메뉴 건너뛰기




Volumn 7, Issue AUG, 2016, Pages

Bacterial communities: Interactions to scale

Author keywords

Bacterial communities; Biodiversity; Competition; Ecology; Interactions; Microbiota; Scaling; Syntrophy

Indexed keywords

BIODIVERSITY; COMPETITION; ECOLOGY; EXPERIMENTAL MODEL; METAGENOMICS; MICROBIAL COMMUNITY; MICROFLORA; NONHUMAN;

EID: 84989162405     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.01234     Document Type: Review
Times cited : (192)

References (171)
  • 1
    • 49449087156 scopus 로고    scopus 로고
    • Factors influencing the establishment of the intestinal microbiota in infancy
    • discussion29-33
    • Adlerberth, I. (2008). Factors influencing the establishment of the intestinal microbiota in infancy. Nestlé Nutr. Workshop Ser. Paediatr. Program. 62, 13-29; discussion29-33. doi: 10.1159/000146245
    • (2008) Nestlé Nutr. Workshop Ser. Paediatr. Program , vol.62 , pp. 13-29
    • Adlerberth, I.1
  • 2
    • 0024228913 scopus 로고
    • Characteristics, dynamics and significance of marine snow
    • Alldredge, A. L., and Silver, M. W. (1988). Characteristics, dynamics and significance of marine snow. Prog. Oceanogr. 20, 41-82. doi: 10.1016/0079-6611(88)90053-5
    • (1988) Prog. Oceanogr , vol.20 , pp. 41-82
    • Alldredge, A.L.1    Silver, M.W.2
  • 3
    • 69049084604 scopus 로고    scopus 로고
    • Sialic acid catabolism confers a competitive advantage to pathogenic Vibrio cholerae in the mouse intestine
    • Almagro-Moreno, S., and Boyd, E. F. (2009). Sialic acid catabolism confers a competitive advantage to pathogenic Vibrio cholerae in the mouse intestine. Infect. Immun. 77, 3807-3816. doi: 10.1128/IAI.00279-09
    • (2009) Infect. Immun , vol.77 , pp. 3807-3816
    • Almagro-Moreno, S.1    Boyd, E.F.2
  • 4
    • 84884680533 scopus 로고    scopus 로고
    • Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells
    • Alteri, C. J., Himpsl, S. D., Pickens, S. R., Lindner, J. R., Zora, J. S., Miller, J. E., et al. (2013). Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells. PLoS Pathog. 9:e1003608. doi: 10.1371/journal.ppat.1003608
    • (2013) PLoS Pathog , vol.9
    • Alteri, C.J.1    Himpsl, S.D.2    Pickens, S.R.3    Lindner, J.R.4    Zora, J.S.5    Miller, J.E.6
  • 5
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R. I., Ludwig, W., and Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
    • (1995) Microbiol. Rev , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 6
    • 84869234725 scopus 로고    scopus 로고
    • Localized cell death focuses mechanical forces during 3D patterning in a biofilm
    • Asally, M., Kittisopikul, M., Rué, P., Du, Y., Hu, Z., Çagatay, T., et al. (2012). Localized cell death focuses mechanical forces during 3D patterning in a biofilm. Proc. Natl. Acad. Sci. U.S.A. 109, 18891-18896. doi: 10.1073/pnas.1212429109
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 18891-18896
    • Asally, M.1    Kittisopikul, M.2    Rué, P.3    Du, Y.4    Hu, Z.5    Çagatay, T.6
  • 7
    • 70349772034 scopus 로고    scopus 로고
    • Quorum sensing and social networking in the microbial world
    • Atkinson, S., and Williams, P. (2009). Quorum sensing and social networking in the microbial world. J. R. Soc. Interface 6, 959-978. doi: 10.1098/rsif.2009.0203
    • (2009) J. R. Soc. Interface , vol.6 , pp. 959-978
    • Atkinson, S.1    Williams, P.2
  • 8
    • 84940663667 scopus 로고    scopus 로고
    • Bile salts modulate the mucin-activated type VI secretion system of pandemic Vibrio cholerae
    • Bachmann, V., Kostiuk, B., Unterweger, D., Diaz-Satizabal, L., Ogg, S., and Pukatzki, S. (2015). Bile salts modulate the mucin-activated type VI secretion system of pandemic Vibrio cholerae. PLoS Negl. Trop. Dis. 9:e0004031. doi: 10.1371/journal.pntd.0004031
    • (2015) PLoS Negl. Trop. Dis , vol.9
    • Bachmann, V.1    Kostiuk, B.2    Unterweger, D.3    Diaz-Satizabal, L.4    Ogg, S.5    Pukatzki, S.6
  • 9
    • 84867576178 scopus 로고    scopus 로고
    • Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis
    • Barger, S. R., Hoefler, B. C., Cubillos-Ruiz, A., Russell, W. K., Russell, D. H., and Straight, P. D. (2012). Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis. Antonie Van Leeuwenhoek 102, 435-445. doi: 10.1007/s10482-012-9769-0
    • (2012) Antonie Van Leeuwenhoek , vol.102 , pp. 435-445
    • Barger, S.R.1    Hoefler, B.C.2    Cubillos-Ruiz, A.3    Russell, W.K.4    Russell, D.H.5    Straight, P.D.6
  • 10
    • 40749084834 scopus 로고    scopus 로고
    • Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract
    • Barman, M., Unold, D., Shifley, K., Amir, E., Hung, K., Bos, N., et al. (2008). Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect. Immun. 76, 907-915. doi: 10.1128/IAI.01432-07
    • (2008) Infect. Immun , vol.76 , pp. 907-915
    • Barman, M.1    Unold, D.2    Shifley, K.3    Amir, E.4    Hung, K.5    Bos, N.6
  • 11
    • 84873723077 scopus 로고    scopus 로고
    • Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions
    • Basler, M., Ho, B. T., and Mekalanos, J. J. (2013). Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell 152, 884-894. doi: 10.1016/j.cell.2013.01.042
    • (2013) Cell , vol.152 , pp. 884-894
    • Basler, M.1    Ho, B.T.2    Mekalanos, J.J.3
  • 12
    • 84969921123 scopus 로고    scopus 로고
    • Antibiotic-induced changes in the intestinal microbiota and disease
    • Becattini, S., Taur, Y., and Pamer, E. G. (2016). Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol. Med. 22, 458-478. doi: 10.1016/j.molmed.2016.04.003
    • (2016) Trends Mol. Med , vol.22 , pp. 458-478
    • Becattini, S.1    Taur, Y.2    Pamer, E.G.3
  • 13
    • 84859426707 scopus 로고    scopus 로고
    • Increasing antagonistic interactions cause bacterial communities to collapse at high diversity
    • Becker, J., Eisenhauer, N., Scheu, S., and Jousset, A. (2012). Increasing antagonistic interactions cause bacterial communities to collapse at high diversity. Ecol. Lett. 15, 468-474. doi: 10.1111/j.1461-0248.2012.01759.x
    • (2012) Ecol. Lett , vol.15 , pp. 468-474
    • Becker, J.1    Eisenhauer, N.2    Scheu, S.3    Jousset, A.4
  • 15
    • 84948732213 scopus 로고    scopus 로고
    • Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
    • Bikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., et al. (2015). Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput. Struct. Biotechnol. J. 13, 390-401. doi: 10.1016/j.csbj.2015.06.001
    • (2015) Comput. Struct. Biotechnol. J , vol.13 , pp. 390-401
    • Bikel, S.1    Valdez-Lara, A.2    Cornejo-Granados, F.3    Rico, K.4    Canizales-Quinteros, S.5    Soberón, X.6
  • 16
    • 0002017255 scopus 로고
    • The meanings of competition
    • Birch, L. C. (1957). The meanings of competition. Am. Nat. 91, 5-18. doi: 10.1086/281957
    • (1957) Am. Nat , vol.91 , pp. 5-18
    • Birch, L.C.1
  • 17
    • 84897654866 scopus 로고    scopus 로고
    • Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition
    • Blanchard, A. E., Celik, V., and Lu, T. (2014). Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition. BMC Syst. Biol. 8:23. doi: 10.1186/1752-0509-8-23
    • (2014) BMC Syst. Biol , vol.8 , pp. 23
    • Blanchard, A.E.1    Celik, V.2    Lu, T.3
  • 18
  • 19
    • 84937839424 scopus 로고    scopus 로고
    • Genomic analyses of pneumococci reveal a wide diversity of bacteriocins-including pneumocyclicin, a novel circular bacteriocin
    • Bogaardt, C., van Tonder, A. J., and Brueggemann, A. B. (2015). Genomic analyses of pneumococci reveal a wide diversity of bacteriocins-including pneumocyclicin, a novel circular bacteriocin. BMC Genomics 16:554. doi: 10.1186/s12864-015-1729-4
    • (2015) BMC Genomics , vol.16 , pp. 554
