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Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis.

Edwards JE, Hermes GDA, Kittelmann S, Nijsse B, Smidt H.

Front Microbiol. 2019 Oct 18;10:2370. doi: 10.3389/fmicb.2019.02370. eCollection 2019.


Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens.

Kers JG, Fischer EAJ, Stegeman JA, Smidt H, Velkers FC.

Microorganisms. 2019 Oct 10;7(10). pii: E431. doi: 10.3390/microorganisms7100431.


Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths.

Indraningrat AAG, Micheller S, Runderkamp M, Sauerland I, Becking LE, Smidt H, Sipkema D.

Mar Drugs. 2019 Oct 11;17(10). pii: E578. doi: 10.3390/md17100578.


Sugar Beet Pectin Supplementation Did Not Alter Profiles of Fecal Microbiota and Exhaled Breath in Healthy Young Adults and Healthy Elderly.

An R, Wilms E, Smolinska A, Hermes GDA, Masclee AAM, de Vos P, Schols HA, van Schooten FJ, Smidt H, Jonkers DMAE, Zoetendal EG, Troost FJ.

Nutrients. 2019 Sep 12;11(9). pii: E2193. doi: 10.3390/nu11092193.


Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation.

Glatter M, Borewicz K, van den Bogert B, Wensch-Dorendorf M, Bochnia M, Greef JM, Bachmann M, Smidt H, Breves G, Zeyner A.

PLoS One. 2019 Aug 8;14(8):e0220553. doi: 10.1371/journal.pone.0220553. eCollection 2019.


Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation.

Koistinen VM, Kärkkäinen O, Borewicz K, Zarei I, Jokkala J, Micard V, Rosa-Sibakov N, Auriola S, Aura AM, Smidt H, Hanhineva K.

Microbiome. 2019 Jul 10;7(1):103. doi: 10.1186/s40168-019-0718-2.


Diversity of tryptophan halogenases in sponges of the genus Aplysina.

Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, Sipkema D.

FEMS Microbiol Ecol. 2019 Aug 1;95(8). pii: fiz108. doi: 10.1093/femsec/fiz108.


Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants.

Peng P, Schneidewind U, Haest PJ, Bosma TNP, Danko AS, Smidt H, Atashgahi S.

Appl Microbiol Biotechnol. 2019 Aug;103(16):6837-6849. doi: 10.1007/s00253-019-09985-8. Epub 2019 Jun 28.


The dark side of technological advances in analysis of microbial ecosystems.

Bailey M, Thomas A, Francis O, Stokes C, Smidt H.

J Anim Sci Biotechnol. 2019 Jun 17;10:49. doi: 10.1186/s40104-019-0357-2. eCollection 2019. Review.


Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content.

Vaidya JD, Hornung BVH, Smidt H, Edwards JE, Plugge CM.

Int J Syst Evol Microbiol. 2019 Aug;69(8):2584-2590. doi: 10.1099/ijsem.0.003544. Epub 2019 Jun 24.


Differences in gut microbiota composition of laying hen lines divergently selected on feather pecking.

van der Eijk JAJ, de Vries H, Kjaer JB, Naguib M, Kemp B, Smidt H, Rodenburg TB, Lammers A.

Poult Sci. 2019 Jun 21. pii: pez336. doi: 10.3382/ps/pez336. [Epub ahead of print]


Correlating Infant Faecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of One-Month Old Breastfed Infants.

Borewicz K, Gu F, Saccenti E, Arts ICW, Penders J, Thijs C, van Leeuwen SS, Lindner C, Nauta A, van Leusen E, Schols HA, Smidt H.

Mol Nutr Food Res. 2019 Apr 24:e1801214. doi: 10.1002/mnfr.201801214. [Epub ahead of print]


Reconstructing functional networks in the human intestinal tract using synthetic microbiomes.

Shetty SA, Smidt H, de Vos WM.

Curr Opin Biotechnol. 2019 Aug;58:146-154. doi: 10.1016/j.copbio.2019.03.009. Epub 2019 Apr 6. Review.


Legionella growth potential of drinking water produced by a reverse osmosis pilot plant.

Learbuch KLG, Lut MC, Liu G, Smidt H, van der Wielen PWJJ.

Water Res. 2019 Jun 15;157:55-63. doi: 10.1016/j.watres.2019.03.037. Epub 2019 Mar 21.


Associated bacteria of Botryococcus braunii (Chlorophyta).

Gouveia JD, Lian J, Steinert G, Smidt H, Sipkema D, Wijffels RH, Barbosa MJ.

PeerJ. 2019 Mar 27;7:e6610. doi: 10.7717/peerj.6610. eCollection 2019.


Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women.

Hechler C, Borewicz K, Beijers R, Saccenti E, Riksen-Walraven M, Smidt H, de Weerth C.

Sci Rep. 2019 Mar 14;9(1):4463. doi: 10.1038/s41598-019-40434-8.


The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.

Elzinga J, van der Oost J, de Vos WM, Smidt H.

