메뉴 건너뛰기




Volumn 7, Issue 6, 2015, Pages 1455-1473

Functionally structured genomes in lactobacillus kunkeei colonizing the honey crop and food products of honeybees and stingless bees

Author keywords

Genome organization; Genome reduction; Honeybee; Lactobacillus kunkeei; Recombination

Indexed keywords

BACTERIAL PROTEIN;

EID: 84979862576     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv079     Document Type: Article
Times cited : (45)

References (102)
  • 1
    • 77954272855 scopus 로고    scopus 로고
    • TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations
    • Abascal F, Zardoya R, Telford MJ. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38:W7-W13.
    • (2010) Nucleic Acids Res. , vol.38 , pp. W7-W13
    • Abascal, F.1    Zardoya, R.2    Telford, M.J.3
  • 2
    • 84879761410 scopus 로고    scopus 로고
    • Do honeybees shape the bacterial community composition in floral nectar?
    • Aizenberg-Gershtein Y, Izhaki I, Halpern M. 2013. Do honeybees shape the bacterial community composition in floral nectar? PLoS One 8:e67556
    • (2013) PLoS One , vol.8
    • Aizenberg-Gershtein, Y.1    Izhaki, I.2    Halpern, M.3
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 5
    • 84891372560 scopus 로고    scopus 로고
    • Microbial ecology of the hive and pollination landscape: Bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera)
    • Anderson KE, et al. 2013. Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera). PLoS One 8:e83125.
    • (2013) PLoS One , vol.8
    • Anderson, K.E.1
  • 6
    • 0032777154 scopus 로고    scopus 로고
    • Insights into the evolutionary process of genome degradation
    • Andersson JO, Andersson SG. 1999. Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev. 9:664-671.
    • (1999) Curr Opin Genet Dev. , vol.9 , pp. 664-671
    • Andersson, J.O.1    Andersson, S.G.2
  • 7
    • 38549153238 scopus 로고    scopus 로고
    • Data growth and its impact on the SCOP database: New developments
    • Andreeva A, et al. 2008. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36:D419-D425.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D419-D425
    • Andreeva, A.1
  • 8
    • 25144519057 scopus 로고    scopus 로고
    • Phylogenetic relationships of honey bees (Hymenoptera:Apinae:Apini) inferred from nuclear and mitochondrial DNA sequence data
    • Arias MC, Sheppard WS. 2005. Phylogenetic relationships of honey bees (Hymenoptera:Apinae:Apini) inferred from nuclear and mitochondrial DNA sequence data. Mol Phylogenet Evol. 37:25-35.
    • (2005) Mol Phylogenet Evol. , vol.37 , pp. 25-35
    • Arias, M.C.1    Sheppard, W.S.2
  • 9
    • 68249086310 scopus 로고    scopus 로고
    • Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii
    • Berglund EC, et al. 2009. Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PLoS Genet. 5:e1000546.
    • (2009) PLoS Genet. , vol.5
    • Berglund, E.C.1
  • 10
    • 84875582587 scopus 로고    scopus 로고
    • The adaptation of temperate bacteriophages to their host genomes
    • Bobay LM, Rocha EP, Touchon M. 2013. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol. 30:737-751.
    • (2013) Mol Biol Evol. , vol.30 , pp. 737-751
    • Bobay, L.M.1    Rocha, E.P.2    Touchon, M.3
  • 11
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 12
    • 4944228947 scopus 로고    scopus 로고
    • Bacteriophage flux in endosymbionts (Wolbachia): Infection frequency, lateral transfer, and recombination rates
    • Bordenstein SR, Wernegreen JJ. 2004. Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates. Mol Biol Evol. 21:1981-1991.
    • (2004) Mol Biol Evol. , vol.21 , pp. 1981-1991
    • Bordenstein, S.R.1    Wernegreen, J.J.2
  • 13
    • 33749431828 scopus 로고    scopus 로고
    • Prophage Finder: A prophage loci prediction tool for prokaryotic genome sequences
    • BoseM, Barber RD. 2006. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. 6:223-227.