    • Bogaardt, C.1    van Tonder, A.J.2    Brueggemann, A.B.3
  • 20
    • 0028325274 scopus 로고
    • Colicins: structures, modes of action, transfer through membranes, and evolution
    • Braun, V., Pilsl, H., and Gross, P. (1994). Colicins: structures, modes of action, transfer through membranes, and evolution. Arch. Microbiol. 161, 199-206. doi: 10.1007/BF00248693
    • (1994) Arch. Microbiol , vol.161 , pp. 199-206
    • Braun, V.1    Pilsl, H.2    Gross, P.3
  • 21
    • 84898771460 scopus 로고    scopus 로고
    • Role of the intestinal microbiota in resistance to colonization by Clostridium difficile
    • Britton, R. A., and Young, V. B. (2014). Role of the intestinal microbiota in resistance to colonization by Clostridium difficile. Gastroenterology 146, 1547-1553. doi: 10.1053/j.gastro.2014.01.059
    • (2014) Gastroenterology , vol.146 , pp. 1547-1553
    • Britton, R.A.1    Young, V.B.2
  • 22
    • 84925500413 scopus 로고    scopus 로고
    • Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
    • Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., et al. (2015). Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205-208. doi: 10.1038/nature13828
    • (2015) Nature , vol.517 , pp. 205-208
    • Buffie, C.G.1    Bucci, V.2    Stein, R.R.3    McKenney, P.T.4    Ling, L.5    Gobourne, A.6
  • 23
    • 84886795788 scopus 로고    scopus 로고
    • Microbiota-mediated colonization resistance against intestinal pathogens
    • Buffie, C. G., and Pamer, E. G. (2013). Microbiota-mediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol. 13, 790-801. doi: 10.1038/nri3535
    • (2013) Nat. Rev. Immunol , vol.13 , pp. 790-801
    • Buffie, C.G.1    Pamer, E.G.2
  • 26
    • 33746865723 scopus 로고    scopus 로고
    • Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics
    • Chater, K. F. (2006). Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361, 761-768. doi: 10.1098/rstb.2005.1758
    • (2006) Philos. Trans. R. Soc. Lond. B Biol. Sci , vol.361 , pp. 761-768
    • Chater, K.F.1
  • 27
    • 84914811256 scopus 로고    scopus 로고
    • An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins
    • Chatzidaki-Livanis, M., Coyne, M. J., and Comstock, L. E. (2014). An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins. Mol. Microbiol. 94, 1361-1374. doi: 10.1111/mmi.12839
    • (2014) Mol. Microbiol , vol.94 , pp. 1361-1374
    • Chatzidaki-Livanis, M.1    Coyne, M.J.2    Comstock, L.E.3
  • 28
    • 84962124787 scopus 로고    scopus 로고
    • Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species
    • Chatzidaki-Livanis, M., Geva-Zatorsky, N., and Comstock, L. E. (2016). Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. Proc. Natl. Acad. Sci. U.S.A. 113, 3627-3632. doi: 10.1073/pnas.1522510113
    • (2016) Proc. Natl. Acad. Sci. U.S.A , vol.113 , pp. 3627-3632
    • Chatzidaki-Livanis, M.1    Geva-Zatorsky, N.2    Comstock, L.E.3
  • 29
    • 2542457427 scopus 로고    scopus 로고
    • Protective effect of exopolysaccharide colanic acid of Escherichia coli O157:H7 to osmotic and oxidative stress
    • Chen, J., Lee, S. M., and Mao, Y. (2004). Protective effect of exopolysaccharide colanic acid of Escherichia coli O157:H7 to osmotic and oxidative stress. Int. J. Food Microbiol. 93, 281-286. doi: 10.1016/j.ijfoodmicro.2003.12.004
    • (2004) Int. J. Food Microbiol , vol.93 , pp. 281-286
    • Chen, J.1    Lee, S.M.2    Mao, Y.3
  • 30
    • 84975503294 scopus 로고    scopus 로고
    • Microbiome sequencing: challenges and opportunities for molecular medicine
    • Clavel, T., Lagkouvardos, I., and Hiergeist, A. (2016). Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev. Mol. Diagn. 16, 795-805. doi: 10.1080/14737159.2016.1184574
    • (2016) Expert Rev. Mol. Diagn , vol.16 , pp. 795-805
    • Clavel, T.1    Lagkouvardos, I.2    Hiergeist, A.3
  • 31
    • 84919884441 scopus 로고    scopus 로고
    • Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy
    • Connell, J. L., Kim, J., Shear, J. B., Bard, A. J., and Whiteley, M. (2014). Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy. Proc. Natl. Acad. Sci. U.S.A. 111, 18255-18260. doi: 10.1073/pnas.1421211111
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. 18255-18260
    • Connell, J.L.1    Kim, J.2    Shear, J.B.3    Bard, A.J.4    Whiteley, M.5
  • 33
  • 34
    • 84863772202 scopus 로고    scopus 로고
    • Production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I
    • Cude, W. N., Mooney, J., Tavanaei, A. A., Hadden, M. K., Frank, A. M., Gulvik, C. A., et al. (2012). Production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I. Appl. Environ. Microbiol. 78, 4771-4780. doi: 10.1128/AEM.00297-12
    • (2012) Appl. Environ. Microbiol , vol.78 , pp. 4771-4780
    • Cude, W.N.1    Mooney, J.2    Tavanaei, A.A.3    Hadden, M.K.4    Frank, A.M.5    Gulvik, C.A.6
  • 35
    • 0037154213 scopus 로고    scopus 로고
    • Chemical warfare between microbes promotes biodiversity
    • Czárán, T. L., Hoekstra, R. F., and Pagie, L. (2002). Chemical warfare between microbes promotes biodiversity. Proc. Natl. Acad. Sci. U.S.A. 99, 786-790. doi: 10.1073/pnas.012399899
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 786-790
    • Czárán, T.L.1    Hoekstra, R.F.2    Pagie, L.3
  • 37
    • 0037325258 scopus 로고    scopus 로고
    • Filamentous phages linked to virulence of Vibrio cholerae
    • Davis, B. M., and Waldor, M. K. (2003). Filamentous phages linked to virulence of Vibrio cholerae. Curr. Opin. Microbiol. 6, 35-42. doi: 10.1016/S1369-5274(02)00005-X
    • (2003) Curr. Opin. Microbiol , vol.6 , pp. 35-42
    • Davis, B.M.1    Waldor, M.K.2
  • 39
    • 84989179649 scopus 로고    scopus 로고
    • Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality
    • De Weirdt, R., and Van de Wiele, T. (2015). Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality. NPJ Biofilms Microbiomes 1:15026. doi: 10.1038/npjbiofilms.2015.26
    • (2015) NPJ Biofilms Microbiomes , vol.1 , pp. 15026
    • De Weirdt, R.1    Van de Wiele, T.2
  • 40
    • 66249123253 scopus 로고    scopus 로고
    • Viability PCR, a culture-independent method for rapid and selective quantification of viable Legionella pneumophila cells in environmental water samples
    • Delgado-Viscogliosi, P., Solignac, L., and Delattre, J.-M. (2009). Viability PCR, a culture-independent method for rapid and selective quantification of viable Legionella pneumophila cells in environmental water samples. Appl. Environ. Microbiol. 75, 3502-3512. doi: 10.1128/AEM.02878-08
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 3502-3512
    • Delgado-Viscogliosi, P.1    Solignac, L.2    Delattre, J.-M.3
  • 41
    • 84860220826 scopus 로고    scopus 로고
    • High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments
    • Dell'Anno, A., Beolchini, F., Rocchetti, L., Luna, G. M., and Danovaro, R. (2012). High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments. Environ. Pollut. 167, 85-92. doi: 10.1016/j.envpol.2012.03.043
    • (2012) Environ. Pollut , vol.167 , pp. 85-92
    • Dell'Anno, A.1    Beolchini, F.2    Rocchetti, L.3    Luna, G.M.4    Danovaro, R.5
  • 42
    • 84951568821 scopus 로고    scopus 로고
    • Gut biogeography of the bacterial microbiota
    • Donaldson, G. P., Lee, S. M., and Mazmanian, S. K. (2016). Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20-32. doi: 10.1038/nrmicro3552
    • (2016) Nat. Rev. Microbiol , vol.14 , pp. 20-32
    • Donaldson, G.P.1    Lee, S.M.2    Mazmanian, S.K.3
  • 43
    • 0000378637 scopus 로고
    • On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzæ
    • Fleming, A. (1929). On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzæ. Br. J. Exp. Pathol. 10:226-236.
