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Volumn 5, Issue , 2015, Pages

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; BACTERIAL GENOME; CLASSIFICATION; FERMENTATION; FOOD CONTROL; GENETIC SELECTION; GENETICS; GENOMICS; INTESTINE FLORA; LACTOBACILLUS REUTERI; PHYLOGENY; SYMBIOSIS;

EID: 84949580253     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep18234     Document Type: Article
Times cited : (53)

References (49)
  • 1
    • 84959852082 scopus 로고    scopus 로고
    • Lactic metabolism revisited: Metabolism of lactic acid bacteria in food fermentations and food biotechnology
    • Gänzle, M. G. Lactic metabolism revisited: Metabolism of lactic acid bacteria in food fermentations and food biotechnology. Curr. Opin. Food Sci. 2, 106-117 (2015).
    • (2015) Curr. Opin. Food Sci , vol.2 , pp. 106-117
    • Gänzle, M.G.1
  • 2
    • 50049098340 scopus 로고    scopus 로고
    • Ecological role of lactobacilli in the gastrointestinal tract: Implications for fundamental and biomedical research
    • Walter, J. Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl. Environ. Microbiol. 74, 4985-4996 (2008).
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 4985-4996
    • Walter, J.1
  • 3
    • 0032858422 scopus 로고    scopus 로고
    • Non-dairy lactic fermentations: The cereal world
    • Vogel, R. F. et al. Non-dairy lactic fermentations: The cereal world. Antonie van Leeuwenhoek 76, 403-411 (1999).
    • (1999) Antonie van Leeuwenhoek , vol.76 , pp. 403-411
    • Vogel, R.F.1
  • 4
    • 77149149718 scopus 로고    scopus 로고
    • Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution
    • Oh, P. L. et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME J. 4, 377-387 (2010).
    • (2011) ISME J , vol.4 , pp. 377-387
    • Oh, P.L.1
  • 5
    • 84908405235 scopus 로고    scopus 로고
    • From prediction to function using evolutionary genomics: Human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions
    • Spinler, J. K. et al. From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Genome Biol. Evol. 6, 1772-1789 (2014).
    • (2014) Genome Biol. Evol , vol.6 , pp. 1772-1789
    • Spinler, J.K.1
  • 6
    • 0037437445 scopus 로고    scopus 로고
    • Contribution of reutericyclin production to the stable persistence of Lactobacillus reuteri in an industrial sourdough fermentation
    • Gänzle, M. G. & Vogel, R. F. Contribution of reutericyclin production to the stable persistence of Lactobacillus reuteri in an industrial sourdough fermentation. Int. J. Food Microbiol. 80, 31-45 (2002).
    • (2002) Int. J. Food Microbiol , vol.80 , pp. 31-45
    • Gänzle, M.G.1    Vogel, R.F.2
  • 7
    • 80052276610 scopus 로고    scopus 로고
    • Microbiological and chemical characterisation of ting, a sorghum-based sourdough product from Botswana
    • Sekwati-Monang, B. & Gänzle, M. G. Microbiological and chemical characterisation of ting, a sorghum-based sourdough product from Botswana. Int. J. Food Microbiol. 150, 115-121 (2011).
    • (2011) Int. J. Food Microbiol , vol.150 , pp. 115-121
    • Sekwati-Monang, B.1    Gänzle, M.G.2
  • 8
    • 0037224663 scopus 로고    scopus 로고
    • Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR-denaturing gradient gel electrophoresis
    • Meroth, C. B., Walter, J., Hertel, C., Brandt, M. J. & Hammes, W. P. Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69, 475-482 (2003).
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 475-482
    • Meroth, C.B.1    Walter, J.2    Hertel, C.3    Brandt, M.J.4    Hammes, W.P.5
  • 9
    • 0001630785 scopus 로고
    • Neue erkenntnisse zum okosystem sauerteig und zur physiologie der sauerteigtypischen stämme lactobacillus sanfrancisco und Lactobacillus pontis
    • Bocker, G., Stolz, P. & Hammes, W. P. Neue Erkenntnisse zum kosystem Sauerteig und zur Physiologie der sauerteigtypischen Stämme Lactobacillus sanfrancisco und Lactobacillus pontis. Getreide Mehl Brot 49, 370-374 (1995).
