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Unravelling plasmidome distribution and interaction with its hosting microbiome.

Brown Kav A, Rozov R, Bogumil D, Sørensen SJ, Hansen LH, Benhar I, Halperin E, Shamir R, Mizrahi I.

Environ Microbiol. 2019 Oct 10. doi: 10.1111/1462-2920.14813. [Epub ahead of print]


Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments.

Cyriaque V, Jacquiod S, Riber L, Abu Al-Soud W, Gillan DC, Sørensen SJ, Wattiez R.

J Hazard Mater. 2019 Sep 6;382:121173. doi: 10.1016/j.jhazmat.2019.121173. [Epub ahead of print]


Interspecies interactions reduce selection for a biofilm optimized variant in a four-species biofilm model.

Røder HL, Liu W, Sørensen SJ, Madsen JS, Burmølle M.

Environ Microbiol. 2019 Sep 12. doi: 10.1111/1462-2920.14802. [Epub ahead of print]


Priority of Early Colonizers but No Effect on Cohabitants in a Synergistic Biofilm Community.

Olsen NMC, Røder HL, Russel J, Madsen JS, Sørensen SJ, Burmølle M.

Front Microbiol. 2019 Aug 23;10:1949. doi: 10.3389/fmicb.2019.01949. eCollection 2019.


Deciphering links between bacterial interactions and spatial organization in multispecies biofilms.

Liu W, Jacquiod S, Brejnrod A, Russel J, Burmølle M, Sørensen SJ.

ISME J. 2019 Aug 27. doi: 10.1038/s41396-019-0494-9. [Epub ahead of print]


Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats.

Heins AL, Johanson T, Han S, Lundin L, Carlquist M, Gernaey KV, Sørensen SJ, Eliasson Lantz A.

Front Bioeng Biotechnol. 2019 Aug 5;7:187. doi: 10.3389/fbioe.2019.00187. eCollection 2019.


Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing.

Gupta S, Mortensen MS, Schjørring S, Trivedi U, Vestergaard G, Stokholm J, Bisgaard H, Krogfelt KA, Sørensen SJ.

Commun Biol. 2019 Aug 5;2:291. doi: 10.1038/s42003-019-0540-1. eCollection 2019.


Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems.

Romero IA, van Dillewijn P, Nesme J, Sørensen SJ, Romero E.

Sci Total Environ. 2019 Nov 15;691:749-759. doi: 10.1016/j.scitotenv.2019.07.087. Epub 2019 Jul 7.


Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil.

Blau K, Jacquiod S, Sørensen SJ, Su JQ, Zhu YG, Smalla K, Jechalke S.

Front Microbiol. 2019 Apr 16;10:725. doi: 10.3389/fmicb.2019.00725. eCollection 2019.


Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce.

Paul Chowdhury S, Babin D, Sandmann M, Jacquiod S, Sommermann L, Sørensen SJ, Fliessbach A, Mäder P, Geistlinger J, Smalla K, Rothballer M, Grosch R.

Environ Microbiol. 2019 Jul;21(7):2426-2439. doi: 10.1111/1462-2920.14631. Epub 2019 Apr 29.


Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps.

Borg Dahl M, Brejnrod AD, Russel J, Sørensen SJ, Schnittler M.

Microb Ecol. 2019 Oct;78(3):764-780. doi: 10.1007/s00248-019-01347-1. Epub 2019 Mar 22.


Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli.

Anjum M, Madsen JS, Nesme J, Jana B, Wiese M, Jasinskytė D, Nielsen DS, Sørensen SJ, Dalsgaard A, Moodley A, Bortolaia V, Guardabassi L.

Antimicrob Agents Chemother. 2019 Apr 25;63(5). pii: e02528-18. doi: 10.1128/AAC.02528-18. Print 2019 May.


Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites.

Li X, Brejnrod AD, Ernst M, Rykær M, Herschend J, Olsen NMC, Dorrestein PC, Rensing C, Sørensen SJ.

Environ Int. 2019 May;126:454-467. doi: 10.1016/j.envint.2019.02.048. Epub 2019 Mar 4.


The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures.

Heins AL, Lundin L, Nunes I, Gernaey KV, Sørensen SJ, Lantz AE.

Biotechnol Prog. 2019 May;35(3):e2796. doi: 10.1002/btpr.2796. Epub 2019 Mar 21.


Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass.

Jakobsen AM, Bahl MI, Buschhardt T, Hansen TB, Al-Soud WA, Brejnrod AD, Sørensen SJ, Nesbakken T, Aabo S.

Int J Food Microbiol. 2019 Apr 16;295:8-18. doi: 10.1016/j.ijfoodmicro.2019.02.003. Epub 2019 Feb 4.


Stability and resilience of the intestinal microbiota in children in daycare - a 12 month cohort study.