    • (1929) Br. J. Exp. Pathol , vol.10 , pp. 226-236
    • Fleming, A.1
  • 44
    • 84867405105 scopus 로고    scopus 로고
    • Competition, not cooperation, dominates interactions among culturable microbial species
    • Foster, K. R., and Bell, T. (2012). Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845-1850. doi: 10.1016/j.cub.2012.08.005
    • (2012) Curr. Biol , vol.22 , pp. 1845-1850
    • Foster, K.R.1    Bell, T.2
  • 45
    • 67649470562 scopus 로고    scopus 로고
    • Metabolic-network-driven analysis of bacterial ecological strategies
    • Freilich, S., Kreimer, A., Borenstein, E., Yosef, N., Sharan, R., Gophna, U., et al. (2009). Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 10:R61. doi: 10.1186/gb-2009-10-6-r61
    • (2009) Genome Biol , vol.10
    • Freilich, S.1    Kreimer, A.2    Borenstein, E.3    Yosef, N.4    Sharan, R.5    Gophna, U.6
  • 46
    • 84455174807 scopus 로고    scopus 로고
    • Competitive and cooperative metabolic interactions in bacterial communities
    • Freilich, S., Zarecki, R., Eilam, O., Segal, E. S., Henry, C. S., Kupiec, M., et al. (2011). Competitive and cooperative metabolic interactions in bacterial communities. Nat. Commun. 2:589. doi: 10.1038/ncomms1597
    • (2011) Nat. Commun , vol.2 , pp. 589
    • Freilich, S.1    Zarecki, R.2    Eilam, O.3    Segal, E.S.4    Henry, C.S.5    Kupiec, M.6
  • 47
    • 79956279962 scopus 로고    scopus 로고
    • Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors
    • Garbeva, P., Silby, M. W., Raaijmakers, J. M., Levy, S. B., and Boer, W. D. (2011). Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME J. 5, 973-985. doi: 10.1038/ismej.2010.196
    • (2011) ISME J , vol.5 , pp. 973-985
    • Garbeva, P.1    Silby, M.W.2    Raaijmakers, J.M.3    Levy, S.B.4    Boer, W.D.5
  • 48
    • 84860003496 scopus 로고    scopus 로고
    • Multi-tier regulation of the streptomycete morphogenetic peptide SapB
    • Gaskell, A. A., Giovinazzo, J. A., Fonte, V., and Willey, J. M. (2012). Multi-tier regulation of the streptomycete morphogenetic peptide SapB. Mol. Microbiol. 84, 501-515. doi: 10.1111/j.1365-2958.2012.08041.x
    • (2012) Mol. Microbiol , vol.84 , pp. 501-515
    • Gaskell, A.A.1    Giovinazzo, J.A.2    Fonte, V.3    Willey, J.M.4
  • 49
    • 80053569422 scopus 로고    scopus 로고
    • Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance
    • Goldfarb, K. C., Karaoz, U., Hanson, C. A., Santee, C. A., Bradford, M. A., Treseder, K. K., et al. (2011). Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front. Microbiol. 2:94. doi: 10.3389/fmicb.2011.00094
    • (2011) Front. Microbiol , vol.2 , pp. 94
    • Goldfarb, K.C.1    Karaoz, U.2    Hanson, C.A.3    Santee, C.A.4    Bradford, M.A.5    Treseder, K.K.6
  • 51
    • 80052371361 scopus 로고    scopus 로고
    • Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry
    • Gonzalez, D. J., Haste, N. M., Hollands, A., Fleming, T. C., Hamby, M., Pogliano, K., et al. (2011). Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry. Microbiology 157, 2485-2492. doi: 10.1099/mic.0.048736-0
    • (2011) Microbiology , vol.157 , pp. 2485-2492
    • Gonzalez, D.J.1    Haste, N.M.2    Hollands, A.3    Fleming, T.C.4    Hamby, M.5    Pogliano, K.6
  • 53
    • 80055098493 scopus 로고    scopus 로고
    • The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes
    • Gray, N. D., Sherry, A., Grant, R. J., Rowan, A. K., Hubert, C. R. J., Callbeck, C. M., et al. (2011). The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ. Microbiol. 13, 2957-2975. doi: 10.1111/j.1462-2920.2011.02570.x
    • (2011) Environ. Microbiol , vol.13 , pp. 2957-2975
    • Gray, N.D.1    Sherry, A.2    Grant, R.J.3    Rowan, A.K.4    Hubert, C.R.J.5    Callbeck, C.M.6
  • 54
    • 33747174849 scopus 로고    scopus 로고
    • Spatial scaling of microbial biodiversity
    • Green, J., and Bohannan, B. J. M. (2006). Spatial scaling of microbial biodiversity. Trends Ecol. Evol. 21, 501-507. doi: 10.1016/j.tree.2006.06.012
    • (2006) Trends Ecol. Evol , vol.21 , pp. 501-507
    • Green, J.1    Bohannan, B.J.M.2
  • 55
    • 84891157577 scopus 로고    scopus 로고
    • Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane
    • Green-Saxena, A., Dekas, A. E., Dalleska, N. F., and Orphan, V. J. (2014). Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane. ISME J. 8, 150-163. doi: 10.1038/ismej.2013.147
    • (2014) ISME J , vol.8 , pp. 150-163
    • Green-Saxena, A.1    Dekas, A.E.2    Dalleska, N.F.3    Orphan, V.J.4
  • 56
    • 84865766850 scopus 로고    scopus 로고
    • The spectral networks paradigm in high throughput mass spectrometry
    • Guthals, A., Watrous, J. D., Dorrestein, P. C., and Bandeira, N. (2012). The spectral networks paradigm in high throughput mass spectrometry. Mol. Biosyst. 8, 2535-2544. doi: 10.1039/c2mb25085c
    • (2012) Mol. Biosyst , vol.8 , pp. 2535-2544
    • Guthals, A.1    Watrous, J.D.2    Dorrestein, P.C.3    Bandeira, N.4
  • 57
    • 84968611431 scopus 로고    scopus 로고
    • Stochastic assembly of bacteria in microwell arrays reveals the importance of confinement in community development
    • Hansen, R. H., Timm, A. C., Timm, C. M., Bible, A. N., Morrell-Falvey, J. L., Pelletier, D. A., et al. (2016). Stochastic assembly of bacteria in microwell arrays reveals the importance of confinement in community development. PLoS ONE 11:e0155080. doi: 10.1371/journal.pone.0155080
    • (2016) PLoS ONE , vol.11
    • Hansen, R.H.1    Timm, A.C.2    Timm, C.M.3    Bible, A.N.4    Morrell-Falvey, J.L.5    Pelletier, D.A.6
  • 58
    • 73949111750 scopus 로고    scopus 로고
    • Bacterial competition: surviving and thriving in the microbial jungle
    • Hibbing, M. E., Fuqua, C., Parsek, M. R., and Peterson, S. B. (2010). Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15-25. doi: 10.1038/nrmicro2259
    • (2010) Nat. Rev. Microbiol , vol.8 , pp. 15-25
    • Hibbing, M.E.1    Fuqua, C.2    Parsek, M.R.3    Peterson, S.B.4
  • 59
    • 2342492833 scopus 로고    scopus 로고
    • Simple prediction of oxygen penetration depth in biofilms for wastewater treatment
    • Hibiya, K., Nagai, J., Tsuneda, S., and Hirata, A. (2004). Simple prediction of oxygen penetration depth in biofilms for wastewater treatment. Biochem. Eng. J. 19, 61-68. doi: 10.1016/j.bej.2003.10.003
    • (2004) Biochem. Eng. J , vol.19 , pp. 61-68
    • Hibiya, K.1    Nagai, J.2    Tsuneda, S.3    Hirata, A.4
  • 60
    • 84864713988 scopus 로고    scopus 로고
    • Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition
    • Hoefler, B. C., Gorzelnik, K. V., Yang, J. Y., Hendricks, N., Dorrestein, P. C., and Straight, P. D. (2012). Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition. Proc. Natl. Acad. Sci. U.S.A. 109, 13082-13087. doi: 10.1073/pnas.1205586109
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 13082-13087
    • Hoefler, B.C.1    Gorzelnik, K.V.2    Yang, J.Y.3    Hendricks, N.4    Dorrestein, P.C.5    Straight, P.D.6
  • 61
    • 84927576346 scopus 로고    scopus 로고
    • 'Imaging mass spectrometry, metabolism, and new views of the microbial world,'
    • eds V. Havlícek and J. Spížek (Hoboken, NJ: John Wiley & Sons, Inc)
    • Hoefler, B. C., and Straight, P. D. (2014). "Imaging mass spectrometry, metabolism, and new views of the microbial world," in Natural Products Analysis: Instrumentation, Methods, and Applications, eds V. Havlícek and J. Spížek (Hoboken, NJ: John Wiley & Sons, Inc), 349-396. doi: 10.1002/9781118876015.ch10
    • (2014) Natural Products Analysis: Instrumentation, Methods, and Applications , pp. 349-396
    • Hoefler, B.C.1    Straight, P.D.2
  • 62
    • 84931022517 scopus 로고    scopus 로고
    • The idiosyncrasy of spatial structure in bacterial competition
    • Hol, F. J. H., Galajda, P., Woolthuis, R. G., Dekker, C., and Keymer, J. E. (2015). The idiosyncrasy of spatial structure in bacterial competition. BMC Res. Notes 8:245. doi: 10.1186/s13104-015-1169-x
    • (2015) BMC Res. Notes , vol.8 , pp. 245
    • Hol, F.J.H.1    Galajda, P.2    Woolthuis, R.G.3    Dekker, C.4    Keymer, J.E.5
  • 63
    • 84958818929 scopus 로고    scopus 로고
    • Bacterial predator-prey dynamics in microscale patchy landscapes
    • Hol, F. J. H., Rotem, O., Jurkevitch, E., Dekker, C., and Koster, D. A. (2016). Bacterial predator-prey dynamics in microscale patchy landscapes. Proc. Biol. Sci. 283:20152154. doi: 10.1098/rspb.2015.2154
    • (2016) Proc. Biol. Sci , vol.283