    • (1995) Getreide Mehl Brot , vol.49 , pp. 370-374
    • Bocker, G.1    Stolz, P.2    Hammes, W.P.3
  • 10
    • 84906342536 scopus 로고    scopus 로고
    • Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology
    • Lin, X. B. & Gänzle, M. G. Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology. Appl. Environ. Microbiol. 80, 5782-5789 (2014).
    • (2014) Appl. Environ. Microbiol , vol.80 , pp. 5782-5789
    • Lin, X.B.1    Gänzle, M.G.2
  • 11
    • 84866153553 scopus 로고    scopus 로고
    • Intestinal origin of sourdough Lactobacillus reuteri isolates as revealed by phylogenetic, genetic, and physiological analysis
    • Su, M. S. W., Oh, P. L., Walter, J. & Gänzle, M. G. Intestinal origin of sourdough Lactobacillus reuteri isolates as revealed by phylogenetic, genetic, and physiological analysis. Appl. Environ. Microbiol. 78, 6777-6780 (2012).
    • (2012) Appl. Environ. Microbiol , vol.78 , pp. 6777-6780
    • Su, M.S.W.1    Oh, P.L.2    Walter, J.3    Gänzle, M.G.4
  • 12
    • 84907033450 scopus 로고    scopus 로고
    • Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach
    • Wilson, C. M. et al. Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach. Appl. Environ. Microbiol. 80, 6104-6113 (2014).
    • (2014) Appl. Environ. Microbiol , vol.80 , pp. 6104-6113
    • Wilson, C.M.1
  • 13
    • 84897061329 scopus 로고    scopus 로고
    • Novel two-component regulatory systems play a role in biofilm formation of Lactobacillus reuteri rodent isolate 100-23
    • Su, M. S. & Gänzle, M. G. Novel two-component regulatory systems play a role in biofilm formation of Lactobacillus reuteri rodent isolate 100-23. Microbiology 160, 795-806 (2014).
    • (2014) Microbiology , vol.160 , pp. 795-806
    • Su, M.S.1    Gänzle, M.G.2
  • 14
    • 84892690253 scopus 로고    scopus 로고
    • Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont
    • Frese, S. A. et al. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet. 9:e1004057 (2013).
    • (2013) PLoS Genet , vol.9 , pp. e1004057
    • Frese, S.A.1
  • 15
    • 79952266302 scopus 로고    scopus 로고
    • The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri
    • Frese, S. A. et al. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet. 7, e1001314 (2011).
    • (2011) PLoS Genet , vol.7 , pp. e1001314
    • Frese, S.A.1
  • 16
    • 84924709775 scopus 로고    scopus 로고
    • Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri
    • Lin, X. B. et al. Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri. Appl. Environ. Microbiol. 81, 2032-2041 (2015).
    • (2015) Appl. Environ. Microbiol , vol.81 , pp. 2032-2041
    • Lin, X.B.1
  • 17
    • 32044464336 scopus 로고    scopus 로고
    • Effect of membrane lateral pressure on the expression of fructosyltransferases in Lactobacillus reuteri
    • Schwab, C. & Gänzle, M. G. Effect of membrane lateral pressure on the expression of fructosyltransferases in Lactobacillus reuteri. Syst. Appl. Microbiol. 29, 89-99 (2006).
    • (2006) Syst. Appl. Microbiol , vol.29 , pp. 89-99
    • Schwab, C.1    Gänzle, M.G.2
  • 18
    • 56049119880 scopus 로고    scopus 로고
    • Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production
    • Morita, H. et al. Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA Res. 15, 151-161 (2008).
    • (2008) DNA Res , vol.15 , pp. 151-161
    • Morita, H.1
  • 19
    • 77956936208 scopus 로고    scopus 로고
    • Metabolic pathway of α -ketoglutarate in Lactobacillus sanfranciscensis and Lactobacillus reuteri during sourdough fermentation
    • Zhang, C. & Ganzle, M. G. Metabolic pathway of α -ketoglutarate in Lactobacillus sanfranciscensis and Lactobacillus reuteri during sourdough fermentation. J. Appl. Microbiol. 109, 1301-1310 (2010).
