title: Genome analysis of Flaviramulus ichthyoenteri Th78(T) in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine.
abstract: BACKGROUND
  Intestinal microbes play significant roles in fish and can be possibly used as probiotics in aquaculture. In our previous study, Flaviramulus ichthyoenteri Th78(T), a novel species in the family Flavobacteriaceae, was isolated from fish intestine and showed strong quorum quenching (QQ) ability. To identify the QQ enzymes in Th78(T) and explore the potential roles of Th78(T) in fish intestine, we sequenced the genome of Th78(T) and performed extensive genomic analysis.
  
  
  RESULTS
  An N-acyl homoserine lactonase FiaL belonging to the metallo-β-lactamase superfamily was identified and the QQ activity of heterologously expressed FiaL was confirmed in vitro. FiaL has relatively little similarity to the known lactonases (25.2 ~ 27.9% identity in amino acid sequence). Various digestive enzymes including alginate lyases and lipases can be produced by Th78(T), and enzymes essential for production of B vitamins such as biotin, riboflavin and folate are predicted. Genes encoding sialic acid lyases, sialidases, sulfatases and fucosidases, which contribute to utilization of mucus, are present in the genome. In addition, genes related to response to different stresses and gliding motility were also identified. Comparative genome analysis shows that Th78(T) has more specific genes involved in carbohydrate transport and metabolism compared to other two isolates in Flavobacteriaceae, both isolated from sediments.
  
  
  CONCLUSIONS
  The genome of Th78(T) exhibits evident advantages for this bacterium to survive in the fish intestine, including production of QQ enzyme, utilization of various nutrients available in the intestine as well as the ability to produce digestive enzymes and vitamins, which also provides an application prospect of Th78(T) to be used as a probiotic in aquaculture.
authors: College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China. yhzhang2011@163.com.
authors: Yunhui
authors: Y
authors: Zhang
authors: College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China. liujiwen333@163.com.
authors: Jiwen
authors: J
authors: Liu
authors: College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China. 98w8h1@163.com.
authors: Kaihao
authors: K
authors: Tang
authors: College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China. yumin@ouc.edu.cn.
authors: Min
authors: M
authors: Yu
authors: Laboratory of Pharmaceutical Microbiology, Ghent University, 9000, Gent, Belgium. tom.coenye@ugent.be.
authors: Tom
authors: T
authors: Coenye
authors: College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, P.R. China. xhzhang@ouc.edu.cn.
authors: Xiao-Hua
authors: XH
authors: Zhang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002265:Carboxylic Ester Hydrolases / Q000235:genetics; D005399:Fishes / Q000382:microbiology*; D041965:Flavobacteriaceae / Q000235:genetics*; D007422:Intestines / Q000382:microbiology; D053038:Quorum Sensing; D017422:Sequence Analysis, DNA; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D002265:Carboxylic Ester Hydrolases; C432003:N-acyl homoserine lactonase; D001618:beta-Lactamases
references: Appl Environ Microbiol. 2008 Mar;74(5):1357-66
references: 18192419
references: Sci Rep. 2013;3:2935
references: 24121744
references: Appl Environ Microbiol. 2010 Aug;76(15):4933-42
references: 20525860
references: J Bacteriol. 2002 Aug;184(15):4304-7
references: 12107150
references: Mol Microbiol. 2014 May;92(4):872-84
references: 24684269
references: Annu Rev Cell Dev Biol. 2005;21:319-46
references: 16212498
references: Appl Environ Microbiol. 2012 Nov;78(22):7985-92
references: 22941089
references: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references: 10592173
references: BMC Genomics. 2010;11:247
references: 20398413
references: Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3526-31
references: 10716724
references: BMC Genomics. 2008;9:75
references: 18261238