Mortensen MS, Hebbelstrup Jensen B, Williams J, Brejnrod AD, O'Brien Andersen L, Röser D, Andreassen BU, Petersen AM, Stensvold CR, Sørensen SJ, Krogfelt KA.

BMC Microbiol. 2018 Dec 22;18(1):223. doi: 10.1186/s12866-018-1367-5.


Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages.

Jacquiod S, Nunes I, Brejnrod A, Hansen MA, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ.

Microbiome. 2018 Dec 13;6(1):223. doi: 10.1186/s40168-018-0606-1.


Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease.

Kanfra X, Liu B, Beerhues L, Sørensen SJ, Heuer H.

Front Plant Sci. 2018 Nov 16;9:1666. doi: 10.3389/fpls.2018.01666. eCollection 2018.


Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial.

Wei S, Mortensen MS, Stokholm J, Brejnrod AD, Thorsen J, Rasmussen MA, Trivedi U, Bisgaard H, Sørensen SJ.

EBioMedicine. 2018 Dec;38:265-272. doi: 10.1016/j.ebiom.2018.11.035. Epub 2018 Nov 23.


Staphylococcus aureus coagulases are exploitable yet stable public goods in clinically relevant conditions.

Trivedi U, Madsen JS, Everett J, Fell C, Russel J, Haaber J, Crosby HA, Horswill AR, Burmølle M, Rumbaugh KP, Sørensen SJ.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11771-E11779. doi: 10.1073/pnas.1804850115. Epub 2018 Nov 21.


Intra- and inter-field diversity of 2,4-dichlorophenoxyacetic acid-degradative plasmids and their tfd catabolic genes in rice fields of the Mekong delta in Vietnam.

Nguyen TPO, Hansen MA, Hansen LH, Horemans B, Sørensen SJ, De Mot R, Springael D.

FEMS Microbiol Ecol. 2019 Jan 1;95(1). doi: 10.1093/femsec/fiy214.


Soil amendment with sewage sludge affects soil prokaryotic community composition, mobilome and resistome.

Wolters B, Fornefeld E, Jechalke S, Su JQ, Zhu YG, Sørensen SJ, Smalla K, Jacquiod S.

FEMS Microbiol Ecol. 2019 Jan 1;95(1). doi: 10.1093/femsec/fiy193.


Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity.

Kang D, Herschend J, Al-Soud WA, Mortensen MS, Gonzalo M, Jacquiod S, Sørensen SJ.

Bioresour Technol. 2018 Dec;270:303-310. doi: 10.1016/j.biortech.2018.09.006. Epub 2018 Sep 4.


Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows.

Zhu Z, Kristensen L, Difford GF, Poulsen M, Noel SJ, Abu Al-Soud W, Sørensen SJ, Lassen J, Løvendahl P, Højberg O.

J Dairy Sci. 2018 Nov;101(11):9847-9862. doi: 10.3168/jds.2017-14366. Epub 2018 Aug 29.


Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives.

Pinilla-Redondo R, Cyriaque V, Jacquiod S, Sørensen SJ, Riber L.

Plasmid. 2018 Sep;99:56-67. doi: 10.1016/j.plasmid.2018.08.002. Epub 2018 Aug 4. Review.


The bacterial microbiota in first-void urine from men with and without idiopathic urethritis.

Frølund M, Wikström A, Lidbrink P, Abu Al-Soud W, Larsen N, Harder CB, Sørensen SJ, Jensen JS, Ahrens P.

PLoS One. 2018 Jul 27;13(7):e0201380. doi: 10.1371/journal.pone.0201380. eCollection 2018.


A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities.

Anjum M, Madsen JS, Espinosa-Gongora C, Jana B, Wiese M, Nielsen DS, Sørensen SJ, Moodley A, Bortolaia V, Guardabassi L.

J Microbiol Methods. 2018 Sep;152:18-26. doi: 10.1016/j.mimet.2018.07.009. Epub 2018 Jul 18.


How Microbial Aggregates Protect against Nanoparticle Toxicity.

Tang J, Wu Y, Esquivel-Elizondo S, Sørensen SJ, Rittmann BE.

Trends Biotechnol. 2018 Nov;36(11):1171-1182. doi: 10.1016/j.tibtech.2018.06.009. Epub 2018 Jul 17. Review.


Enhanced bacterial mutualism through an evolved biofilm phenotype.

Røder HL, Herschend J, Russel J, Andersen MF, Madsen JS, Sørensen SJ, Burmølle M.

ISME J. 2018 Nov;12(11):2608-2618. doi: 10.1038/s41396-018-0165-2. Epub 2018 Jul 5.


An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer.

Madsen JS, Hylling O, Jacquiod S, Pécastaings S, Hansen LH, Riber L, Vestergaard G, Sørensen SJ.

ISME J. 2018 Sep;12(9):2330-2334. doi: 10.1038/s41396-018-0183-0. Epub 2018 Jun 13.


Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm.

