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Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes.

Huys GR, Raes J.

Curr Opin Microbiol. 2018 Aug;44:1-8. doi: 10.1016/j.mib.2018.05.002. Epub 2018 Jun 13. Review.


Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany.

Cho GS, Li B, Rostalsky A, Fiedler G, Rösch N, Igbinosa E, Kabisch J, Bockelmann W, Hammer P, Huys G, Franz CMAP.

Front Microbiol. 2018 Mar 27;9:536. doi: 10.3389/fmicb.2018.00536. eCollection 2018.


Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources.

Huys G, Purohit P, Tan CH, Snauwaert C, Vos P, Saffar HA, Obaid IA, Busse HJ, Seemann T, Albert MJ.

Int J Syst Evol Microbiol. 2017 May;67(5):1415-1421. doi: 10.1099/ijsem.0.001832. Epub 2017 Jun 5.


Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex mainly recovered from clinical samples in different countries.

Cosgaya C, Marí-Almirall M, Van Assche A, Fernández-Orth D, Mosqueda N, Telli M, Huys G, Higgins PG, Seifert H, Lievens B, Roca I, Vila J.

Int J Syst Evol Microbiol. 2016 Oct;66(10):4105-4111. doi: 10.1099/ijsem.0.001318. Epub 2016 Jul 15.


Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC.

Machiels K, Sabino J, Vandermosten L, Joossens M, Arijs I, de Bruyn M, Eeckhaut V, Van Assche G, Ferrante M, Verhaegen J, Van Steen K, Van Immerseel F, Huys G, Verbeke K, Wolthuis A, de Buck Van Overstraeten A, D'Hoore A, Rutgeerts P, Vermeire S.

Gut. 2017 Jan;66(1):79-88. doi: 10.1136/gutjnl-2015-309398. Epub 2015 Sep 30.


Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs.

Becker AA, Janssens GP, Snauwaert C, Hesta M, Huys G.

PLoS One. 2015 Apr 23;10(4):e0123933. doi: 10.1371/journal.pone.0123933. eCollection 2015.


Wheat bran extract alters colonic fermentation and microbial composition, but does not affect faecal water toxicity: a randomised controlled trial in healthy subjects.

Windey K, De Preter V, Huys G, Broekaert WF, Delcour JA, Louat T, Herman J, Verbeke K.

Br J Nutr. 2015 Jan 28;113(2):225-38. doi: 10.1017/S0007114514003523. Epub 2014 Dec 12.


Probiotics: an update.

Vandenplas Y, Huys G, Daube G.

J Pediatr (Rio J). 2015 Jan-Feb;91(1):6-21. doi: 10.1016/j.jped.2014.08.005. Epub 2014 Oct 23. Review.


Psychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014.

Pothakos V, Taminiau B, Huys G, Nezer C, Daube G, Devlieghere F.

Int J Food Microbiol. 2014 Nov 17;191:157-63. doi: 10.1016/j.ijfoodmicro.2014.09.013. Epub 2014 Sep 19.


Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.

Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, Robertson L.

Syst Appl Microbiol. 2014 Jul;37(5):329-35. doi: 10.1016/j.syapm.2014.05.003. Epub 2014 May 27. Erratum in: Syst Appl Microbiol. 2014 Oct;37(7):541-2.


Monitoring psychrotrophic lactic acid bacteria contamination in a ready-to-eat vegetable salad production environment.

Pothakos V, Snauwaert C, De Vos P, Huys G, Devlieghere F.

Int J Food Microbiol. 2014 Aug 18;185:7-16. doi: 10.1016/j.ijfoodmicro.2014.05.009. Epub 2014 May 15.


Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003.

Christiaen SE, O'Connell Motherway M, Bottacini F, Lanigan N, Casey PG, Huys G, Nelis HJ, van Sinderen D, Coenye T.

PLoS One. 2014 May 28;9(5):e98111. doi: 10.1371/journal.pone.0098111. eCollection 2014.


Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae.

Becker AA, Hesta M, Hollants J, Janssens GP, Huys G.

BMC Microbiol. 2014 Feb 18;14:43. doi: 10.1186/1471-2180-14-43.


Psychrotrophic members of Leuconostoc gasicomitatum, Leuconostoc gelidum and Lactococcus piscium dominate at the end of shelf-life in packaged and chilled-stored food products in Belgium.

Pothakos V, Snauwaert C, De Vos P, Huys G, Devlieghere F.

