Bifidobacterium longum BB-46.

Bianchi F, Larsen N, de Mello Tieghi T, Adorno MAT, Kot W, Saad SMI, Jespersen L, Sivieri K.

Appl Microbiol Biotechnol. 2018 Oct;102(20):8827-8840. doi: 10.1007/s00253-018-9234-8. Epub 2018 Aug 18.


Neonatal gut and immune maturation is determined more by postnatal age than by postconceptional age in moderately preterm pigs.

Ren S, Hui Y, Obelitz-Ryom K, Brandt AB, Kot W, Nielsen DS, Thymann T, Sangild PT, Nguyen DN.

Am J Physiol Gastrointest Liver Physiol. 2018 Nov 1;315(5):G855-G867. doi: 10.1152/ajpgi.00169.2018. Epub 2018 Aug 17.


Effect of the dietary polyacetylenes falcarinol and falcarindiol on the gut microbiota composition in a rat model of colorectal cancer.

Kobaek-Larsen M, Nielsen DS, Kot W, Krych Ł, Christensen LP, Baatrup G.

BMC Res Notes. 2018 Jun 27;11(1):411. doi: 10.1186/s13104-018-3527-y.


Gut microbiota recovery and immune response in ampicillin-treated mice.

Castro-Mejía JL, Jakesevic M, Fabricius NF, Krych Ł, Nielsen DS, Kot W, Bendtsen KM, Vogensen FK, Hansen CHF, Hansen AK.

Res Vet Sci. 2018 Jun;118:357-364. doi: 10.1016/j.rvsc.2018.03.013. Epub 2018 Mar 27.


Oral insulin does not alter gut microbiota composition of NOD mice.

Kihl P, Krych L, Buschard K, Wesley JD, Kot W, Hansen AK, Nielsen DS, von Herrath MG.

Diabetes Metab Res Rev. 2018 Sep;34(6):e3010. doi: 10.1002/dmrr.3010. Epub 2018 May 1.


Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches.

Muhammed MK, Olsen ML, Kot W, Neve H, Castro-Mejía JL, Janzen T, Hansen LH, Nielsen DS, Sørensen SJ, Heller KJ, Vogensen FK.

Int J Food Microbiol. 2018 May 2;272:61-72. doi: 10.1016/j.ijfoodmicro.2018.02.012. Epub 2018 Feb 21.


Genome Sequencing of dsDNA-Containing Bacteriophages Directly from a Single Plaque.

Kot W.

Methods Mol Biol. 2018;1681:179-184. doi: 10.1007/978-1-4939-7343-9_13.


Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR.

Krych Ł, Kot W, Bendtsen KMB, Hansen AK, Vogensen FK, Nielsen DS.

J Microbiol Methods. 2018 Jan;144:1-7. doi: 10.1016/j.mimet.2017.10.015. Epub 2017 Oct 28.


In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina.

Behrendt L, Raina JB, Lutz A, Kot W, Albertsen M, Halkjær-Nielsen P, Sørensen SJ, Larkum AW, Kühl M.

ISME J. 2017 Oct 31. doi: 10.1038/ismej.2017.192. [Epub ahead of print]


The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages.

Nielsen TK, Carstens AB, Browne P, Lametsch R, Neve H, Kot W, Hansen LH.

Sci Rep. 2017 Oct 19;7(1):13566. doi: 10.1038/s41598-017-13911-1.


Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures.

Muhammed MK, Kot W, Neve H, Mahony J, Castro-Mejía JL, Krych L, Hansen LH, Nielsen DS, Sørensen SJ, Heller KJ, van Sinderen D, Vogensen FK.

Appl Environ Microbiol. 2017 Sep 15;83(19). pii: e00888-17. doi: 10.1128/AEM.00888-17. Print 2017 Oct 1.


Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1.

Kot W, Sabri M, Gingras H, Ouellette M, Tremblay DM, Moineau S.

Genome Announc. 2017 Jul 13;5(28). pii: e00333-17. doi: 10.1128/genomeA.00333-17.


Degradation of mecoprop in polluted landfill leachate and waste water in a moving bed biofilm reactor.

Escolà Casas M, Nielsen TK, Kot W, Hansen LH, Johansen A, Bester K.

Water Res. 2017 Sep 15;121:213-220. doi: 10.1016/j.watres.2017.05.031. Epub 2017 May 17.


Immunological effects of reduced mucosal integrity in the early life of BALB/c mice.

Bendtsen KM, Hansen CHF, Krych Ł, Skovgaard K, Kot W, Vogensen FK, Hansen AK.

PLoS One. 2017 May 1;12(5):e0176662. doi: 10.1371/journal.pone.0176662. eCollection 2017.


Sensitivity to oxazolone induced dermatitis is transferable with gut microbiota in mice.

Zachariassen LF, Krych L, Engkilde K, Nielsen DS, Kot W, Hansen CH, Hansen AK.

Sci Rep. 2017 Mar 14;7:44385. doi: 10.1038/srep44385.


Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures.

Frantzen CA, Kot W, Pedersen TB, Ardö YM, Broadbent JR, Neve H, Hansen LH, Dal Bello F, Østlie HM, Kleppen HP, Vogensen FK, Holo H.

Front Microbiol. 2017 Feb 3;8:132. doi: 10.3389/fmicb.2017.00132. eCollection 2017.


Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species.

Szymczak P, Janzen T, Neves AR, Kot W, Hansen LH, Lametsch R, Neve H, Franz CMAP, Vogensen FK.

Appl Environ Microbiol. 2017 Feb 15;83(5). pii: e02748-16. doi: 10.1128/AEM.02748-16. Print 2017 Mar 1.