references: Appl Environ Microbiol. 2000 Apr;66(4):1692-7
references: 10742262
references: Microbiol Mol Biol Rev. 2004 Mar;68(1):132-53
references: 15007099
references: Int J Syst Evol Microbiol. 2013 Dec;63(Pt 12):4477-83
references: 23859948
references: Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S19
references: 21995734
references: J Bacteriol. 2005 Oct;187(20):6943-52
references: 16199564
references: Science. 1998 Apr 10;280(5361):295-8
references: 9535661
references: Curr Microbiol. 1999 Aug;39(2):68-72
references: 10398829
references: Trends Microbiol. 2003 Jun;11(6):248-53
references: 12823939
references: J Appl Microbiol. 2010 Jan;108(1):139-47
references: 19548884
references: Environ Microbiol. 2006 Dec;8(12):2201-13
references: 17107561
references: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references: 9023104
references: Infect Immun. 2002 Dec;70(12):7161-4
references: 12438402
references: Genome Biol Evol. 2014 Jan;6(1):133-48
references: 24391155
references: Biol Chem. 1998 Jan;379(1):1-18
references: 9504711
references: Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1845-9
references: 16166676
references: J Bacteriol. 1997 May;179(9):3004-12
references: 9139920
references: Appl Environ Microbiol. 2009 Nov;75(21):6864-75
references: 19717629
references: Bioinformatics. 2007 Mar 15;23(6):673-9
references: 17237039
references: Nucleic Acids Res. 2005;33(17):5691-702
references: 16214803
references: J Biol Chem. 2012 Jul 13;287(29):24605-17
references: 22593568
references: Trends Microbiol. 1994 Aug;2(8):271-7
references: 7981969
references: J Biol Chem. 1999 Nov 5;274(45):31751-4
references: 10542193
references: Appl Microbiol Biotechnol. 2011 Feb;89(4):903-15
references: 21088832
references: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4638-43
references: 11930013
references: Appl Environ Microbiol. 2005 Sep;71(9):4966-71
references: 16151074
references: J Biosci Bioeng. 2012 Jan;113(1):20-5
references: 22019407
references: Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8724-9
references: 18552178
references: J Bacteriol. 1991 May;173(9):3000-9
references: 1902216
references: Appl Environ Microbiol. 2010 Apr;76(8):2524-30
references: 20173075
references: J Bacteriol. 2010 Mar;192(5):1201-11
references: 20038590
references: J Bacteriol. 2013 Jan;195(2):270-8
references: 23123910
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
references: 17130148
references: Appl Environ Microbiol. 2013 Nov;79(21):6813-22
references: 23995932
references: Genome Biol Evol. 2013;5(1):187-99
references: 23292138
references: BMC Genomics. 2013;14:707
references: 24131871
references: Nucleic Acids Res. 2007;35(9):3100-8
references: 17452365
references: Trends Microbiol. 2002 Jun;10(6):254-7
references: 12088651
references: J Bacteriol. 2011 Sep;193(17):4545-6
references: 21725025
references: J Bacteriol. 1997 Sep;179(17):5271-81
references: 9286976
references: FEMS Immunol Med Microbiol. 2008 Mar;52(2):145-54
references: 18081845
references: FEMS Microbiol Ecol. 2002 Feb 1;39(2):91-100
references: 19709188
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40
references: 18953034
references: Appl Environ Microbiol. 2003 Aug;69(8):4989-93
references: 12902298
references: Can J Microbiol. 2006 Dec;52(12):1266-71
references: 17473897
references: Appl Environ Microbiol. 2003 Nov;69(11):6949-53
references: 14602662
references: Nucleic Acids Res. 2001 Jan 1;29(1):41-3
references: 11125044
references: Dis Aquat Organ. 2005 Jun 14;65(1):43-52
references: 16042042
references: Annu Rev Microbiol. 2001;55:49-75
references: 11544349
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Science. 1997 Oct 24;278(5338):631-7
references: 9381173
references: ScientificWorldJournal. 2002 Mar 5;2:558-72
references: 12805983
references: Microbiology. 2003 Jun;149(Pt 6):1541-50
references: 12777494
references: FEMS Microbiol Rev. 2001 Aug;25(4):365-404
references: 11524130
references: BMC Evol Biol. 2009;9:118
references: 19470179
references: Genome Res. 2010 Feb;20(2):265-72
references: 20019144