    • (2006) Silico Biol. , vol.6 , pp. 223-227
    • Bose, M.1    Barber, R.D.2
  • 14
    • 79956122403 scopus 로고    scopus 로고
    • Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations
    • Boucher Y, et al. 2011. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2:e00335-10.
    • (2011) MBio , vol.2 , pp. e00335-e00410
    • Boucher, Y.1
  • 15
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen TC, Philippe H, Bryant D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665-2681.
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 16
    • 84886875528 scopus 로고    scopus 로고
    • Proteins of novel lactic acid bacteria from Apis mellifera mellifera: An insight into the production of known extra-cellular proteins during microbial stress
    • Butler E, et al. 2013. Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress. BMC Microbiol. 13:235.
    • (2013) BMC Microbiol. , vol.13 , pp. 235
    • Butler, E.1
  • 17
    • 85021346400 scopus 로고    scopus 로고
    • A pilot study investigating lactic acid bacterial symbionts from the honeybee in inhibiting human chronic wound pathogens
    • Butler E, et al. 2014. A pilot study investigating lactic acid bacterial symbionts from the honeybee in inhibiting human chronic wound pathogens. Int Wound J. doi: 10.1111/iwj.12360
    • (2014) Int Wound J.
    • Butler, E.1
  • 18
    • 0037716585 scopus 로고    scopus 로고
    • Prophage insertion sites
    • Campbell A. 2003. Prophage insertion sites. Res Microbiol. 154:277-282.
    • (2003) Res Microbiol. , vol.154 , pp. 277-282
    • Campbell, A.1
  • 19
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldon, T.3
  • 21
    • 24044433279 scopus 로고    scopus 로고
    • ACT: The artemis comparison tool
    • Carver TJ, et al. 2005. ACT: the Artemis Comparison Tool. Bioinformatics 21:3422-3423.
    • (2005) Bioinformatics , vol.21 , pp. 3422-3423
    • Carver, T.J.1
  • 22
    • 0029048945 scopus 로고
    • RRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation
    • Condon C, Liveris D, Squires C, Schwartz I, Squires CL. 1995. rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J Bacteriol. 177:4152-4156.
    • (1995) J Bacteriol. , vol.177 , pp. 4152-4156
    • Condon, C.1    Liveris, D.2    Squires, C.3    Schwartz, I.4    Squires, C.L.5
  • 23
    • 33645055663 scopus 로고    scopus 로고
    • Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes
    • Couturier E, Rocha EP. 2006. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol. 59:1506-1518.
    • (2006) Mol Microbiol. , vol.59 , pp. 1506-1518
    • Couturier, E.1    Rocha, E.P.2
  • 24
    • 77956193448 scopus 로고    scopus 로고
    • ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147.
    • (2010) PLoS One , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 25
    • 34249027580 scopus 로고    scopus 로고
    • Inference of bacterial microevolution using multilocus sequence data
    • Didelot X, Falush D. 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251-1266.
    • (2007) Genetics , vol.175 , pp. 1251-1266
    • Didelot, X.1    Falush, D.2
  • 26
    • 28044436397 scopus 로고    scopus 로고
    • Accelerated evolution associated with genome reduction in a free-living prokaryote
    • Dufresne A, Garczarek L, Partensky F. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:R14.
    • (2005) Genome Biol. , vol.6 , pp. R14
    • Dufresne, A.1    Garczarek, L.2    Partensky, F.3
  • 27
    • 0031801913 scopus 로고    scopus 로고
    • Lactobacillus kunkeei sp. Nov.: A spoilage organism associated with grape juice fermentations
    • Edwards CG, Haag KM, Collins MD, Hutson RA, Huang YC. 1998. Lactobacillus kunkeei sp. nov.: a spoilage organism associated with grape juice fermentations. J Appl Microbiol. 84:698-702.