Food Microbiol. 2014 May;39:61-7. doi: 10.1016/ Epub 2013 Nov 19.


Gut microbiota affects sensitivity to acute DSS-induced colitis independently of host genotype.

Brinkman BM, Becker A, Ayiseh RB, Hildebrand F, Raes J, Huys G, Vandenabeele P.

Inflamm Bowel Dis. 2013 Nov;19(12):2560-7. doi: 10.1097/MIB.0b013e3182a8759a.


The Italian Hafnia alvei strain LMG 27376 is Hafnia paralvei.

Savini V, Argentieri AV, Marrollo R, Carretto E, Fazii P, D'Antonio D, Huys G.

Vet Microbiol. 2013 Dec 27;167(3-4):742-3. doi: 10.1016/j.vetmic.2013.07.026. Epub 2013 Aug 6. No abstract available.


Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

Hamet MF, Londero A, Medrano M, Vercammen E, Van Hoorde K, Garrote GL, Huys G, Vandamme P, Abraham AG.

Food Microbiol. 2013 Dec;36(2):327-34. doi: 10.1016/ Epub 2013 Jul 5.


Acinetobacter kookii sp. nov., isolated from soil.

Choi JY, Ko G, Jheong W, Huys G, Seifert H, Dijkshoorn L, Ko KS.

Int J Syst Evol Microbiol. 2013 Dec;63(Pt 12):4402-6. doi: 10.1099/ijs.0.047969-0. Epub 2013 Aug 15.


Amoxicillin-clavulanic acid resistance in fecal Enterobacteriaceae from patients with cystic fibrosis and healthy siblings.

Duytschaever G, Huys G, Boulanger L, De Boeck K, Vandamme P.

J Cyst Fibros. 2013 Dec;12(6):780-3. doi: 10.1016/j.jcf.2013.06.006. Epub 2013 Jul 16.


Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC).

Huys G, Botteldoorn N, Delvigne F, De Vuyst L, Heyndrickx M, Pot B, Dubois JJ, Daube G.

Mol Nutr Food Res. 2013 Aug;57(8):1479-504. doi: 10.1002/mnfr.201300065. Epub 2013 Jun 25.


Dysbiosis of bifidobacteria and Clostridium cluster XIVa in the cystic fibrosis fecal microbiota.

Duytschaever G, Huys G, Bekaert M, Boulanger L, De Boeck K, Vandamme P.

J Cyst Fibros. 2013 May;12(3):206-15. doi: 10.1016/j.jcf.2012.10.003. Epub 2012 Nov 11.


Selective culturing and genus-specific PCR detection for identification of Aeromonas in tissue samples to assist the medico-legal diagnosis of death by drowning.

Huys G, Coopman V, Van Varenbergh D, Cordonnier J.

Forensic Sci Int. 2012 Sep 10;221(1-3):11-5. doi: 10.1016/j.forsciint.2012.03.017. Epub 2012 Apr 11.


Food fermentations: microorganisms with technological beneficial use.

Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, Hammes WP, Harnett J, Huys G, Laulund S, Ouwehand A, Powell IB, Prajapati JB, Seto Y, Ter Schure E, Van Boven A, Vankerckhoven V, Zgoda A, Tuijtelaars S, Hansen EB.

Int J Food Microbiol. 2012 Mar 15;154(3):87-97. doi: 10.1016/j.ijfoodmicro.2011.12.030. Epub 2011 Dec 31. Review. Erratum in: Int J Food Microbiol. 2012 Jun 1;156(3):301.


Cross-sectional and longitudinal comparisons of the predominant fecal microbiota compositions of a group of pediatric patients with cystic fibrosis and their healthy siblings.

Duytschaever G, Huys G, Bekaert M, Boulanger L, De Boeck K, Vandamme P.

Appl Environ Microbiol. 2011 Nov;77(22):8015-24. doi: 10.1128/AEM.05933-11. Epub 2011 Sep 16.


Safety assessment of probiotics for human use.

Sanders ME, Akkermans LM, Haller D, Hammerman C, Heimbach J, Hörmannsperger G, Huys G, Levy DD, Lutgendorff F, Mack D, Phothirath P, Solano-Aguilar G, Vaughan E.

Gut Microbes. 2010 May-Jun;1(3):164-85. doi: 10.4161/gmic.1.3.12127. Epub 2010 Mar 4. Review.


Diversity and dynamics of bacterial populations during spontaneous sorghum fermentations used to produce ting, a South African food.