    • Hol, F.J.H.1    Rotem, O.2    Jurkevitch, E.3    Dekker, C.4    Koster, D.A.5
  • 64
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. doi: 10.1038/nature11234
    • (2012) Nature , vol.486 , pp. 207-214
  • 65
    • 84927521343 scopus 로고    scopus 로고
    • Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms
    • Hunting, E. R., Vijver, M. G., van der Geest, H. G., Mulder, C., Kraak, M. H. S., Breure, A. M., et al. (2015). Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms. Front. Microbiol. 6:105. doi: 10.3389/fmicb.2015.00105
    • (2015) Front. Microbiol , vol.6 , pp. 105
    • Hunting, E.R.1    Vijver, M.G.2    van der Geest, H.G.3    Mulder, C.4    Kraak, M.H.S.5    Breure, A.M.6
  • 67
    • 84867746452 scopus 로고    scopus 로고
    • Metabolic specialization and the assembly of microbial communities
    • Johnson, D. R., Goldschmidt, F., Lilja, E. E., and Ackermann, M. (2012). Metabolic specialization and the assembly of microbial communities. ISME J. 6, 1985-1991. doi: 10.1038/ismej.2012.46
    • (2012) ISME J , vol.6 , pp. 1985-1991
    • Johnson, D.R.1    Goldschmidt, F.2    Lilja, E.E.3    Ackermann, M.4
  • 68
    • 84930678786 scopus 로고    scopus 로고
    • Counteraction of antibiotic production and degradation stabilizes microbial communities
    • Kelsic, E. D., Zhao, J., Vetsigian, K., and Kishony, R. (2015). Counteraction of antibiotic production and degradation stabilizes microbial communities. Nature 521, 516-519. doi: 10.1038/nature14485
    • (2015) Nature , vol.521 , pp. 516-519
    • Kelsic, E.D.1    Zhao, J.2    Vetsigian, K.3    Kishony, R.4
  • 69
    • 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., and Bohannan, B. J. M. (2002). Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418, 171-174. doi: 10.1038/nature00823
    • (2002) Nature , vol.418 , pp. 171-174
    • Kerr, B.1    Riley, M.A.2    Feldman, M.W.3    Bohannan, B.J.M.4
  • 70
    • 57449090900 scopus 로고    scopus 로고
    • Defined spatial structure stabilizes a synthetic multispecies bacterial community
    • Kim, H. J., Boedicker, J. Q., Choi, J. W., and Ismagilov, R. F. (2008). Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proc. Natl. Acad. Sci. U.S.A. 105, 18188-18193. doi: 10.1073/pnas.0807935105
    • (2008) Proc. Natl. Acad. Sci. U.S.A , vol.105 , pp. 18188-18193
    • Kim, H.J.1    Boedicker, J.Q.2    Choi, J.W.3    Ismagilov, R.F.4
  • 71
    • 79951492842 scopus 로고    scopus 로고
    • Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii)
    • Kim, H. J., Du, W., and Ismagilov, R. F. (2011). Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii). Integr. Biol. (Camb). 3, 126-133. doi: 10.1039/c0ib00019a
    • (2011) Integr. Biol. (Camb) , vol.3 , pp. 126-133
    • Kim, H.J.1    Du, W.2    Ismagilov, R.F.3
  • 73
    • 84907346425 scopus 로고    scopus 로고
    • Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition
    • Koch, G., Yepes, A., Förstner, K. U., Wermser, C., Stengel, S. T., Modamio, J., et al. (2014). Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition. Cell 158, 1060-1071. doi: 10.1016/j.cell.2014.06.046
    • (2014) Cell , vol.158 , pp. 1060-1071
    • Koch, G.1    Yepes, A.2    Förstner, K.U.3    Wermser, C.4    Stengel, S.T.5    Modamio, J.6
  • 74
    • 0000644552 scopus 로고
    • Untersuchungen ueber Bakterien V. Die Aetiologie der Milzbrand-Krankheit, begruendent auf die Entwicklungsgeschichte des Bacillus anthracis
    • Koch, R. (1876). Untersuchungen ueber Bakterien V. Die Aetiologie der Milzbrand-Krankheit, begruendent auf die Entwicklungsgeschichte des Bacillus anthracis. Beitr. Z. Biol. Pflanz. 2, 277-310.
    • (1876) Beitr. Z. Biol. Pflanz , vol.2 , pp. 277-310
    • Koch, R.1
  • 75
    • 84945964162 scopus 로고    scopus 로고
    • Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract
    • Kommineni, S., Bretl, D. J., Lam, V., Chakraborty, R., Hayward, M., Simpson, P., et al. (2015). Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. Nature 526, 719-722. doi: 10.1038/nature15524
    • (2015) Nature , vol.526 , pp. 719-722
    • Kommineni, S.1    Bretl, D.J.2    Lam, V.3    Chakraborty, R.4    Hayward, M.5    Simpson, P.6
  • 76
    • 84864058204 scopus 로고    scopus 로고
    • Selection-driven gene loss in bacteria
    • Koskiniemi, S., Sun, S., Berg, O. G., and Andersson, D. I. (2012). Selection-driven gene loss in bacteria. PLoS Genet. 8:e1002787. doi: 10.1371/journal.pgen.1002787
    • (2012) PLoS Genet , vol.8
    • Koskiniemi, S.1    Sun, S.2    Berg, O.G.3    Andersson, D.I.4
  • 78
    • 27144509129 scopus 로고    scopus 로고
    • Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm
    • Kreth, J., Merritt, J., Shi, W., and Qi, F. (2005). Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm. J. Bacteriol. 187, 7193-7203. doi: 10.1128/JB.187.21.7193-7203.2005
    • (2005) J. Bacteriol , vol.187 , pp. 7193-7203
    • Kreth, J.1    Merritt, J.2    Shi, W.3    Qi, F.4
  • 79
    • 46049097957 scopus 로고    scopus 로고
    • Streptococcal antagonism in oral biofilms: Streptococcus sanguinis and Streptococcus gordonii interference with Streptococcus mutans
    • Kreth, J., Zhang, Y., and Herzberg, M. C. (2008). Streptococcal antagonism in oral biofilms: Streptococcus sanguinis and Streptococcus gordonii interference with Streptococcus mutans. J. Bacteriol. 190, 4632-4640. doi: 10.1128/JB.00276-08
    • (2008) J. Bacteriol , vol.190 , pp. 4632-4640
    • Kreth, J.1    Zhang, Y.2    Herzberg, M.C.3
  • 80
    • 84939825194 scopus 로고    scopus 로고
    • Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
    • Lebeis, S. L., Paredes, S. H., Lundberg, D. S., Breakfield, N., Gehring, J., McDonald, M., et al. (2015). Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860-864. doi: 10.1126/science.aaa8764
    • (2015) Science , vol.349 , pp. 860-864
    • Lebeis, S.L.1    Paredes, S.H.2    Lundberg, D.S.3    Breakfield, N.4    Gehring, J.5    McDonald, M.6
  • 81
    • 84978716069 scopus 로고    scopus 로고
    • Promising antibiotic discovered in microbial 'dark matter'
    • Ledford, H. (2015). Promising antibiotic discovered in microbial 'dark matter'. Nature doi: 10.1038/nature.2015.16675
    • (2015) Nature
    • Ledford, H.1
  • 82
    • 84863668598 scopus 로고    scopus 로고
    • Repeated, selection-driven genome reduction of accessory genes in experimental populations
    • Lee, M. C., and Marx, C. J. (2012). Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet. 8:e1002651. doi: 10.1371/journal.pgen.1002651
    • (2012) PLoS Genet , vol.8
    • Lee, M.C.1    Marx, C.J.2
  • 83
    • 0027101175 scopus 로고
    • The problem of pattern and scale in ecology
    • Levin, S. A. (1992). The problem of pattern and scale in ecology. Ecology 73, 1943-1967. doi: 10.2307/1941447
    • (1992) Ecology , vol.73 , pp. 1943-1967
    • Levin, S.A.1
  • 84
    • 84877279350 scopus 로고    scopus 로고
    • Platforms for antibiotic discovery
    • Lewis, K. (2013). Platforms for antibiotic discovery. Nat. Rev. Drug Discov. 12, 371-387. doi: 10.1038/nrd3975
    • (2013) Nat. Rev. Drug Discov , vol.12 , pp. 371-387
    • Lewis, K.1
  • 85
    • 52049092682 scopus 로고    scopus 로고
    • Worlds within worlds: evolution of the vertebrate gut microbiota
    • Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R., and Gordon, J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776-788. doi: 10.1038/nrmicro1978
    • (2008) Nat. Rev. Microbiol , vol.6 , pp. 776-788
    • Ley, R.E.1    Lozupone, C.A.2    Hamady, M.3    Knight, R.4    Gordon, J.I.5
  • 86
    • 0037394611 scopus 로고    scopus 로고
    • Microbiology of the phyllosphere
    • Lindow, S. E., and Brandl, M. T. (2003). Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875-1883. doi: 10.1128/AEM.69.4.1875
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 1875-1883
    • Lindow, S.E.1    Brandl, M.T.2
  • 87
    • 84922937832 scopus 로고    scopus 로고
    • A new antibiotic kills pathogens without detectable resistance
    • Ling, L. L., Schneider, T., Peoples, A. J., Spoering, A. L., Engels, I., Conlon, B. P., et al. (2015). A new antibiotic kills pathogens without detectable resistance. Nature 517, 455-459. doi: 10.1038/nature14098
    • (2015) Nature , vol.517 , pp. 455-459
    • Ling, L.L.1    Schneider, T.2    Peoples, A.J.3    Spoering, A.L.4    Engels, I.5    Conlon, B.P.6
  • 88
    • 79952609857 scopus 로고    scopus 로고