    • (2011) J. Appl. Microbiol , vol.109 , pp. 1301-1310
    • Zhang, C.1    Gänzle, M.G.2
  • 20
    • 80052197161 scopus 로고    scopus 로고
    • Contribution of glutamate decarboxylase in Lactobacillus reuteri to acid resistance and persistence in sourdough fermentation
    • Su, M. S. W., Schlicht, S. & Gänzle, M. G. Contribution of glutamate decarboxylase in Lactobacillus reuteri to acid resistance and persistence in sourdough fermentation. Microb. Cell Factories 10 (Suppl 1), S8 (2011).
    • (2011) Microb. Cell Factories , vol.10 , pp. S8
    • Su, M.S.W.1    Schlicht, S.2    Gänzle, M.G.3
  • 21
    • 84870178114 scopus 로고    scopus 로고
    • Killing as means of promoting biodiversity
    • Abrudan, M. I., Brown, S. & Rozen, D. E. Killing as means of promoting biodiversity. Biochem Soc. Trans. 40, 1512-1516 (2012).
    • (2012) Biochem Soc. Trans , vol.40 , pp. 1512-1516
    • Abrudan, M.I.1    Brown, S.2    Rozen, D.E.3
  • 22
    • 67650074198 scopus 로고    scopus 로고
    • Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
    • Lefébure, T. & Stanhope, M. J. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 19, 1224-1232 (2009).
    • (2009) Genome Res , vol.19 , pp. 1224-1232
    • Lefébure, T.1    Stanhope, M.J.2
  • 23
    • 34548846699 scopus 로고    scopus 로고
    • Evolution of the core and pan-genome of Streptococcus: Positive selection, recombination, and genome composition
    • Lefébure, T. & Stanhope, M. J. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8, R71 (2007).
    • (2007) Genome Biol , vol.8 , pp. R71
    • Lefébure, T.1    Stanhope, M.J.2
  • 24
    • 51349158939 scopus 로고    scopus 로고
    • Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
    • Orsi, R. H., Sun, Q. & Wiedmann, M. Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes. BMC Evol. Biol. 8, 233 (2008).
    • (2008) BMC Evol. Biol , vol.8 , pp. 233
    • Orsi, R.H.1    Sun, Q.2    Wiedmann, M.3
  • 25
    • 72249097352 scopus 로고    scopus 로고
    • Growth rate-dependent global effects on gene expression in bacteria
    • Klumpp, S., Zhang, Z. & Hwa, T. Growth rate-dependent global effects on gene expression in bacteria. Cell 139, 1366-1375.
    • Cell , vol.139 , pp. 1366-1375
    • Klumpp, S.1    Zhang, Z.2    Hwa, T.3
  • 26
    • 80052250365 scopus 로고    scopus 로고
    • Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs
    • Vogel, R. F. et al. Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs. Microb Cell Fact. 10 Suppl 1, S6 (2011).
    • (2011) Microb Cell Fact , vol.10 , Issue.6
    • Vogel, R.F.1
  • 27
    • 77954696677 scopus 로고    scopus 로고
    • Ecology of exopolysaccharide formation by lactic acid bacteria: Sucrose utilization, stress tolerance, and biofilm formation] Bacterial polysaccharides
    • [Ullrich, M. (Ed.)][263-278] Caister Academic Press Norfolk
    • Gänzle, M. G. & Schwab, C. [Ecology of exopolysaccharide formation by lactic acid bacteria: Sucrose utilization, stress tolerance, and biofilm formation] Bacterial polysaccharides. Current innovations and future trends. [Ullrich, M. (Ed.)][263-278](Caister Academic Press Norfolk, 2009).
    • (2009) Current Innovations and Future Trends
    • Gänzle, M.G.1    Schwab, C.2
  • 28
    • 33748917136 scopus 로고    scopus 로고
    • Carbohydrate, peptide and lipid metabolism of lactobacilli in sourdough
    • Gänzle, M. G., Vermeulen, N. & Vogel, R. F. Carbohydrate, peptide and lipid metabolism of lactobacilli in sourdough. Food Microbiol. 24, 128-138 (2007).
    • (2007) Food Microbiol , vol.24 , pp. 128-138
    • Gänzle, M.G.1    Vermeulen, N.2    Vogel, R.F.3
  • 29
    • 84884191741 scopus 로고    scopus 로고
    • The carbohydrate metabolism signature of Lactococcus lactis strain A12 reveals its sourdough ecosystem origin
    • Passerini, D. et al. The carbohydrate metabolism signature of Lactococcus lactis strain A12 reveals its sourdough ecosystem origin. Appl. Environ. Microbiol. 79, 5844-5852 (2013).