    • (1998) J Appl Microbiol. , vol.84 , pp. 698-702
    • Edwards, C.G.1    Haag, K.M.2    Collins, M.D.3    Hutson, R.A.4    Huang, Y.C.5
  • 28
    • 84930640210 scopus 로고    scopus 로고
    • Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
    • Ellegaard KM, et al. 2015. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genomics 16:284.
    • (2015) BMC Genomics , vol.16 , pp. 284
    • Ellegaard, K.M.1
  • 30
    • 84857933933 scopus 로고    scopus 로고
    • Characterization and emended description of Lactobacillus kunkeei as a fructophilic lactic acid bacterium
    • Endo A, et al. 2012. Characterization and emended description of Lactobacillus kunkeei as a fructophilic lactic acid bacterium. Int J Syst Evol Microbiol. 62:500-504.
    • (2012) Int J Syst Evol Microbiol. , vol.62 , pp. 500-504
    • Endo, A.1
  • 31
    • 84881248839 scopus 로고    scopus 로고
    • The gut microbiota of insects - Diversity in structure and function
    • Engel P, Moran NA. 2013. The gut microbiota of insects - diversity in structure and function. FEMS Microbiol Rev. 37:699-735.
    • (2013) FEMS Microbiol Rev. , vol.37 , pp. 699-735
    • Engel, P.1    Moran, N.A.2
  • 32
    • 84907585369 scopus 로고    scopus 로고
    • Hidden diversity in honey bee gut symbionts detected by single-cell genomics
    • Engel P, Stepanauskas R, Moran NA. 2014. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genet. 10:e1004596.
    • (2014) PLoS Genet. , vol.10
    • Engel, P.1    Stepanauskas, R.2    Moran, N.A.3
  • 33
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 34
    • 82355180987 scopus 로고    scopus 로고
    • Bees brought to their knees: Microbes affecting honey bee health
    • Evans JD, Schwarz RS. 2011. Bees brought to their knees: microbes affecting honey bee health. Trends Microbiol. 19:614-620.
    • (2011) Trends Microbiol. , vol.19 , pp. 614-620
    • Evans, J.D.1    Schwarz, R.S.2
  • 35
    • 84891782659 scopus 로고    scopus 로고
    • Pfam: The protein families database
    • Finn RD, et al. 2014. Pfam: the protein families database. Nucleic Acids Res. 42:D222-D230.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D222-D230
    • Finn, R.D.1
  • 36
    • 73449086690 scopus 로고    scopus 로고
    • Novel lactic acid bacteria inhibiting Paenibacillus larvae in honey bee larvae
    • Forsgren E, Olofsson TC, Vásquez A, Fries I. 2010. Novel lactic acid bacteria inhibiting Paenibacillus larvae in honey bee larvae. Apidologie 41:99-108.
    • (2010) Apidologie , vol.41 , pp. 99-108
    • Forsgren, E.1    Olofsson, T.C.2    Vásquez, A.3    Fries, I.4
  • 38
    • 0345055819 scopus 로고    scopus 로고
    • Modeling of growth of Lactobacillus sanfranciscensis and Candida milleri in response to process parameters of sourdough fermentation
    • Ganzle MG, Ehmann M, Hammes WP. 1998. Modeling of growth of Lactobacillus sanfranciscensis and Candida milleri in response to process parameters of sourdough fermentation. Appl Environ Microbiol. 64:2616-2623.
    • (1998) Appl Environ Microbiol. , vol.64 , pp. 2616-2623
    • Ganzle, M.G.1    Ehmann, M.2    Hammes, W.P.3
  • 39
    • 34547579396 scopus 로고    scopus 로고
    • CRISPRFinder: Aweb tool to identify clustered regularly interspaced short palindromic repeats
    • Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: aweb tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52-W57.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W52-W57
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 40
    • 84868369211 scopus 로고    scopus 로고
    • Streamlining and core genome conservation among highly divergent members of the SAR11 clade
    • Grote J, et al. 2012. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. MBio 3:e00252-12.
    • (2012) MBio , vol.3 , pp. e00252-e00312
    • Grote, J.1
  • 41
    • 84875987691 scopus 로고    scopus 로고
    • A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella
    • Guy L, et al. 2013. A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella. PLoS Genet. 9:e1003393.