    • Real-time mapping of a hydrogen peroxide concentration profile across a polymicrobial bacterial biofilm using scanning electrochemical microscopy
    • Liu, X., Ramsey, M. M., Chen, X., Koley, D., Whiteley, M., and Bard, A. J. (2011). Real-time mapping of a hydrogen peroxide concentration profile across a polymicrobial bacterial biofilm using scanning electrochemical microscopy. Proc. Natl. Acad. Sci. U.S.A. 108, 2668-2673. doi: 10.1073/pnas.1018391108
    • (2011) Proc. Natl. Acad. Sci. U.S.A , vol.108 , pp. 2668-2673
    • Liu, X.1    Ramsey, M.M.2    Chen, X.3    Koley, D.4    Whiteley, M.5    Bard, A.J.6
  • 89
    • 84942027277 scopus 로고    scopus 로고
    • Competition for space during bacterial colonization of a surface
    • Lloyd, D. P., and Allen, R. J. (2015). Competition for space during bacterial colonization of a surface. J. R. Soc. Interface 12:0608. doi: 10.1098/rsif.2015.0608
    • (2015) J. R. Soc. Interface , vol.12 , pp. 0608
    • Lloyd, D.P.1    Allen, R.J.2
  • 90
  • 91
    • 78149470831 scopus 로고    scopus 로고
    • Comparison of 61 sequenced Escherichia coli genomes
    • Lukjancenko, O., Wassenaar, T. M., and Ussery, D. W. (2010). Comparison of 61 sequenced Escherichia coli genomes. Microb. Ecol. 60, 708-720. doi: 10.1007/s00248-010-9717-3
    • (2010) Microb. Ecol , vol.60 , pp. 708-720
    • Lukjancenko, O.1    Wassenaar, T.M.2    Ussery, D.W.3
  • 92
    • 84949114770 scopus 로고    scopus 로고
    • Bacterial growth laws reflect the evolutionary importance of energy efficiency
    • Maitra, A., and Dill, K. A. (2015). Bacterial growth laws reflect the evolutionary importance of energy efficiency. Proc. Natl. Acad. Sci. U.S.A. 112, 406-411. doi: 10.1073/pnas.1421138111
    • (2015) Proc. Natl. Acad. Sci. U.S.A , vol.112 , pp. 406-411
    • Maitra, A.1    Dill, K.A.2
  • 93
    • 84877955615 scopus 로고    scopus 로고
    • The weak shall inherit: bacteriocin-mediated interactions in bacterial populations
    • Majeed, H., Lampert, A., Ghazaryan, L., and Gillor, O. (2013). The weak shall inherit: bacteriocin-mediated interactions in bacterial populations. PLoS ONE 8:e63837. doi: 10.1371/journal.pone.0063837
    • (2013) PLoS ONE , vol.8
    • Majeed, H.1    Lampert, A.2    Ghazaryan, L.3    Gillor, O.4
  • 94
    • 85047696106 scopus 로고    scopus 로고
    • Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities
    • Mallon, C. A., Poly, F., Le Roux, X., Marring, I., van Elsas, J. D., and Salles, J. F. (2015). Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 96, 915-926. doi: 10.1890/14-1001.1
    • (2015) Ecology , vol.96 , pp. 915-926
    • Mallon, C.A.1    Poly, F.2    Le Roux, X.3    Marring, I.4    van Elsas, J.D.5    Salles, J.F.6
  • 95
    • 84925665336 scopus 로고    scopus 로고
    • Slow and steady wins the race: a bacterial exploitative competition strategy in fluctuating environments
    • Mao, J., Blanchard, A. E., and Lu, T. (2015). Slow and steady wins the race: a bacterial exploitative competition strategy in fluctuating environments. ACS Synth. Biol. 4, 240-248. doi: 10.1021/sb4002008
    • (2015) ACS Synth. Biol , vol.4 , pp. 240-248
    • Mao, J.1    Blanchard, A.E.2    Lu, T.3
  • 96
    • 84960919584 scopus 로고    scopus 로고
    • Shaping the growth behaviour of biofilms initiated from bacterial aggregates
    • Melaugh, G., Hutchison, J., Kragh, K. N., Irie, Y., Roberts, A., Bjarnsholt, T., et al. (2016). Shaping the growth behaviour of biofilms initiated from bacterial aggregates. PLoS ONE 11:e0149683. doi: 10.1371/journal.pone.0149683
    • (2016) PLoS ONE , vol.11
    • Melaugh, G.1    Hutchison, J.2    Kragh, K.N.3    Irie, Y.4    Roberts, A.5    Bjarnsholt, T.6
  • 97
    • 85015352699 scopus 로고    scopus 로고
    • Diverse ecological strategies are encoded by Streptococcus pneumoniae bacteriocin-like peptides
    • Miller, E. L., Abrudan, M. I., Roberts, I. S., and Rozen, D. E. (2016). Diverse ecological strategies are encoded by Streptococcus pneumoniae bacteriocin-like peptides. Genome Biol. Evol. 8, 1072-1090. doi: 10.1093/gbe/evw055
    • (2016) Genome Biol. Evol , vol.8 , pp. 1072-1090
    • Miller, E.L.1    Abrudan, M.I.2    Roberts, I.S.3    Rozen, D.E.4
  • 98
    • 84858979136 scopus 로고    scopus 로고
    • The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities
    • Moffitt, J. R., Lee, J. B., and Cluzel, P. (2012). The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities. Lab Chip 12, 1487-1494. doi: 10.1039/c2lc00009a
    • (2012) Lab Chip , vol.12 , pp. 1487-1494
    • Moffitt, J.R.1    Lee, J.B.2    Cluzel, P.3
  • 99
    • 25144507240 scopus 로고    scopus 로고
    • Spatial organization of dual-species bacterial aggregates on leaf surfaces
    • Monier, J.-M., and Lindow, S. E. (2005). Spatial organization of dual-species bacterial aggregates on leaf surfaces. Appl. Environ. Microbiol. 71, 5484-5493. doi: 10.1128/AEM.71.9.5484-5493.2005
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 5484-5493
    • Monier, J.-M.1    Lindow, S.E.2
  • 100
    • 84928137945 scopus 로고    scopus 로고
    • Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island
    • Moon, B. Y., Park, J. Y., Hwang, S. Y., Robinson, D. A., Thomas, J. C., Fitzgerald, J. R., et al. (2015). Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island. Sci. Rep. 5:9784. doi: 10.1038/srep09784
    • (2015) Sci. Rep , vol.5 , pp. 9784
    • Moon, B.Y.1    Park, J.Y.2    Hwang, S.Y.3    Robinson, D.A.4    Thomas, J.C.5    Fitzgerald, J.R.6
  • 103
    • 84938291252 scopus 로고    scopus 로고
    • Black Queen evolution: the role of leakiness in structuring microbial communities
    • Morris, J. J. (2015). Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet. 31, 475-482. doi: 10.1016/j.tig.2015.05.004
    • (2015) Trends Genet , vol.31 , pp. 475-482
    • Morris, J.J.1
  • 104
    • 84860511582 scopus 로고    scopus 로고
    • The Black Queen hypothesis: evolution of dependencies through adaptive gene loss
    • Morris, J. J., Lenski, R. E., and Zinser, E. R. (2012). The Black Queen hypothesis: evolution of dependencies through adaptive gene loss. MBio 3, 1-7. doi: 10.1128/mBio.00036-12
    • (2012) MBio , vol.3 , pp. 1-7
    • Morris, J.J.1    Lenski, R.E.2    Zinser, E.R.3
  • 106
    • 84906330901 scopus 로고    scopus 로고
    • Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus
    • Müller, S., Strack, S. N., Hoefler, B. C., Straight, P. D., Kearns, D. B., and Kirby, J. R. (2014). Bacillaene and sporulation protect Bacillus subtilis from predation by Myxococcus xanthus. Appl. Environ. Microbiol. 80, 5603-5610. doi: 10.1128/AEM.01621-14
    • (2014) Appl. Environ. Microbiol , vol.80 , pp. 5603-5610
    • Müller, S.1    Strack, S.N.2    Hoefler, B.C.3    Straight, P.D.4    Kearns, D.B.5    Kirby, J.R.6
  • 107
    • 0031959006 scopus 로고    scopus 로고
    • Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
    • Muyzer, G., and Smalla, K. (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73, 127-141. doi: 10.1023/A:1000669317571
    • (1998) Antonie Van Leeuwenhoek , vol.73 , pp. 127-141
    • Muyzer, G.1    Smalla, K.2
  • 108
    • 45749149209 scopus 로고    scopus 로고
    • Coexistence of antibiotic-producing and antibiotic-sensitive bacteria in biofilms is mediated by resistant bacteria
    • Narisawa, N., Haruta, S., Arai, H., Ishii, M., and Igarashi, Y. (2008). Coexistence of antibiotic-producing and antibiotic-sensitive bacteria in biofilms is mediated by resistant bacteria. Appl. Environ. Microbiol. 74, 3887-3894. doi: 10.1128/AEM.02497-07
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 3887-3894
    • Narisawa, N.1    Haruta, S.2    Arai, H.3    Ishii, M.4    Igarashi, Y.5
  • 109
    • 77950560416 scopus 로고    scopus 로고
    • Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species
    • Nichols, D., Cahoon, N., Trakhtenberg, E. M., Pham, L., Mehta, A., Belanger, A., et al. (2010). Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl. Environ. Microbiol. 76, 2445-2450. doi: 10.1128/AEM.01754-09
    • (2010) Appl. Environ. Microbiol , vol.76 , pp. 2445-2450
    • Nichols, D.1    Cahoon, N.2    Trakhtenberg, E.M.3    Pham, L.4    Mehta, A.5    Belanger, A.6
  • 110
    • 34547579868 scopus 로고    scopus 로고
    • Genotypic microbial community profiling: a critical technical review
    • Nocker, A., Burr, M., and Camper, A. K. (2007). Genotypic microbial community profiling: a critical technical review. Microb. Ecol. 54, 276-289. doi: 10.1007/s00248-006-9199-5
    • (2007) Microb. Ecol , vol.54 , pp. 276-289