Madoroba E, Steenkamp ET, Theron J, Scheirlinck I, Cloete TE, Huys G.

Syst Appl Microbiol. 2011 May;34(3):227-34. doi: 10.1016/j.syapm.2010.11.016. Epub 2011 Feb 6.


Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives.

Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S.

Gut. 2011 May;60(5):631-7. doi: 10.1136/gut.2010.223263. Epub 2011 Jan 5.


High-throughput method for comparative analysis of denaturing gradient gel electrophoresis profiles from human fecal samples reveals significant increases in two bifidobacterial species after inulin-type prebiotic intake.

Joossens M, Huys G, Van Steen K, Cnockaert M, Vermeire S, Rutgeerts P, Verbeke K, Vandamme P, De Preter V.

FEMS Microbiol Ecol. 2011 Feb;75(2):343-9. doi: 10.1111/j.1574-6941.2010.01008.x. Epub 2010 Dec 6.


Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations.

Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, Huys G, Vandamme P, Van Hummelen P, De Vuyst L.

Appl Environ Microbiol. 2011 Jan;77(2):618-26. doi: 10.1128/AEM.02028-10. Epub 2010 Nov 19.


Selection, application and monitoring of Lactobacillus paracasei strains as adjunct cultures in the production of Gouda-type cheeses.

Van Hoorde K, Van Leuven I, Dirinck P, Heyndrickx M, Coudijzer K, Vandamme P, Huys G.

Int J Food Microbiol. 2010 Dec 15;144(2):226-35. doi: 10.1016/j.ijfoodmicro.2010.05.007. Epub 2010 May 20.


Antibiotic susceptibility of members of the Lactobacillus acidophilus group using broth microdilution and molecular identification of their resistance determinants.

Mayrhofer S, van Hoek AH, Mair C, Huys G, Aarts HJ, Kneifel W, Domig KJ.

Int J Food Microbiol. 2010 Nov 15;144(1):81-7. doi: 10.1016/j.ijfoodmicro.2010.08.024. Epub 2010 Oct 1.


Lactic acid bacteria community dynamics and metabolite production of rye sourdough fermentations share characteristics of wheat and spelt sourdough fermentations.

Weckx S, Van der Meulen R, Maes D, Scheirlinck I, Huys G, Vandamme P, De Vuyst L.

Food Microbiol. 2010 Dec;27(8):1000-8. doi: 10.1016/ Epub 2010 Jun 25.


Tolerance and safety of the potentially probiotic strain Lactobacillus rhamnosus PRSF-L477: a randomised, double-blind placebo-controlled trial in healthy volunteers.

Wind RD, Tolboom H, Klare I, Huys G, Knol J.

Br J Nutr. 2010 Dec;104(12):1806-16. doi: 10.1017/S0007114510002746. Epub 2010 Aug 9.


Community dynamics of bacteria in sourdough fermentations as revealed by their metatranscriptome.

Weckx S, Van der Meulen R, Allemeersch J, Huys G, Vandamme P, Van Hummelen P, De Vuyst L.

Appl Environ Microbiol. 2010 Aug;76(16):5402-8. doi: 10.1128/AEM.00570-10. Epub 2010 Jun 25.


Molecular basis and transferability of tetracycline resistance in Enterococcus italicus LMG 22195 from fermented milk.

Zago M, Huys G, Giraffa G.

Int J Food Microbiol. 2010 Aug 15;142(1-2):234-6. doi: 10.1016/j.ijfoodmicro.2010.05.022. Epub 2010 Jun 4.


Intra- and interlaboratory performances of two commercial antimicrobial susceptibility testing methods for bifidobacteria and nonenterococcal lactic acid bacteria.

Huys G, D'Haene K, Cnockaert M, Tosi L, Danielsen M, Flórez AB, Mättö J, Axelsson L, Korhonen J, Mayrhofer S, Egervärn M, Giacomini M, Vandamme P.

Antimicrob Agents Chemother. 2010 Jun;54(6):2567-74. doi: 10.1128/AAC.00407-10. Epub 2010 Apr 12.


Yeast species composition differs between artisan bakery and spontaneous laboratory sourdoughs.

Vrancken G, De Vuyst L, Van der Meulen R, Huys G, Vandamme P, Daniel HM.

FEMS Yeast Res. 2010 Jun;10(4):471-81. doi: 10.1111/j.1567-1364.2010.00621.x. Epub 2010 Mar 10.


Influence of pasteurization, brining conditions and production environment on the microbiota of artisan Gouda-type cheeses.