    • (2013) PLoS Genet. , vol.9
    • Guy, L.1
  • 42
    • 77956519355 scopus 로고    scopus 로고
    • GenoPlotR: Comparative gene and genome visualization in R
    • Guy L, Kultima JR, Andersson SG. 2010. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26:2334-2335.
    • (2010) Bioinformatics , vol.26 , pp. 2334-2335
    • Guy, L.1    Kultima, J.R.2    Andersson, S.G.3
  • 43
    • 33947231236 scopus 로고    scopus 로고
    • Mutational bias suggests that replication termination occurs near the dif site, not at ter sites
    • Hendrickson H, Lawrence JG. 2007. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. MolMicrobiol. 64:42-56.
    • (2007) MolMicrobiol. , vol.64 , pp. 42-56
    • Hendrickson, H.1    Lawrence, J.G.2
  • 44
    • 64449088715 scopus 로고    scopus 로고
    • Comparative analysis of CRISPR loci in lactic acid bacteria genomes
    • Horvath P, et al. 2009. Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol. 131:62-70.
    • (2009) Int J Food Microbiol. , vol.131 , pp. 62-70
    • Horvath, P.1
  • 45
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1
  • 46
    • 77954209892 scopus 로고    scopus 로고
    • The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell
    • Junier T, Zdobnov EM. 2010. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26:1669-1670.
    • (2010) Bioinformatics , vol.26 , pp. 1669-1670
    • Junier, T.1    Zdobnov, E.M.2
  • 47
    • 79954577654 scopus 로고    scopus 로고
    • Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture
    • Kent BN, et al. 2011. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol Evol. 3:209-218.
    • (2011) Genome Biol Evol. , vol.3 , pp. 209-218
    • Kent, B.N.1
  • 48
    • 65249166565 scopus 로고    scopus 로고
    • Themosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans
    • Klasson L, et al. 2009. Themosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc Natl Acad Sci U S A. 106:5725-5730.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 5725-5730
    • Klasson, L.1
  • 49
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3100-3108
    • Lagesen, K.1
  • 50
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 51
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 52
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 53
    • 77954430217 scopus 로고    scopus 로고
    • Amolecular phylogeny of the genus Apis suggests that the giant honey bee of the Philippines, A. Breviligula Maa, and the plains honey bee of southern India, A. Indica Fabricius, are valid species
    • Lo N, Gloag RS, Anderson DL, Oldroyd BP. 2010. Amolecular phylogeny of the genus Apis suggests that the giant honey bee of the Philippines, A. breviligula Maa, and the plains honey bee of southern India, A. indica Fabricius, are valid species. Syst Entomol. 35:226-233.
    • (2010) Syst Entomol. , vol.35 , pp. 226-233
    • Lo, N.1    Gloag, R.S.2    Anderson, D.L.3    Oldroyd, B.P.4
  • 54
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 55
    • 79956157571 scopus 로고    scopus 로고
    • Evolution and classification of the CRISPR-Cas systems
    • Makarova KS, et al. 2011. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 9:467-477.
    • (2011) Nat Rev Microbiol. , vol.9 , pp. 467-477
    • Makarova, K.S.1
  • 56
    • 78751670451 scopus 로고    scopus 로고
    • A simple and distinctive microbiota associated with honey bees and bumble bees
    • Martinson VG, et al. 2011. A simple and distinctive microbiota associated with honey bees and bumble bees. Mol Ecol. 20:619-628.
    • (2011) Mol Ecol. , vol.20 , pp. 619-628
    • Martinson, V.G.1
  • 57
    • 79251604784 scopus 로고    scopus 로고
    • The terminal region of the E. Coli chromosome localises at the periphery of the nucleoid
    • Meile JC, et al. 2011. The terminal region of the E. coli chromosome localises at the periphery of the nucleoid. BMC Microbiol. 11:28.
    • (2011) BMC Microbiol. , vol.11 , pp. 28
    • Meile, J.C.1
  • 58
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira A, Ochman H, Moran NA. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-596.