    • Nocker, A.1    Burr, M.2    Camper, A.K.3
  • 111
    • 33748746842 scopus 로고    scopus 로고
    • Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells
    • Nocker, A., Cheung, C.-Y., and Camper, A. K. (2006). Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67, 310-320. doi: 10.1016/j.mimet.2006.04.015
    • (2006) J. Microbiol. Methods , vol.67 , pp. 310-320
    • Nocker, A.1    Cheung, C.-Y.2    Camper, A.K.3
  • 112
    • 84962367282 scopus 로고    scopus 로고
    • Clostridium difficile infection: a review of current and emerging therapies
    • Ofosu, A. (2016). Clostridium difficile infection: a review of current and emerging therapies. Ann. Gastroenterol. 29, 147-154. doi: 10.20524/aog.2016.0006
    • (2016) Ann. Gastroenterol , vol.29 , pp. 147-154
    • Ofosu, A.1
  • 113
    • 0031034881 scopus 로고    scopus 로고
    • The reason for as well as the consequence of the Cambrian explosion in animal evolution
    • Ohno, S. (1997). The reason for as well as the consequence of the Cambrian explosion in animal evolution. J. Mol. Evol. 44(Suppl. 1), S23-S27. doi: 10.1007/PL00000055
    • (1997) J. Mol. Evol , vol.44 , pp. S23-S27
    • Ohno, S.1
  • 115
    • 84965045968 scopus 로고    scopus 로고
    • Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens
    • Pamer, E. G., Dethlefsen, L., Huse, S., Sogin, M. L., Relman, D. A., Ubeda, C., et al. (2016). Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science 352, 535-538. doi: 10.1126/science.aad9382
    • (2016) Science , vol.352 , pp. 535-538
    • Pamer, E.G.1    Dethlefsen, L.2    Huse, S.3    Sogin, M.L.4    Relman, D.A.5    Ubeda, C.6
  • 116
    • 80051647407 scopus 로고    scopus 로고
    • A microfluidic concentrator array for quantitative predation assays of predatory microbes
    • Park, S., Kim, D., Mitchell, R. J., and Kim, T. (2011). A microfluidic concentrator array for quantitative predation assays of predatory microbes. Lab Chip 11, 2916-2923. doi: 10.1039/c1lc20230h
    • (2011) Lab Chip , vol.11 , pp. 2916-2923
    • Park, S.1    Kim, D.2    Mitchell, R.J.3    Kim, T.4
  • 117
    • 11444252559 scopus 로고    scopus 로고
    • Sociomicrobiology: the connections between quorum sensing and biofilms
    • Parsek, M. R., and Greenberg, E. P. (2005). Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol. 13, 27-33. doi: 10.1016/j.tim.2004.11.007
    • (2005) Trends Microbiol , vol.13 , pp. 27-33
    • Parsek, M.R.1    Greenberg, E.P.2
  • 119
    • 0028826917 scopus 로고
    • Bacillaene, a novel inhibitor of procaryotic protein synthesis produced by Bacillus subtilis: production, taxonomy, isolation, physico-chemical characterization and biological activity
    • Patel, P. S., Huang, S., Fisher, S., Pirnik, D., Aklonis, C., Dean, L., et al. (1995). Bacillaene, a novel inhibitor of procaryotic protein synthesis produced by Bacillus subtilis: production, taxonomy, isolation, physico-chemical characterization and biological activity. J. Antibiot. (Tokyo) 48, 997-1003. doi: 10.7164/antibiotics.48.997
    • (1995) J. Antibiot. (Tokyo) , vol.48 , pp. 997-1003
    • Patel, P.S.1    Huang, S.2    Fisher, S.3    Pirnik, D.4    Aklonis, C.5    Dean, L.6
  • 120
    • 84876462101 scopus 로고    scopus 로고
    • Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network
    • Pérez-Gutiérrez, R.-A., López-Ramírez, V., Islas, á., Alcaraz, L. D., Hernández-González, I., Olivera, B. C. L., et al. (2013). Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network. ISME J. 7, 487-497. doi: 10.1038/ismej.2012.119
    • (2013) ISME J , vol.7 , pp. 487-497
    • Pérez-Gutiérrez, R.-A.1    López-Ramírez, V.2    Islas, Á.3    Alcaraz, L.D.4    Hernández-González, I.5    Olivera, B.C.L.6
  • 121
    • 44349119350 scopus 로고    scopus 로고
    • Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
    • Pernthaler, A., Dekas, A. E., Brown, C. T., Goffredi, S. K., Embaye, T., and Orphan, V. J. (2008). Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc. Natl. Acad. Sci. U.S.A. 105, 7052-7057. doi: 10.1073/pnas.0711303105
    • (2008) Proc. Natl. Acad. Sci. U.S.A , vol.105 , pp. 7052-7057
    • Pernthaler, A.1    Dekas, A.E.2    Brown, C.T.3    Goffredi, S.K.4    Embaye, T.5    Orphan, V.J.6
  • 122
    • 84877020842 scopus 로고    scopus 로고
    • Stool substitute transplant therapy for the eradication of Clostridium difficile infection: "RePOOPulating" the gut
    • Petrof, E. O., Gloor, G. B., Vanner, S. J., Weese, S. J., Carter, D., Daigneault, M. C., et al. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: "RePOOPulating" the gut. Microbiome 1:3. doi: 10.1186/2049-2618-1-3
    • (2013) Microbiome , vol.1 , pp. 3
    • Petrof, E.O.1    Gloor, G.B.2    Vanner, S.J.3    Weese, S.J.4    Carter, D.5    Daigneault, M.C.6
  • 123
    • 84939233322 scopus 로고    scopus 로고
    • Metabolic interactions in microbial communities: Untangling the Gordian knot
    • Ponomarova, O., and Patil, K. R. (2015). Metabolic interactions in microbial communities: Untangling the Gordian knot. Curr. Opin. Microbiol. 27, 37-44. doi: 10.1016/j.mib.2015.06.014
    • (2015) Curr. Opin. Microbiol , vol.27 , pp. 37-44
    • Ponomarova, O.1    Patil, K.R.2
  • 124
    • 84930799613 scopus 로고    scopus 로고
    • Inhibition of Cell Differentiation in Bacillus subtilis by Pseudomonas protegens
    • Powers, M. J., Sanabria-Valentín, E., Bowers, A. A., and Shank, E. A. (2015). Inhibition of Cell Differentiation in Bacillus subtilis by Pseudomonas protegens. J. Bacteriol. 197, 2129-2138. doi: 10.1128/JB.02535-14
    • (2015) J. Bacteriol , vol.197 , pp. 2129-2138
    • Powers, M.J.1    Sanabria-Valentín, E.2    Bowers, A.A.3    Shank, E.A.4
  • 125
    • 84881446358 scopus 로고    scopus 로고
    • Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia
    • Prokopenko, M. G., Hirst, M. B., De Brabandere, L., Lawrence, D. J. P., Berelson, W. M., Granger, J., et al. (2013). Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia. Nature 500, 194-198. doi: 10.1038/nature12365
    • (2013) Nature , vol.500 , pp. 194-198
    • Prokopenko, M.G.1    Hirst, M.B.2    De Brabandere, L.3    Lawrence, D.J.P.4    Berelson, W.M.5    Granger, J.6
  • 126
    • 84880787578 scopus 로고    scopus 로고
    • Data-independent microbial metabolomics with ambient ionization mass spectrometry
    • Rath, C. M., Yang, J. Y., Alexandrov, T., and Dorrestein, P. C. (2013). Data-independent microbial metabolomics with ambient ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 24, 1167-1176. doi: 10.1007/s13361-013-0608-y
    • (2013) J. Am. Soc. Mass Spectrom , vol.24 , pp. 1167-1176
    • Rath, C.M.1    Yang, J.Y.2    Alexandrov, T.3    Dorrestein, P.C.4
  • 127
    • 34548305141 scopus 로고    scopus 로고
    • Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games
    • Reichenbach, T., Mobilia, M., and Frey, E. (2007). Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 448, 1046-1049. doi: 10.1038/nature06095
    • (2007) Nature , vol.448 , pp. 1046-1049
    • Reichenbach, T.1    Mobilia, M.2    Frey, E.3
  • 128
    • 84858866774 scopus 로고    scopus 로고
    • Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere
    • Remus-Emsermann, M. N. P., Tecon, R., Kowalchuk, G. A., and Leveau, J. H. J. (2012). Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere. ISME J. 6, 756-765. doi: 10.1038/ismej.2011.209
    • (2012) ISME J , vol.6 , pp. 756-765
    • Remus-Emsermann, M.N.P.1    Tecon, R.2    Kowalchuk, G.A.3    Leveau, J.H.J.4
  • 129
    • 84959059778 scopus 로고    scopus 로고
    • Mechanisms of competition in biofilm communities
    • Rendueles, O., and Ghigo, J. (2015). Mechanisms of competition in biofilm communities. Microbiol. Spectr. 3, 1-18. doi: 10.1128/microbiolspec. MB-0009-2014
    • (2015) Microbiol. Spectr , vol.3 , pp. 1-18
    • Rendueles, O.1    Ghigo, J.2
  • 130
    • 0033105191 scopus 로고    scopus 로고
    • The ecological role of bacteriocins in bacterial competition
    • Riley, M. A., and Gordon, D. M. (1999). The ecological role of bacteriocins in bacterial competition. Trends Microbiol. 7, 129-133. doi: 10.1016/S0966-842X(99)01459-6
    • (1999) Trends Microbiol , vol.7 , pp. 129-133
    • Riley, M.A.1    Gordon, D.M.2
  • 131
    • 67349250428 scopus 로고    scopus 로고
    • The gut microbiota shapes intestinal immune responses during health and disease
    • Round, J. L., and Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313-323. doi: 10.1038/nri2515