Whey powders are a rich source and excellent storage matrix for dairy bacteriophages.

Wagner N, Brinks E, Samtlebe M, Hinrichs J, Atamer Z, Kot W, Franz CMAP, Neve H, Heller KJ.

Int J Food Microbiol. 2017 Jan 16;241:308-317. doi: 10.1016/j.ijfoodmicro.2016.10.037. Epub 2016 Nov 1.


Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer.

Madsen JS, Riber L, Kot W, Basfeld A, Burmølle M, Hansen LH, Sørensen SJ.

PLoS One. 2016 Sep 14;11(9):e0162390. doi: 10.1371/journal.pone.0162390. eCollection 2016.


Clear Plaque Mutants of Lactococcal Phage TP901-1.

Kot W, Kilstrup M, Vogensen FK, Hammer K.

PLoS One. 2016 Jun 3;11(6):e0155233. doi: 10.1371/journal.pone.0155233. eCollection 2016.


Characterisation of a novel enterobacteria phage, CAjan, isolated from rat faeces.

Carstens AB, Kot W, Lametsch R, Neve H, Hansen LH.

Arch Virol. 2016 Aug;161(8):2219-26. doi: 10.1007/s00705-016-2901-0. Epub 2016 May 26.


Genome Sequence of Selenium-Solubilizing Bacterium Caulobacter vibrioides T5M6.

Wang Y, Qin Y, Kot W, Zhang F, Zheng S, Wang G, Hansen LH, Rensing C.

Genome Announc. 2016 Feb 11;4(1). pii: e01721-15. doi: 10.1128/genomeA.01721-15.


Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut.

Castro-Mejía JL, Muhammed MK, Kot W, Neve H, Franz CM, Hansen LH, Vogensen FK, Nielsen DS.

Microbiome. 2015 Nov 17;3:64. doi: 10.1186/s40168-015-0131-4.


Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition.

León-Sobrino C, Kot WP, Garrett RA.

Mol Microbiol. 2016 Feb;99(4):719-28. doi: 10.1111/mmi.13263. Epub 2015 Nov 27.


A novel bacteriophage cocktail reduces and disperses Pseudomonas aeruginosa biofilms under static and flow conditions.

Alves DR, Perez-Esteban P, Kot W, Bean JE, Arnot T, Hansen LH, Enright MC, Jenkins AT.

Microb Biotechnol. 2016 Jan;9(1):61-74. doi: 10.1111/1751-7915.12316. Epub 2015 Sep 8.


Complete Genome Sequences of Four Novel Escherichia coli Bacteriophages Belonging to New Phage Groups.

Carstens AB, Kot W, Hansen LH.

Genome Announc. 2015 Jul 16;3(4). pii: e00741-15. doi: 10.1128/genomeA.00741-15.


Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33.

Li X, Kot W, Wang D, Zheng S, Wang G, Hansen LH, Rensing C.

Genome Announc. 2015 May 7;3(3). pii: e00406-15. doi: 10.1128/genomeA.00406-15.


Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark.

Nielsen TK, Kot W, Sørensen SR, Hansen LH.

Genome Announc. 2015 Feb 12;3(1). pii: e01529-14. doi: 10.1128/genomeA.01529-14.


Combined use of bacteriophage K and a novel bacteriophage to reduce Staphylococcus aureus biofilm formation.

Alves DR, Gaudion A, Bean JE, Perez Esteban P, Arnot TC, Harper DR, Kot W, Hansen LH, Enright MC, Jenkins AT.

Appl Environ Microbiol. 2014 Nov;80(21):6694-703. doi: 10.1128/AEM.01789-14. Epub 2014 Aug 22.


Complete Genome Sequences of Four Novel Lactococcus lactis Phages Distantly Related to the Rare 1706 Phage Species.

Kot W, Neve H, Vogensen FK, Heller KJ, Sørensen SJ, Hansen LH.

Genome Announc. 2014 Jul 10;2(4). pii: e00265-14. doi: 10.1128/genomeA.00265-14.


Genome Sequence of Leuconostoc mesenteroides subsp. cremoris Strain T26, Isolated from Mesophilic Undefined Cheese Starter.

Pedersen TB, Kot WP, Hansen LH, Sørensen SJ, Broadbent JR, Vogensen FK, Ardö Y.

Genome Announc. 2014 Jun 5;2(3). pii: e00485-14. doi: 10.1128/genomeA.00485-14.


Genome Sequences of Two Leuconostoc pseudomesenteroides Strains Isolated from Danish Dairy Starter Cultures.

Pedersen TB, Kot WP, Hansen LH, Sørensen SJ, Broadbent JR, Vogensen FK, Ardö Y.

Genome Announc. 2014 Jun 5;2(3). pii: e00484-14. doi: 10.1128/genomeA.00484-14.


Bacteriophages of leuconostoc, oenococcus, and weissella.

Kot W, Neve H, Heller KJ, Vogensen FK.

Front Microbiol. 2014 Apr 28;5:186. doi: 10.3389/fmicb.2014.00186. eCollection 2014. Review.


Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

Kot W, Hansen LH, Neve H, Hammer K, Jacobsen S, Pedersen PD, Sørensen SJ, Heller KJ, Vogensen FK.

Int J Food Microbiol. 2014 Apr 17;176:29-37. doi: 10.1016/j.ijfoodmicro.2014.01.019. Epub 2014 Feb 5.


DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque.

Kot W, Vogensen FK, Sørensen SJ, Hansen LH.

J Virol Methods. 2014 Feb;196:152-6. doi: 10.1016/j.jviromet.2013.10.040. Epub 2013 Nov 14.


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