Flemming, H.-C. et al. Biofilms: an emergent form of bacterial life. Nat. Rev. Microbiol. 14, 563. https://doi.org/10.1038/nrmicro.2016.94 (2016).
Boddey, J. A., Flegg, C. P., Day, C. J., Beacham, I. R. & Peak, I. R. Temperature-regulated microcolony formation by Burkholderia pseudomallei requires pilA and enhances association with cultured human cells. Infect. Immunity 74, 5374–5381. https://doi.org/10.1128/iai.00569-06 (2006).
Lister, J. L. & Horswill, A. R. Staphylococcus aureus biofilms: recent developments in biofilm dispersal. Front. Cell. Infect. Microbiol. https://doi.org/10.3389/fcimb.2014.00178 (2014).
Whitchurch, C. B., Tolker-Nielsen, T., Ragas, P. C. & Mattick, J. S. Extracellular DNA required for bacterial biofilm formation. Science 295, 1487–1487. https://doi.org/10.1126/science.295.5559.1487 (2002).
Foster, T. J., Geoghegan, J. A., Ganesh, V. K. & Höök, M. Adhesion, invasion and evasion: the many functions of the surface proteins of Staphylococcus aureus. Nat. Rev. Microbiol. 12, 49. https://doi.org/10.1038/nrmicro3161 (2013).
Mack, D. et al. The intercellular adhesin involved in biofilm accumulation of Staphylococcus epidermidis is a linear beta-1,6-linked glucosaminoglycan: purification and structural analysis. J. Bacteriol. 178, 175–183 (1996).
Limoli, D. H., Jones, C. J. & Wozniak, D. J. Bacterial extracellular polysaccharides in biofilm formation and function. Microbiol. Spectrum. https://doi.org/10.1128/microbiolspec.MB-0011-2014 (2015).
Gallaher, T. K., Wu, S., Webster, P. & Aguilera, R. Identification of biofilm proteins in non-typeable Haemophilus Influenzae. BMC Microbiol. 6, 65. https://doi.org/10.1186/1471-2180-6-65 (2006).
Hu, W. et al. DNA builds and strengthens the extracellular matrix in Myxococcus xanthus biofilms by interacting with exopolysaccharides. PLoS ONE 7, e51905. https://doi.org/10.1371/journal.pone.0051905 (2012).
Boles, B. R. & Horswill, A. R. Staphylococcal biofilm disassembly. Trends Microbiol. 19, 449–455. https://doi.org/10.1016/j.tim.2011.06.004 (2011).
Reen, F. J. et al. Bile signalling promotes chronic respiratory infections and antibiotic tolerance. Sci. Rep. 6, 29768 (2016).
Duanis-Assaf, D., Steinberg, D., Chai, Y. & Shemesh, M. The LuxS based quorum sensing governs lactose induced biofilm formation by Bacillus subtilis. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.01517 (2016).
Le, K. Y. & Otto, M. Quorum-sensing regulation in staphylococci-an overview. Front. Microbiol. 6, 1174–1174. https://doi.org/10.3389/fmicb.2015.01174 (2015).
Qi, L. et al. Relationship between antibiotic resistance, biofilm formation, and biofilm-specific resistance in Acinetobacter baumannii. Front. Microbiol. 7, 483–483. https://doi.org/10.3389/fmicb.2016.00483 (2016).
O’Callaghan, A. & van Sinderen, D. Bifidobacteria and their role as members of the human gut microbiota. Front. Microbiol. 7, 925–925. https://doi.org/10.3389/fmicb.2016.00925 (2016).
Hill, C. et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11, 506. https://doi.org/10.1038/nrgastro.2014.66 (2014).
Sánchez, B., Ruiz, L., Gueimonde, M., Ruas-Madiedo, P. & Margolles, A. Adaptation of bifidobacteria to the gastrointestinal tract and functional consequences. Pharmacol. Res. 69, 127–136. https://doi.org/10.1016/j.phrs.2012.11.004 (2013).
Holm, R., Müllertz, A. & Mu, H. Bile salts and their importance for drug absorption. Int. J. Pharm. 453, 44–55. https://doi.org/10.1016/j.ijpharm.2013.04.003 (2013).
Islam, K. B. M. S. et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 141, 1773–1781. https://doi.org/10.1053/j.gastro.2011.07.046 (2011).