    • (2009) Nat. Rev. Immunol , vol.9 , pp. 313-323
    • Round, J.L.1    Mazmanian, S.K.2
  • 132
    • 77956996314 scopus 로고    scopus 로고
    • Soil bacterial and fungal communities across a pH gradient in an arable soil
    • Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., et al. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340-1351. doi: 10.1038/ismej.2010.58
    • (2010) ISME J , vol.4 , pp. 1340-1351
    • Rousk, J.1    Bååth, E.2    Brookes, P.C.3    Lauber, C.L.4    Lozupone, C.5    Caporaso, J.G.6
  • 133
    • 84901996995 scopus 로고    scopus 로고
    • Microfluidics expanding the frontiers of microbial ecology
    • Rusconi, R., Garren, M., and Stocker, R. (2014). Microfluidics expanding the frontiers of microbial ecology. Annu. Rev. Biophys. 43, 65-91. doi: 10.1146/annurev-biophys-051013-022916
    • (2014) Annu. Rev. Biophys , vol.43 , pp. 65-91
    • Rusconi, R.1    Garren, M.2    Stocker, R.3
  • 134
    • 79960184167 scopus 로고    scopus 로고
    • Secondary metabolites of soil Bacillus spp
    • Sansinenea, E., and Ortiz, A. (2011). Secondary metabolites of soil Bacillus spp. Biotechnol. Lett. 33, 1523-1538. doi: 10.1007/s10529-011-0617-5
    • (2011) Biotechnol. Lett , vol.33 , pp. 1523-1538
    • Sansinenea, E.1    Ortiz, A.2
  • 135
    • 82755197345 scopus 로고    scopus 로고
    • Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus
    • Shank, E. A., Klepac-Ceraj, V., Collado-Torres, L., Powers, G. E., Losick, R., and Kolter, R. (2011). Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc. Natl. Acad. Sci. U.S.A. 108, E1236-E1243. doi: 10.1073/pnas.1103630108
    • (2011) Proc. Natl. Acad. Sci. U.S.A , vol.108 , pp. E1236-E1243
    • Shank, E.A.1    Klepac-Ceraj, V.2    Collado-Torres, L.3    Powers, G.E.4    Losick, R.5    Kolter, R.6
  • 136
    • 84917741051 scopus 로고    scopus 로고
    • Donor feces infusion for eradication of extended spectrum beta-lactamase producing Escherichia coli in a patient with end stage renal disease
    • Singh, R., van Nood, E., Nieuwdorp, M., van Dam, B., ten Berge, I. J. M., Geerlings, S. E., et al. (2014). Donor feces infusion for eradication of extended spectrum beta-lactamase producing Escherichia coli in a patient with end stage renal disease. Clin. Microbiol. Infect. 20, O977-O978. doi: 10.1111/1469-0691.12683
    • (2014) Clin. Microbiol. Infect , vol.20 , pp. O977-O978
    • Singh, R.1    van Nood, E.2    Nieuwdorp, M.3    van Dam, B.4    ten Berge, I.J.M.5    Geerlings, S.E.6
  • 137
    • 84940941884 scopus 로고    scopus 로고
    • MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis
    • Singhal, N., Kumar, M., Kanaujia, P. K., and Virdi, J. S. (2015). MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front. Microbiol. 6:791. doi: 10.3389/fmicb.2015.00791
    • (2015) Front. Microbiol , vol.6 , pp. 791
    • Singhal, N.1    Kumar, M.2    Kanaujia, P.K.3    Virdi, J.S.4
  • 138
    • 73549083223 scopus 로고    scopus 로고
    • Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem
    • Song, H., Payne, S., Gray, M., and You, L. (2009). Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Nat. Chem. Biol. 5, 929-935. doi: 10.1038/nchembio.244
    • (2009) Nat. Chem. Biol , vol.5 , pp. 929-935
    • Song, H.1    Payne, S.2    Gray, M.3    You, L.4
  • 140
    • 84892708007 scopus 로고    scopus 로고
    • Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
    • Stein, R. R., Bucci, V., Toussaint, N. C., Buffie, C. G., Rätsch, G., Pamer, E. G., et al. (2013). Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9:e1003388. doi: 10.1371/journal.pcbi.1003388
    • (2013) PLoS Comput. Biol , vol.9
    • Stein, R.R.1    Bucci, V.2    Toussaint, N.C.3    Buffie, C.G.4    Rätsch, G.5    Pamer, E.G.6
  • 141
    • 84953319558 scopus 로고    scopus 로고
    • Inference of network dynamics and metabolic interactions in the gut microbiome
    • Steinway, S. N., Biggs, M. B., Loughran, T. P., Papin, J. A., and Albert, R. (2015). Inference of network dynamics and metabolic interactions in the gut microbiome. PLoS Comput. Biol. 11:e1004338. doi: 10.1371/journal.pcbi.1004338
    • (2015) PLoS Comput. Biol , vol.11
    • Steinway, S.N.1    Biggs, M.B.2    Loughran, T.P.3    Papin, J.A.4    Albert, R.5
  • 142
    • 39149100341 scopus 로고    scopus 로고
    • Physiological heterogeneity in biofilms
    • Stewart, P. S., and Franklin, M. J. (2008). Physiological heterogeneity in biofilms. Nat. Rev. Microbiol. 6, 199-210. doi: 10.1038/nrmicro1838
    • (2008) Nat. Rev. Microbiol , vol.6 , pp. 199-210
    • Stewart, P.S.1    Franklin, M.J.2
  • 143
    • 0034922338 scopus 로고    scopus 로고
    • Detachment, surface migration, and other dynamic behavior in bacterial biofilms revealed by digital time-lapse imaging
    • Stoodley, P., Hall-Stoodley, L., and Lappin-Scott, H. M. (2001a). Detachment, surface migration, and other dynamic behavior in bacterial biofilms revealed by digital time-lapse imaging. Methods Enzymol. 337, 306-319. doi: 10.1016/S0076-6879(01)37023-4
    • (2001) Methods Enzymol , vol.337 , pp. 306-319
    • Stoodley, P.1    Hall-Stoodley, L.2    Lappin-Scott, H.M.3
  • 146
    • 33745472449 scopus 로고    scopus 로고
    • Interactions between Streptomyces coelicolor and Bacillus subtilis: role of surfactants in raising aerial structures
    • Straight, P. D., Willey, J. M., and Kolter, R. (2006). Interactions between Streptomyces coelicolor and Bacillus subtilis: role of surfactants in raising aerial structures. J. Bacteriol. 188, 4918-4925. doi: 10.1128/JB.00162-06
    • (2006) J. Bacteriol , vol.188 , pp. 4918-4925
    • Straight, P.D.1    Willey, J.M.2    Kolter, R.3
  • 147
    • 84953314233 scopus 로고    scopus 로고
    • Escape from lethal bacterial competition through coupled activation of antibiotic resistance and a mobilized subpopulation
    • Stubbendieck, R. M., and Straight, P. D. (2015). Escape from lethal bacterial competition through coupled activation of antibiotic resistance and a mobilized subpopulation. PLoS Genet. 11:e1005722. doi: 10.1371/journal.pgen.1005722
    • (2015) PLoS Genet , vol.11
    • Stubbendieck, R.M.1    Straight, P.D.2
  • 148
    • 84982830487 scopus 로고    scopus 로고
    • Multifaceted interfaces of bacterial competition
    • Stubbendieck, R. M., and Straight, P. D. (2016). Multifaceted interfaces of bacterial competition. J. Bacteriol. 198, JB.275-16. doi: 10.1128/JB.00275-16
    • (2016) J. Bacteriol , vol.198
    • Stubbendieck, R.M.1    Straight, P.D.2
  • 149
    • 33646678737 scopus 로고    scopus 로고
    • Biodiversity, definition of
    • Swingland, I. R. (2001). Biodiversity, definition of. Encycl. Biodivers. 1, 377-391. doi: 10.1016/B0-12-226865-2/00027-4
    • (2001) Encycl. Biodivers , vol.1 , pp. 377-391
    • Swingland, I.R.1
  • 150
    • 84917709090 scopus 로고    scopus 로고
    • A hidden pitfall in the preparation of agar media undermines microorganism cultivability
    • Tanaka, T., Kawasaki, K., Daimon, S., Kitagawa, W., Yamamoto, K., Tamaki, H., et al. (2014). A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl. Environ. Microbiol. 80, 7659-7666. doi: 10.1128/AEM.02741-14
    • (2014) Appl. Environ. Microbiol , vol.80 , pp. 7659-7666
    • Tanaka, T.1    Kawasaki, K.2    Daimon, S.3    Kitagawa, W.4    Yamamoto, K.5    Tamaki, H.6
  • 151
    • 59649101124 scopus 로고    scopus 로고
    • Secondary metabolites produced by the marine bacterium Halobacillus salinus that inhibit quorum sensing-controlled phenotypes in gram-negative bacteria
    • Teasdale, M. E., Liu, J., Wallace, J., Akhlaghi, F., and Rowley, D. C. (2009). Secondary metabolites produced by the marine bacterium Halobacillus salinus that inhibit quorum sensing-controlled phenotypes in gram-negative bacteria. Appl. Environ. Microbiol. 75, 567-572. doi: 10.1128/AEM.00632-08
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 567-572
    • Teasdale, M.E.1    Liu, J.2    Wallace, J.3    Akhlaghi, F.4    Rowley, D.C.5
  • 152
    • 80054806900 scopus 로고    scopus 로고
    • Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota
    • Thiennimitr, P., Winter, S. E., Winter, M. G., Xavier, M. N., Tolstikov, V., Huseby, D. L., et al. (2011). Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc. Natl. Acad. Sci. U.S.A. 108, 17480-17485. doi: 10.1073/pnas.1107857108
    • (2011) Proc. Natl. Acad. Sci. U.S.A , vol.108 , pp. 17480-17485
    • Thiennimitr, P.1    Winter, S.E.2    Winter, M.G.3    Xavier, M.N.4    Tolstikov, V.5    Huseby, D.L.6