    • (2001) Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 59
    • 84860486227 scopus 로고    scopus 로고
    • Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees
    • Moran NA, Hansen AK, Powell JE, Sabree ZL. 2012. Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees. PLoS One 7:e36393.
    • (2012) PLoS One , vol.7
    • Moran, N.A.1    Hansen, A.K.2    Powell, J.E.3    Sabree, Z.L.4
  • 60
    • 58449125407 scopus 로고    scopus 로고
    • Genomics and evolution of heritable bacterial symbionts
    • Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 42:165-190.
    • (2008) Annu Rev Genet. , vol.42 , pp. 165-190
    • Moran, N.A.1    McCutcheon, J.P.2    Nakabachi, A.3
  • 61
    • 39449118068 scopus 로고    scopus 로고
    • Learning how to live together: Genomic insights into prokaryote-animal symbioses
    • Moya A, Pereto J, Gil R, Latorre A. 2008. Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat Rev Genet. 9:218-229.
    • (2008) Nat Rev Genet. , vol.9 , pp. 218-229
    • Moya, A.1    Pereto, J.2    Gil, R.3    Latorre, A.4
  • 62
    • 84867684328 scopus 로고    scopus 로고
    • Fructophilic Lactobacillus kunkeei and Lactobacillus brevis isolated from fresh flowers, bees and beehives
    • Neveling DP, Endo A, Dicks LM. 2012. Fructophilic Lactobacillus kunkeei and Lactobacillus brevis isolated from fresh flowers, bees and beehives. Curr Microbiol. 65:507-515.
    • (2012) Curr Microbiol. , vol.65 , pp. 507-515
    • Neveling, D.P.1    Endo, A.2    Dicks, L.M.3
  • 63
    • 84907046552 scopus 로고    scopus 로고
    • Lactobacillus apinorum sp. Nov., Lactobacillus mellifer sp. Nov., Lactobacillus mellis sp. Nov., Lactobacillus melliventris sp. Nov., Lactobacillus kimbladii sp. Nov., Lactobacillus helsingborgensis sp. Nov. and Lactobacillus kullabergensis sp. Nov., isolated from the honey stomach of the honeybee Apis mellifera
    • Olofsson TC, Alsterfjord M, Nilson B, Butler E, Vasquez A. 2014. Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera. Int J Syst Evol Microbiol. 64:3109-3119.
    • (2014) Int J Syst Evol Microbiol. , vol.64 , pp. 3109-3119
    • Olofsson, T.C.1    Alsterfjord, M.2    Nilson, B.3    Butler, E.4    Vasquez, A.5
  • 64
    • 85022185060 scopus 로고    scopus 로고
    • Lactic acid bacterial symbionts in honeybees - An unknown key to honey's antimicrobial and therapeutic activities
    • Olofsson TC, Butler E, et al. 2014. Lactic acid bacterial symbionts in honeybees - an unknown key to honey's antimicrobial and therapeutic activities. Int Wound J. doi: 10.1111/iwj.12345
    • (2014) Int Wound J.
    • Olofsson, T.C.1    Butler, E.2
  • 65
    • 50249182791 scopus 로고    scopus 로고
    • Detection and identification of a novel lactic acid bacterial flora within the honey stomach of the honeybee Apis mellifera
    • Olofsson TC, Vasquez A. 2008. Detection and identification of a novel lactic acid bacterial flora within the honey stomach of the honeybee Apis mellifera. Curr Microbiol. 57:356-363.
    • (2008) Curr Microbiol. , vol.57 , pp. 356-363
    • Olofsson, T.C.1    Vasquez, A.2
  • 66
    • 84856644726 scopus 로고    scopus 로고
    • A scientific note on the lactic acid bacterial flora within the honeybee subspecies; Apis mellifera (Buckfast), A. M. Scutellata, A. M. Mellifera, and A. M. Monticola
    • Olofsson TC, Vásquez A, Sammataro D, Macharia J. 2011. A scientific note on the lactic acid bacterial flora within the honeybee subspecies; Apis mellifera (Buckfast), A. m. scutellata, A. m. mellifera, and A. m. monticola. Apidologie 42:696-699.