Van Hoorde K, Heyndrickx M, Vandamme P, Huys G.

Food Microbiol. 2010 May;27(3):425-33. doi: 10.1016/ Epub 2009 Dec 11.


Multiplex PCR method for detection of three Aeromonas enterotoxin genes.

Kingombe CI, D'Aoust JY, Huys G, Hofmann L, Rao M, Kwan J.

Appl Environ Microbiol. 2010 Jan;76(2):425-33. doi: 10.1128/AEM.01357-09. Epub 2009 Nov 20.


Diversity of lactic acid bacteria from modified atmosphere packaged sliced cooked meat products at sell-by date assessed by PCR-denaturing gradient gel electrophoresis.

Audenaert K, D'Haene K, Messens K, Ruyssen T, Vandamme P, Huys G.

Food Microbiol. 2010 Feb;27(1):12-8. doi: 10.1016/ Epub 2009 May 4.


Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2.

Huys G, Cnockaert M, Abbott SL, Janda JM, Vandamme P.

Int J Syst Evol Microbiol. 2010 Aug;60(Pt 8):1725-8. doi: 10.1099/ijs.0.018606-0. Epub 2009 Sep 4.


Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria.

Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, Huys G, Vandamme P, Van Hummelen P, De Vuyst L.

Appl Environ Microbiol. 2009 Oct;75(20):6488-95. doi: 10.1128/AEM.01055-09. Epub 2009 Aug 14.


Human vaginal Lactobacillus rhamnosus harbor mutation in 23S rRNA associated with erythromycin resistance.

Begovic J, Huys G, Mayo B, D'Haene K, Florez AB, Lozo J, Kojic M, Strahinic I, Topisirovic L.

Res Microbiol. 2009 Jul-Aug;160(6):421-6. doi: 10.1016/j.resmic.2009.07.005. Epub 2009 Jul 18.


Prevalence and transmission of antimicrobial resistance among Aeromonas populations from a duckweed aquaculture based hospital sewage water recycling system in Bangladesh.

Rahman M, Huys G, Kühn I, Rahman M, Möllby R.

Antonie Van Leeuwenhoek. 2009 Oct;96(3):313-21. doi: 10.1007/s10482-009-9348-1. Epub 2009 May 21.


Polyphasic taxonomic characterization of Lactobacillus rossiae isolates from Belgian and Italian sourdoughs reveals intraspecific heterogeneity.

Scheirlinck I, Van der Meulen R, Vrancken G, De Vuyst L, Settanni L, Vandamme P, Huys G.

Syst Appl Microbiol. 2009 Apr;32(2):151-6. doi: 10.1016/j.syapm.2008.12.006. Epub 2009 Feb 7.


Diversity of lactic acid bacteria in two Flemish artisan raw milk Gouda-type cheeses.

Van Hoorde K, Verstraete T, Vandamme P, Huys G.

Food Microbiol. 2008 Oct;25(7):929-35. doi: 10.1016/ Epub 2008 Jun 21.


Genotypic diversity, antimicrobial resistance, and virulence factors of human isolates and probiotic cultures constituting two intraspecific groups of Enterococcus faecium isolates.

Vankerckhoven V, Huys G, Vancanneyt M, Snauwaert C, Swings J, Klare I, Witte W, Van Autgaerden T, Chapelle S, Lammens C, Goossens H.

Appl Environ Microbiol. 2008 Jul;74(14):4247-55. doi: 10.1128/AEM.02474-07. Epub 2008 May 16.


Comparison of broth microdilution, Etest, and agar disk diffusion methods for antimicrobial susceptibility testing of Lactobacillus acidophilus group members.

Mayrhofer S, Domig KJ, Mair C, Zitz U, Huys G, Kneifel W.

Appl Environ Microbiol. 2008 Jun;74(12):3745-8. doi: 10.1128/AEM.02849-07. Epub 2008 Apr 25.


Phenotypic and molecular assessment of antimicrobial resistance in Lactobacillus paracasei strains of food origin.

Huys G, D'Haene K, Danielsen M, Mättö J, Egervärn M, Vandamme P.

J Food Prot. 2008 Feb;71(2):339-44.


Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

Scheirlinck I, Van der Meulen R, Van Schoor A, Vancanneyt M, De Vuyst L, Vandamme P, Huys G.

Appl Environ Microbiol. 2008 Apr;74(8):2414-23. doi: 10.1128/AEM.02771-07. Epub 2008 Feb 29.

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