Begley, M., Gahan, C. G. & Hill, C. The interaction between bacteria and bile. FEMS Microbiol. Rev. 29, 625–651. https://doi.org/10.1016/j.femsre.2004.09.003 (2005).
Ruiz, L., Margolles, A. & Sanchez, B. Bile resistance mechanisms in Lactobacillus and Bifidobacterium. Front. Microbiol. 4, 396. https://doi.org/10.3389/fmicb.2013.00396 (2013).
Price, C. E., Reid, S. J., Driessen, A. J. & Abratt, V. R. The Bifidobacterium longum NCIMB 702259T ctr gene codes for a novel cholate transporter. Appl. Environ. Microbiol. 72, 923–926. https://doi.org/10.1128/aem.72.1.923-926.2006 (2006).
Gueimonde, M., Garrigues, C., van Sinderen, D., de los Reyes-Gavilan, C. G. & Margolles, A. Bile-inducible efflux transporter from Bifidobacterium longum NCC2705, conferring bile resistance. Appl. Environ. Microbiol. 75, 3153–3160. https://doi.org/10.1128/aem.00172-09 (2009).
Ruiz, L., Zomer, A., O’Connell-Motherway, M., van Sinderen, D. & Margolles, A. Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics. Appl. Environ. Microbiol. 78, 1123–1131. https://doi.org/10.1128/aem.06060-11 (2012).
Ruiz, L., Sánchez, B., Ruas-Madiedo, P., De Los Reyes-Gavilán, C. G. & Margolles, A. Cell envelope changes in Bifidobacterium animalis ssp. lactis as a response to bile. FEMS Microbiol. Lett. 274, 316–322. https://doi.org/10.1111/j.1574-6968.2007.00854.x (2007).
Gómez Zavaglia, A., Kociubinski, G., Pérez, P., Disalvo, E. & De Antoni, G. Effect of bile on the lipid composition and surface properties of bifidobacteria. J. Appl. Microbiol. 93, 794–799. https://doi.org/10.1046/j.1365-2672.2002.01747.x (2002).
An, H. et al. Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol. Cell. Proteom. 13, 2558–2572. https://doi.org/10.1074/mcp.M114.039156 (2014).
Sanchez, B., de los Reyes-Gavilan, C. G. & Margolles, A. The F1F0-ATPase of Bifidobacterium animalis is involved in bile tolerance. Environ. Microbiol. 8, 1825–1833. https://doi.org/10.1111/j.1462-2920.2006.01067.x (2006).
Sanchez, B., Noriega, L., Ruas-Madiedo, P., de los Reyes-Gavilan, C. G. & Margolles, A. Acquired resistance to bile increases fructose-6-phosphate phosphoketolase activity in Bifidobacterium. FEMS Microbiol. Lett. 235, 35–41. https://doi.org/10.1016/j.femsle.2004.04.009 (2004).
Sanchez, B. et al. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J. Bacteriol. 187, 5799–5808. https://doi.org/10.1128/jb.187.16.5799-5808.2005 (2005).
Noriega, L., Gueimonde, M., Sanchez, B., Margolles, A. & de los Reyes-Gavilan, C. G. Effect of the adaptation to high bile salts concentrations on glycosidic activity, survival at low PH and cross-resistance to bile salts in Bifidobacterium. Int. J. Food Microbiol. 94, 79–86. https://doi.org/10.1016/j.ijfoodmicro.2004.01.003 (2004).
Tanaka, H., Hashiba, H., Kok, J. & Mierau, I. Bile salt hydrolase of Bifidobacterium longum-biochemical and genetic characterization. Appl. Environ. Microbiol. 66, 2502–2512. https://doi.org/10.1128/aem.66.6.2502-2512.2000 (2000).
Noriega, L., Cuevas, I., Margolles, A. & de los Reyes-Gavilán, C. G. Deconjugation and bile salts hydrolase activity by Bifidobacterium strains with acquired resistance to bile. Int. Dairy J. 16, 850–855. https://doi.org/10.1016/j.idairyj.2005.09.008 (2006).
Ambalam, P., Kondepudi, K. K., Nilsson, I., Wadstrom, T. & Ljungh, A. Bile enhances cell surface hydrophobicity and biofilm formation of bifidobacteria. Appl. Biochem. Biotechnol. 172, 1970–1981. https://doi.org/10.1007/s12010-013-0596-1 (2014).