    • (2011) Apidologie , vol.42 , pp. 696-699
    • Olofsson, T.C.1    Vásquez, A.2    Sammataro, D.3    Macharia, J.4
  • 67
    • 77953023066 scopus 로고    scopus 로고
    • GenePRIMP: A gene prediction improvement pipeline for prokaryotic genomes
    • Pati A, et al. 2010. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 7:455-457.
    • (2010) Nat Methods. , vol.7 , pp. 455-457
    • Pati, A.1
  • 68
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson WR. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183:63-98.
    • (1990) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 69
    • 84864134721 scopus 로고    scopus 로고
    • SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
    • Pruesse E, Peplies J, Glockner FO. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829.
    • (2012) Bioinformatics , vol.28 , pp. 1823-1829
    • Pruesse, E.1    Peplies, J.2    Glockner, F.O.3
  • 70
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. 2005. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33:D501-D504.
    • (2005) Nucleic Acids Res. , vol.33 , pp. D501-D504
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 71
    • 84858077472 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Punta M, et al. 2012. The Pfam protein families database. Nucleic Acids Res. 40:D290-D301.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D290-D301
    • Punta, M.1
  • 72
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast C, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D590-D596
    • Quast, C.1
  • 73
    • 34247621729 scopus 로고    scopus 로고
    • Phylogenetic analysis of honey bee behavioral evolution
    • Raffiudin R, Crozier RH. 2007. Phylogenetic analysis of honey bee behavioral evolution. Mol Phylogenet Evol. 43:543-552.
    • (2007) Mol Phylogenet Evol. , vol.43 , pp. 543-552
    • Raffiudin, R.1    Crozier, R.H.2
  • 74
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 75
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 76
    • 60849134825 scopus 로고    scopus 로고
    • Specialization and geographic isolation among Wolbachia symbionts from ants and lycaenid butterflies
    • Russell JA, et al. 2009. Specialization and geographic isolation among Wolbachia symbionts from ants and lycaenid butterflies. Evolution 63:624-640.
    • (2009) Evolution , vol.63 , pp. 624-640
    • Russell, J.A.1
  • 77
    • 84864058226 scopus 로고    scopus 로고
    • Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees
    • Sabree ZL, Hansen AK, Moran NA. 2012. Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees. PLoS One 7:e41250.
    • (2012) PLoS One , vol.7
    • Sabree, Z.L.1    Hansen, A.K.2    Moran, N.A.3
  • 78
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 79
    • 0023274170 scopus 로고
    • The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias
    • Sharp PM, Li WH. 1987. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol. 4:222-230.
    • (1987) Mol Biol Evol. , vol.4 , pp. 222-230
    • Sharp, P.M.1    Li, W.H.2
  • 80
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
    • (2001) Bioinformatics , vol.17 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 81
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 82
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 83
    • 63549147824 scopus 로고    scopus 로고
    • DIYA: A bacterial annotation pipeline for any genomics lab
    • Stewart AC, Osborne B, Read TD. 2009. DIYA: a bacterial annotation pipeline for any genomics lab. Bioinformatics 25:962-963.
    • (2009) Bioinformatics , vol.25 , pp. 962-963
    • Stewart, A.C.1    Osborne, B.2    Read, T.D.3
  • 84
    • 84901049718 scopus 로고    scopus 로고
    • Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo
    • Tal A, Arbel-Goren R, Costantino N, Court DL, Stavans J. 2014. Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo. Proc Natl Acad Sci U S A. 111:7308-7312.
    • (2014) Proc Natl Acad Sci U S A. , vol.111 , pp. 7308-7312
    • Tal, A.1    Arbel-Goren, R.2    Costantino, N.3    Court, D.L.4    Stavans, J.5
  • 85
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33-36.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 86
    • 77953809752 scopus 로고    scopus 로고
    • Evolutionary microbial genomics: Insights into bacterial host adaptation
    • Toft C, Andersson SG. 2010. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet. 11:465-475.