Microbiol Mol Biol Rev. 2019 Mar 13;83(2). pii: e00054-18. doi: 10.1128/MMBR.00054-18. Print 2019 May 15. Review.


The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life.

Borewicz K, Suarez-Diez M, Hechler C, Beijers R, de Weerth C, Arts I, Penders J, Thijs C, Nauta A, Lindner C, Van Leusen E, Vaughan EE, Smidt H.

Sci Rep. 2019 Feb 21;9(1):2434. doi: 10.1038/s41598-018-38268-x.


Toll-Like Receptor-Dependent Immunomodulatory Activity of Pycnogenol®.

Verlaet A, van der Bolt N, Meijer B, Breynaert A, Naessens T, Konstanti P, Smidt H, Hermans N, Savelkoul HFJ, Teodorowicz M.

Nutrients. 2019 Jan 22;11(2). pii: E214. doi: 10.3390/nu11020214.


High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria.

Versluis D, de J Bello González T, Zoetendal EG, Passel MWJV, Smidt H.

PLoS One. 2019 Jan 17;14(1):e0210970. doi: 10.1371/journal.pone.0210970. eCollection 2019.


Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds.

Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D.

Front Microbiol. 2018 Dec 12;9:3079. doi: 10.3389/fmicb.2018.03079. eCollection 2018. Review.


Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater.

van der Waals MJ, Plugge C, Meima-Franke M, de Waard P, Bodelier PLE, Smidt H, Gerritse J.

Water Res. 2019 Jan 1;148:314-323. doi: 10.1016/j.watres.2018.10.050. Epub 2018 Oct 22.


Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces.

Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM.

Int J Syst Evol Microbiol. 2018 Dec;68(12):3741-3746. doi: 10.1099/ijsem.0.003041. Epub 2018 Oct 23.


Non-invasive continuous real-time in vivo analysis of microbial hydrogen production shows adaptation to fermentable carbohydrates in mice.

Fernández-Calleja JMS, Konstanti P, Swarts HJM, Bouwman LMS, Garcia-Campayo V, Billecke N, Oosting A, Smidt H, Keijer J, van Schothorst EM.

Sci Rep. 2018 Oct 18;8(1):15351. doi: 10.1038/s41598-018-33619-0.


Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future.

Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP.

Front Microbiol. 2018 Sep 25;9:2161. doi: 10.3389/fmicb.2018.02161. eCollection 2018. Review.


Do apes smell like humans? The role of skin bacteria and volatiles of primates in mosquito host selection.

Verhulst NO, Umanets A, Weldegergis BT, Maas JPA, Visser TM, Dicke M, Smidt H, Takken W.

J Exp Biol. 2018 Nov 16;221(Pt 22). pii: jeb185959. doi: 10.1242/jeb.185959.


Gut Microbiota and Body Weight in School-Aged Children: The KOALA Birth Cohort Study.

Mbakwa CA, Hermes GDA, Penders J, Savelkoul PHM, Thijs C, Dagnelie PC, Mommers M, Zoetendal EG, Smidt H, Arts ICW.

Obesity (Silver Spring). 2018 Nov;26(11):1767-1776. doi: 10.1002/oby.22320. Epub 2018 Oct 8.


Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent.

Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H.

Int J Syst Evol Microbiol. 2018 Nov;68(11):3479-3486. doi: 10.1099/ijsem.0.003012. Epub 2018 Sep 18.


Sex differences in lipid metabolism are affected by presence of the gut microbiota.

Baars A, Oosting A, Lohuis M, Koehorst M, El Aidy S, Hugenholtz F, Smidt H, Mischke M, Boekschoten MV, Verkade HJ, Garssen J, van der Beek EM, Knol J, de Vos P, van Bergenhenegouwen J, Fransen F.

Sci Rep. 2018 Sep 7;8(1):13426. doi: 10.1038/s41598-018-31695-w.


Age-dependent changes in GI physiology and microbiota: time to reconsider?

An R, Wilms E, Masclee AAM, Smidt H, Zoetendal EG, Jonkers D.

Gut. 2018 Dec;67(12):2213-2222. doi: 10.1136/gutjnl-2017-315542. Epub 2018 Sep 7. Review.


Short-Term Microbiota Manipulation and Forearm Substrate Metabolism in Obese Men: A Randomized, Double-Blind, Placebo-Controlled Trial.

Reijnders D, Goossens GH, Hermes GDA, Smidt H, Zoetendal EG, Blaak EE.

Obes Facts. 2018;11(4):318-326. doi: 10.1159/000492114. Epub 2018 Aug 9.


Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut.

Atashgahi S, Shetty SA, Smidt H, de Vos WM.

Front Physiol. 2018 Jul 10;9:888. doi: 10.3389/fphys.2018.00888. eCollection 2018. Review.


The effect of the algal microbiome on industrial production of microalgae.

Lian J, Wijffels RH, Smidt H, Sipkema D.

Microb Biotechnol. 2018 Sep;11(5):806-818. doi: 10.1111/1751-7915.13296. Epub 2018 Jul 5. Review.