  • 153
    • 84908234204 scopus 로고    scopus 로고
    • Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism
    • Tong, M., McHardy, I., Ruegger, P., Goudarzi, M., Kashyap, P. C., Haritunians, T., et al. (2014). Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. 8, 2193-2206. doi: 10.1038/ismej.2014.64
    • (2014) ISME J , vol.8 , pp. 2193-2206
    • Tong, M.1    McHardy, I.2    Ruegger, P.3    Goudarzi, M.4    Kashyap, P.C.5    Haritunians, T.6
  • 154
    • 84868094808 scopus 로고    scopus 로고
    • Interspecies modulation of bacterial development through iron competition and siderophore piracy
    • Traxler, M. F., Seyedsayamdost, M. R., Clardy, J., and Kolter, R. (2012). Interspecies modulation of bacterial development through iron competition and siderophore piracy. Mol. Microbiol. 86, 628-644. doi: 10.1111/mmi.12008
    • (2012) Mol. Microbiol , vol.86 , pp. 628-644
    • Traxler, M.F.1    Seyedsayamdost, M.R.2    Clardy, J.3    Kolter, R.4
  • 155
    • 84883430904 scopus 로고    scopus 로고
    • Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome
    • Traxler, M. F., Watrous, J. D., Alexandrov, T., Dorrestein, P. C., and Kolter, R. (2013). Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome. MBio 4, 1-12. doi: 10.1128/mBio.00459-13
    • (2013) MBio , vol.4 , pp. 1-12
    • Traxler, M.F.1    Watrous, J.D.2    Alexandrov, T.3    Dorrestein, P.C.4    Kolter, R.5
  • 156
    • 85016191902 scopus 로고    scopus 로고
    • Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa
    • Trosvik, P., and de Muinck, E. J. (2015). Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa. Microbiome 3:44. doi: 10.1186/s40168-015-0107-4
    • (2015) Microbiome , vol.3 , pp. 44
    • Trosvik, P.1    de Muinck, E.J.2
  • 157
    • 84923374734 scopus 로고    scopus 로고
    • Biotic interactions and temporal dynamics of the human gastrointestinal microbiota
    • Trosvik, P., de Muinck, E. J., and Stenseth, N. C. (2015). Biotic interactions and temporal dynamics of the human gastrointestinal microbiota. ISME J. 9, 533-541. doi: 10.1038/ismej.2014.147
    • (2015) ISME J , vol.9 , pp. 533-541
    • Trosvik, P.1    de Muinck, E.J.2    Stenseth, N.C.3
  • 158
    • 84901585888 scopus 로고    scopus 로고
    • The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations
    • van Vliet, S., Hol, F. J. H., Weenink, T., Galajda, P., and Keymer, J. E. (2014). The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations. BMC Microbiol. 14:116. doi: 10.1186/1471-2180-14-116
    • (2014) BMC Microbiol , vol.14 , pp. 116
    • van Vliet, S.1    Hol, F.J.H.2    Weenink, T.3    Galajda, P.4    Keymer, J.E.5
  • 159
    • 84892976247 scopus 로고    scopus 로고
    • Bacterial competition reveals differential regulation of the pks genes by Bacillus subtilis
    • Vargas-Bautista, C., Rahlwes, K., and Straight, P. (2014). Bacterial competition reveals differential regulation of the pks genes by Bacillus subtilis. J. Bacteriol. 196, 717-728. doi: 10.1128/JB.01022-13
    • (2014) J. Bacteriol , vol.196 , pp. 717-728
    • Vargas-Bautista, C.1    Rahlwes, K.2    Straight, P.3
  • 160
    • 84887884513 scopus 로고    scopus 로고
    • Phylogenetic distance and species richness interactively affect the productivity of bacterial communities
    • Venail, P. A., and Vives, M. J. (2013a). Phylogenetic distance and species richness interactively affect the productivity of bacterial communities. Ecology 94, 2529-2536. doi: 10.1890/12-2002.1
    • (2013) Ecology , vol.94 , pp. 2529-2536
    • Venail, P.A.1    Vives, M.J.2
  • 161
    • 84883423388 scopus 로고    scopus 로고
    • Positive effects of bacterial diversity on ecosystem functioning driven by complementarity effects in a bioremediation context
    • Venail, P. A., and Vives, M. J. (2013b). Positive effects of bacterial diversity on ecosystem functioning driven by complementarity effects in a bioremediation context. PLoS ONE 8:e72561. doi: 10.1371/journal.pone.0072561
    • (2013) PLoS ONE , vol.8
    • Venail, P.A.1    Vives, M.J.2
  • 162
    • 70350517259 scopus 로고    scopus 로고
    • Social conflict in centimeter-and global-scale populations of the bacterium Myxococcus xanthus
    • Vos, M., and Velicer, G. J. (2009). Social conflict in centimeter-and global-scale populations of the bacterium Myxococcus xanthus. Curr. Biol. 19, 1763-1767. doi: 10.1016/j.cub.2009.08.061
    • (2009) Curr. Biol , vol.19 , pp. 1763-1767
    • Vos, M.1    Velicer, G.J.2
  • 163
    • 0001007431 scopus 로고
    • Leaf area and competition for light between plant species using direct sunlight transmission
    • Walker, G. K., Blackshaw, R. E., and Dekker, J. (1988). Leaf area and competition for light between plant species using direct sunlight transmission. Weed Technol. 2, 159-165.
    • (1988) Weed Technol , vol.2 , pp. 159-165
    • Walker, G.K.1    Blackshaw, R.E.2    Dekker, J.3
  • 164
    • 84898792630 scopus 로고    scopus 로고
    • Angucyclines as signals modulate the behaviors of Streptomyces coelicolor
    • Wang, W., Ji, J., Li, X., Wang, J., Li, S., Pan, G., et al. (2014). Angucyclines as signals modulate the behaviors of Streptomyces coelicolor. Proc. Natl. Acad. Sci. U.S.A. 111, 5688-5693. doi: 10.1073/pnas.1324253111
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. 5688-5693
    • Wang, W.1    Ji, J.2    Li, X.3    Wang, J.4    Li, S.5    Pan, G.6
  • 165
    • 27944442272 scopus 로고    scopus 로고
    • Quorum sensing: cell-to-cell communication in bacteria
    • Waters, C. M., and Bassler, B. L. (2005). Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319-346. doi: 10.1146/annurev.cellbio.21.012704.131001
    • (2005) Annu. Rev. Cell Dev. Biol , vol.21 , pp. 319-346
    • Waters, C.M.1    Bassler, B.L.2
  • 166
    • 84887777195 scopus 로고    scopus 로고
    • Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry
    • Watrous, J., Roach, P., Heath, B., Alexandrov, T., Laskin, J., and Dorrestein, P. C. (2013). Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry. Anal. Chem. 85, 10385-10391. doi: 10.1021/ac4023154
    • (2013) Anal. Chem , vol.85 , pp. 10385-10391
    • Watrous, J.1    Roach, P.2    Heath, B.3    Alexandrov, T.4    Laskin, J.5    Dorrestein, P.C.6
  • 167
    • 77955670903 scopus 로고    scopus 로고
    • Myxobacterial secondary metabolites: bioactivities and modes-of-action
    • Weissman, K. J., and Müller, R. (2010). Myxobacterial secondary metabolites: bioactivities and modes-of-action. Nat. Prod. Rep. 27, 1276-1295. doi: 10.1039/c001260m
    • (2010) Nat. Prod. Rep , vol.27 , pp. 1276-1295
    • Weissman, K.J.1    Müller, R.2
  • 168
    • 73549086351 scopus 로고    scopus 로고
    • Translating metabolic exchange with imaging mass spectrometry
    • Yang, Y.-L., Xu, Y., Straight, P., and Dorrestein, P. C. (2009). Translating metabolic exchange with imaging mass spectrometry. Nat. Chem. Biol. 5, 885-887. doi: 10.1038/nchembio.252
    • (2009) Nat. Chem. Biol , vol.5 , pp. 885-887
    • Yang, Y.-L.1    Xu, Y.2    Straight, P.3    Dorrestein, P.C.4
  • 169
    • 84931264579 scopus 로고    scopus 로고
    • Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach
    • Zapién-Campos, R., Olmedo-álvarez, G., and Santillán, M. (2015). Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach. Front. Microbiol. 6:489. doi: 10.3389/fmicb.2015.00489
    • (2015) Front. Microbiol , vol.6 , pp. 489
    • Zapién-Campos, R.1    Olmedo-álvarez, G.2    Santillán, M.3
  • 170
    • 84926466253 scopus 로고    scopus 로고
    • Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice
    • Zhang, Y., Zhao, F., Deng, Y., Zhao, Y., and Ren, H. (2015). Metagenomic and metabolomic analysis of the toxic effects of trichloroacetamide-induced gut microbiome and urine metabolome perturbations in mice. J. Proteome Res. 14, 1752-1761. doi: 10.1021/pr5011263
    • (2015) J. Proteome Res , vol.14 , pp. 1752-1761
    • Zhang, Y.1    Zhao, F.2    Deng, Y.3    Zhao, Y.4    Ren, H.5
  • 171
    • 84882779412 scopus 로고    scopus 로고
    • Involvement of gshAB in the interspecies competition within oral biofilm
    • Zheng, X., Zhang, K., Zhou, X., Liu, C., Li, M., Li, Y., et al. (2013). Involvement of gshAB in the interspecies competition within oral biofilm. J. Dent. Res. 92, 819-824. doi: 10.1177/0022034513498598
    • (2013) J. Dent. Res , vol.92 , pp. 819-824
    • Zheng, X.1    Zhang, K.2    Zhou, X.3    Liu, C.4    Li, M.5    Li, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.