    • (2013) Appl. Environ. Microbiol , vol.79 , pp. 5844-5852
    • Passerini, D.1
  • 30
    • 84901923222 scopus 로고    scopus 로고
    • Gene expression of lactobacilli in murine forestomach biofilms
    • Schwab, C., Tweit, A. T., Schleper, C. & Urich, T. Gene expression of lactobacilli in murine forestomach biofilms. Microb. Biotechnol. 7, 347-359 (2014).
    • (2014) Microb. Biotechnol , vol.7 , pp. 347-359
    • Schwab, C.1    Tweit, A.T.2    Schleper, C.3    Urich, T.4
  • 31
    • 84926433439 scopus 로고    scopus 로고
    • Fermented foods as experimentally tractable microbial ecosystems
    • Wolfe, B. E. & Dutton, R. J. Fermented foods as experimentally tractable microbial ecosystems. Cell 161, 49-55 (2015).
    • (2015) Cell , vol.161 , pp. 49-55
    • Wolfe, B.E.1    Dutton, R.J.2
  • 32
    • 0018347481 scopus 로고
    • Association of rat, pig, and fowl biotypes of lactobacilli with the stomach of gnotobiotic mice
    • Wesney, E. & Tannock, G. W. Association of rat, pig, and fowl biotypes of lactobacilli with the stomach of gnotobiotic mice. Microb. Ecol. 5, 35-42 (1979).
    • (1979) Microb. Ecol , vol.5 , pp. 35-42
    • Wesney, E.1    Tannock, G.W.2
  • 33
    • 40549120596 scopus 로고    scopus 로고
    • The RAST Server: Rapid annotations using subsystems technology
    • Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2009).
    • (2009) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1
  • 34
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403 (2004).
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 35
    • 79551599525 scopus 로고    scopus 로고
    • Mugsy: Fast multiple alignment of closely related whole genomes
    • Angiuoli, S. V. & Salzberg, S. L. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27, 334-342 (2010).
    • (2011) Bioinformatics , vol.27 , pp. 334-342
    • Angiuoli, S.V.1    Salzberg, S.L.2
  • 36
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577 (2007).
    • (2007) Syst. Biol , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 37
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-Analysis of large phylogenies
    • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-Analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 38
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 41
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar R. ., C.1
  • 42
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • (Web Server issue), W609-612
    • Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34 (Web Server issue), W609-612 (2006).
    • (2006) Nucleic Acids Res , vol.34
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 43
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 44
    • 8544225780 scopus 로고    scopus 로고
    • Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    • Wong, W. S., Yang, Z., Goldman, N. & Nielsen, R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041-1051 (2004).
    • (2004) Genetics , vol.168 , pp. 1041-1051
    • Wong, W.S.1    Yang, Z.2    Goldman, N.3    Nielsen, R.4
  • 45
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical bayes inference of amino acid sites under positive selection
    • Yang, Z., Wong, W. S. & Nielsen, R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22, 1107-1118 (2005).
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.2    Nielsen, R.3
  • 46
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang, J., Nielsen, R. & Yang, Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472-2479 (2005).
    • (2005) Mol. Biol. Evol , vol.22 , pp. 2472-2479
    • Zhang, J.1    Nielsen, R.2    Yang, Z.3
  • 47
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: An updated version includes eukaryotes
    • Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 48
    • 84903525876 scopus 로고    scopus 로고
    • Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough
    • Lin, X. B. & Gänzle, M. G. Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough. Int. J. Food Microbiol. 186, 42-48 (2014).
    • (2014) Int. J. Food Microbiol , vol.186 , pp. 42-48
    • Lin, X.B.1    Gänzle, M.G.2
  • 49
    • 0037062936 scopus 로고    scopus 로고
    • Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors
    • Kerr, B., Riley, M. A., Feldman, M. W. & Bohannan, B. J. M. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418, 171-174 (2002).
    • (2002) Nature , vol.418 , pp. 171-174
    • Kerr, B.1    Riley, M.A.2    Feldman, M.W.3    Bohannan, B.J.M.4


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