Fifty Percent Human - how art brings us in touch with our microbial cohabitants.

Bäumel S, Tytgat HLP, Nemec B, Schmidt R, Chia LW, Smidt H.

Microb Biotechnol. 2018 Jul;11(4):571-574. doi: 10.1111/1751-7915.13285.


Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats.

Marozava S, Vargas-López R, Tian Y, Merl-Pham J, Braster M, Meckenstock RU, Smidt H, Röling WFM, Westerhoff HV.

Environ Microbiol. 2018 Jul;20(7):2652-2669. doi: 10.1111/1462-2920.14295.


Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam.

Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D.

PeerJ. 2018 Jun 8;6:e4970. doi: 10.7717/peerj.4970. eCollection 2018.


Prospects for harnessing biocide resistance for bioremediation and detoxification.

Atashgahi S, Sánchez-Andrea I, Heipieper HJ, van der Meer JR, Stams AJM, Smidt H.

Science. 2018 May 18;360(6390):743-746. doi: 10.1126/science.aar3778. Review.


Correction to: Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges.

Versluis D, McPherson K, van Passel MWJ, Smidt H, Sipkema D.

Mar Biotechnol (NY). 2018 Aug;20(4):557. doi: 10.1007/s10126-018-9829-1.


In Vitro Fermentation Behavior of Isomalto/Malto-Polysaccharides Using Human Fecal Inoculum Indicates Prebiotic Potential.

Gu F, Borewicz K, Richter B, van der Zaal PH, Smidt H, Buwalda PL, Schols HA.

Mol Nutr Food Res. 2018 Jun;62(12):e1800232. doi: 10.1002/mnfr.201800232. Epub 2018 May 28.


Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut.

Hugenholtz F, Davids M, Schwarz J, Müller M, Tomé D, Schaap P, Hooiveld GJEJ, Smidt H, Kleerebezem M.

PLoS One. 2018 Apr 17;13(4):e0194066. doi: 10.1371/journal.pone.0194066. eCollection 2018.


Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice.

Kok DEG, Rusli F, van der Lugt B, Lute C, Laghi L, Salvioli S, Picone G, Franceschi C, Smidt H, Vervoort J, Kampman E, Müller M, Steegenga WT.

J Nutr Biochem. 2018 Jun;56:152-164. doi: 10.1016/j.jnutbio.2018.01.001. Epub 2018 Mar 20.


Studying microbial functionality within the gut ecosystem by systems biology.

Hornung B, Martins Dos Santos VAP, Smidt H, Schaap PJ.

Genes Nutr. 2018 Mar 6;13:5. doi: 10.1186/s12263-018-0594-6. eCollection 2018. Review.


A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways.

Atashgahi S, Hornung B, van der Waals MJ, da Rocha UN, Hugenholtz F, Nijsse B, Molenaar D, van Spanning R, Stams AJM, Gerritse J, Smidt H.

Sci Rep. 2018 Mar 14;8(1):4490. doi: 10.1038/s41598-018-22617-x.


Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens.

Kers JG, Velkers FC, Fischer EAJ, Hermes GDA, Stegeman JA, Smidt H.

Front Microbiol. 2018 Feb 16;9:235. doi: 10.3389/fmicb.2018.00235. eCollection 2018. Review.


Optimized procedures for generating an enhanced, near physiological 2D culture system from porcine intestinal organoids.

van der Hee B, Loonen LMP, Taverne N, Taverne-Thiele JJ, Smidt H, Wells JM.

Stem Cell Res. 2018 Apr;28:165-171. doi: 10.1016/j.scr.2018.02.013. Epub 2018 Feb 20.


Anaerobic degradation of a mixture of MtBE, EtBE, TBA, and benzene under different redox conditions.

van der Waals MJ, Pijls C, Sinke AJC, Langenhoff AAM, Smidt H, Gerritse J.

Appl Microbiol Biotechnol. 2018 Apr;102(7):3387-3397. doi: 10.1007/s00253-018-8853-4. Epub 2018 Feb 24.


The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows.

Vaidya JD, van den Bogert B, Edwards JE, Boekhorst J, van Gastelen S, Saccenti E, Plugge CM, Smidt H.

Front Microbiol. 2018 Jan 31;9:92. doi: 10.3389/fmicb.2018.00092. eCollection 2018.


Occupancy strongly influences faecal microbial composition of wild lemurs.

Umanets A, de Winter I, IJdema F, Ramiro-Garcia J, van Hooft P, Heitkönig IMA, Prins HHT, Smidt H.

FEMS Microbiol Ecol. 2018 Mar 1;94(3). doi: 10.1093/femsec/fiy017.


Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.

Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, Sipkema D.

Genome Biol Evol. 2018 Jan 1;10(1):125-142. doi: 10.1093/gbe/evx271.


Organohalide respiration in pristine environments: implications for the natural halogen cycle.

Atashgahi S, Häggblom MM, Smidt H.

Environ Microbiol. 2018 Mar;20(3):934-948. doi: 10.1111/1462-2920.14016. Epub 2017 Dec 15. Review.


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