    • (2010) Nat Rev Genet. , vol.11 , pp. 465-475
    • Toft, C.1    Andersson, S.G.2
  • 87
    • 84907976382 scopus 로고    scopus 로고
    • The chromosomal accommodation and domestication of mobile genetic elements
    • Touchon M, Bobay LM, Rocha EP. 2014. The chromosomal accommodation and domestication of mobile genetic elements. Curr Opin Microbiol. 22 C:22-29.
    • (2014) Curr Opin Microbiol. , vol.22 C , pp. 22-29
    • Touchon, M.1    Bobay, L.M.2    Rocha, E.P.3
  • 88
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • UniProt Consortium. 2014. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42:D191-D198.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D191-D198
    • UniProt Consortium1
  • 89
    • 84858050440 scopus 로고    scopus 로고
    • Symbionts as major modulators of insect health: Lactic acid bacteria and honeybees
    • Vasquez A, et al. 2012. Symbionts as major modulators of insect health: lactic acid bacteria and honeybees. PLoS One 7:e33188.
    • (2012) PLoS One , vol.7
    • Vasquez, A.1
  • 90
    • 69549122175 scopus 로고    scopus 로고
    • The lactic acid bacteria involved in the production of bee pollen and bee bread
    • Vásquez A, Olofsson TC. 2009. The lactic acid bacteria involved in the production of bee pollen and bee bread. J Apic Res. 48:189-195.
    • (2009) J Apic Res. , vol.48 , pp. 189-195
    • Vásquez, A.1    Olofsson, T.C.2
  • 91
    • 60749131160 scopus 로고    scopus 로고
    • A scientific note on the lactic acid bacterial flora in honeybees in the USA - A comparison with bees from Sweden
    • Vásquez A, Olofsson TC, Sammataro D. 2009. A scientific note on the lactic acid bacterial flora in honeybees in the USA - a comparison with bees from Sweden. Apidologie 40:26-28.
    • (2009) Apidologie , vol.40 , pp. 26-28
    • Vásquez, A.1    Olofsson, T.C.2    Sammataro, D.3
  • 92
    • 80052250365 scopus 로고    scopus 로고
    • Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs
    • Vogel RF, et al. 2011. Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs. Microb Cell Fact. 10(Suppl. 1):S6.
    • (2011) Microb Cell Fact. , vol.10 , pp. S6
    • Vogel, R.F.1
  • 93
    • 84882705545 scopus 로고    scopus 로고
    • Microbial gut diversity of Africanized and European honey bee larval instars
    • Vojvodic S, Rehan SM, Anderson KE. 2013. Microbial gut diversity of Africanized and European honey bee larval instars. PLoS One 8:e72106.
    • (2013) PLoS One , vol.8
    • Vojvodic, S.1    Rehan, S.M.2    Anderson, K.E.3
  • 94
    • 58549084151 scopus 로고    scopus 로고
    • A comparison of homologous recombination rates in bacteria and archaea
    • Vos M, Didelot X. 2009. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3:199-208.
    • (2009) ISME J. , vol.3 , pp. 199-208
    • Vos, M.1    Didelot, X.2
  • 96
    • 0029149572 scopus 로고
    • Evolution and phylogeny of Wolbachia: Reproductive parasites of arthropods
    • Werren JH, Zhang W, Guo LR. 1995. Evolution and phylogeny of Wolbachia: reproductive parasites of arthropods. Proc Biol Sci. 261:55-63.
    • (1995) Proc Biol Sci. , vol.261 , pp. 55-63
    • Werren, J.H.1    Zhang, W.2    Guo, L.R.3
  • 98
    • 0037082414 scopus 로고    scopus 로고
    • Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: Sublocation preference of integrase subfamilies
    • Williams KP. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res. 30:866-875.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 866-875
    • Williams, K.P.1
  • 99
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 100
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan - An integration platform for the signature-recognition methods in InterPro
    • Zdobnov EM, Apweiler R. 2001. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847-848.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 101
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.