Liu W, Russel J, Burmølle M, Sørensen SJ, Madsen JS.

ISME J. 2018 Aug;12(8):1940-1951. doi: 10.1038/s41396-018-0112-2. Epub 2018 Apr 18.


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.


Nutrient Fortification of Human Donor Milk Affects Intestinal Function and Protein Metabolism in Preterm Pigs.

Sun J, Li Y, Nguyen DN, Mortensen MS, van den Akker CHP, Skeath T, Pors SE, Pankratova S, Rudloff S, Sørensen SJ, Burrin DG, Thymann T, Sangild PT.

J Nutr. 2018 Mar 1;148(3):336-347. doi: 10.1093/jn/nxx033.


Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization.

Wolters B, Jacquiod S, Sørensen SJ, Widyasari-Mehta A, Bech TB, Kreuzig R, Smalla K.

FEMS Microbiol Ecol. 2018 Apr 1;94(4). doi: 10.1093/femsec/fiy027.


Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers.

Zupančič J, Raghupathi PK, Houf K, Burmølle M, Sørensen SJ, Gunde-Cimerman N.

Front Microbiol. 2018 Jan 30;9:21. doi: 10.3389/fmicb.2018.00021. eCollection 2018.


Publisher Correction: Maturation of the gut microbiome and risk of asthma in childhood.

Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H.

Nat Commun. 2018 Feb 13;9(1):704. doi: 10.1038/s41467-018-03150-x.


Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan.

Raghupathi PK, Liu W, Sabbe K, Houf K, Burmølle M, Sørensen SJ.

Front Microbiol. 2018 Jan 9;8:2649. doi: 10.3389/fmicb.2017.02649. eCollection 2017.


Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities.

Raghupathi PK, Zupančič J, Brejnrod AD, Jacquiod S, Houf K, Burmølle M, Gunde-Cimerman N, Sørensen SJ.

Appl Environ Microbiol. 2018 Feb 14;84(5). pii: e02755-17. doi: 10.1128/AEM.02755-17. Print 2018 Mar 1.


Fluorescence Recovery Allows the Implementation of a Fluorescence Reporter Gene Platform Applicable for the Detection and Quantification of Horizontal Gene Transfer in Anoxic Environments.

Pinilla-Redondo R, Riber L, Sørensen SJ.

Appl Environ Microbiol. 2018 Mar 1;84(6). pii: e02507-17. doi: 10.1128/AEM.02507-17. Print 2018 Mar 15.


Maturation of the gut microbiome and risk of asthma in childhood.

Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H.

Nat Commun. 2018 Jan 10;9(1):141. doi: 10.1038/s41467-017-02573-2. Erratum in: Nat Commun. 2018 Feb 13;9(1):704.


Bacterial social interactions and the emergence of community-intrinsic properties.

Madsen JS, Sørensen SJ, Burmølle M.

Curr Opin Microbiol. 2018 Apr;42:104-109. doi: 10.1016/j.mib.2017.11.018. Epub 2017 Dec 1. Review.


A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community.

Herschend J, Damholt ZBV, Marquard AM, Svensson B, Sørensen SJ, Hägglund P, Burmølle M.

Sci Rep. 2017 Nov 28;7(1):16483. doi: 10.1038/s41598-017-16633-6.


Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period.

Zhu Z, Noel SJ, Difford GF, Al-Soud WA, Brejnrod A, Sørensen SJ, Lassen J, Løvendahl P, Højberg O.

PLoS One. 2017 Nov 8;12(11):e0187858. doi: 10.1371/journal.pone.0187858. eCollection 2017.


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]


A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil.

Ghodsalavi B, Svenningsen NB, Hao X, Olsson S, Nicolaisen MH, Al-Soud WA, Sørensen SJ, Nybroe O.

PLoS One. 2017 Oct 27;12(10):e0187116. doi: 10.1371/journal.pone.0187116. eCollection 2017.


Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome.

Jacquiod S, Cyriaque V, Riber L, Al-Soud WA, Gillan DC, Wattiez R, Sørensen SJ.

J Hazard Mater. 2018 Feb 15;344:299-307. doi: 10.1016/j.jhazmat.2017.09.046. Epub 2017 Sep 28.


Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies.

Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M.

Mol Ecol Resour. 2018 Mar;18(2):306-318. doi: 10.1111/1755-0998.12725. Epub 2017 Nov 4.


Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation.

Jurburg SD, Nunes I, Brejnrod A, Jacquiod S, Priemé A, Sørensen SJ, Van Elsas JD, Salles JF.

Front Microbiol. 2017 Sep 25;8:1832. doi: 10.3389/fmicb.2017.01832. eCollection 2017.


Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.


Antagonism correlates with metabolic similarity in diverse bacteria.

Russel J, Røder HL, Madsen JS, Burmølle M, Sørensen SJ.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):10684-10688. doi: 10.1073/pnas.1706016114. Epub 2017 Sep 18.

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