Pumbwe, L. et al. Bile salts enhance bacterial co-aggregation, bacterial-intestinal epithelial cell adhesion, biofilm formation and antimicrobial resistance of Bacteroides fragilis. Microb. Pathog. 43, 78–87. https://doi.org/10.1016/j.micpath.2007.04.002 (2007).
Lebeer, S., Verhoeven, T. L., Perea Velez, M., Vanderleyden, J. & De Keersmaecker, S. C. Impact of environmental and genetic factors on biofilm formation by the probiotic strain Lactobacillus rhamnosus GG. Appl. Environ. Microbiol. 73, 6768–6775. https://doi.org/10.1128/aem.01393-07 (2007).
Macfarlane, S. & Macfarlane, G. T. Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut. Appl. Environ. Microbiol. 72, 6204–6211. https://doi.org/10.1128/aem.00754-06 (2006).
Macfarlane, M. J. H. G. T. M. S. Bacterial growth and metabolism on surfaces in the large intestine. Microb. Ecol. Health Dis. 12, 64–72. https://doi.org/10.1080/089106000750060314 (2000).
Pereira, C. S., Thompson, J. A. & Xavier, K. B. AI-2-mediated signalling in bacteria. FEMS Microbiol. Rev. 37, 156–181. https://doi.org/10.1111/j.1574-6976.2012.00345.x (2013).
Hammer, B. K. & Bassler, B. L. Quorum sensing controls biofilm formation in Vibrio cholerae. Mol. Microbiol. 50, 101–104. https://doi.org/10.1046/j.1365-2958.2003.03688.x (2003).
Solano, C., Echeverz, M. & Lasa, I. Biofilm dispersion and quorum sensing. Curr. Opin. Microbiol. 18, 96–104. https://doi.org/10.1016/j.mib.2014.02.008 (2014).
Sun, Z., He, X., Brancaccio, V. F., Yuan, J. & Riedel, C. U. Bifidobacteria exhibit LuxS-dependent autoinducer 2 activity and biofilm formation. PLoS ONE 9, e88260. https://doi.org/10.1371/journal.pone.0088260 (2014).
Christiaen, S. E. et al. Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003. PLoS ONE 9, e98111. https://doi.org/10.1371/journal.pone.0098111 (2014).
Yuan, J. et al. A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705. Mol. Cell. Proteom. 5, 1105–1118. https://doi.org/10.1074/mcp.M500410-MCP200 (2006).
D’Urzo, N. et al. Acidic pH strongly enhances in vitro biofilm formation by a subset of hypervirulent ST-17 Streptococcus agalactiae strains. Appl. Environ. Microbiol. 80, 2176–2185. https://doi.org/10.1128/aem.03627-13 (2014).
O’Neill, E. et al. Association between methicillin susceptibility and biofilm regulation in Staphylococcus aureus isolates from device-related infections. J. Clin. Microbiol. 45, 1379–1388. https://doi.org/10.1128/jcm.02280-06 (2007).
Hung, D. T., Zhu, J., Sturtevant, D. & Mekalanos, J. J. Bile acids stimulate biofilm formation in Vibrio cholerae. Mol. Microbiol. 59, 193–201. https://doi.org/10.1111/j.1365-2958.2005.04846.x (2006).
Maze, A., O’Connell-Motherway, M., Fitzgerald, G. F., Deutscher, J. & van Sinderen, D. Identification and characterization of a fructose phosphotransferase system in Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 73, 545–553. https://doi.org/10.1128/aem.01496-06 (2007).
Lanigan, N., Bottacini, F., Casey, P. G., O’Connell Motherway, M. & van Sinderen, D. Genome-wide search for genes required for bifidobacterial growth under iron-limitation. Front. Microbiol. 8, 964. https://doi.org/10.3389/fmicb.2017.00964 (2017).
Ruiz, L., Motherway, M. O., Lanigan, N. & van Sinderen, D. Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003. PLoS ONE 8, e64699. https://doi.org/10.1371/journal.pone.0064699 (2013).
Fanning, S. et al. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc. Natl. Acad. Sci. USA. 109, 2108–2113. https://doi.org/10.1073/pnas.1115621109 (2012).
Alonso-Casajus, N. et al. Glycogen phosphorylase, the product of the glgP Gene, catalyzes glycogen breakdown by removing glucose units from the nonreducing ends in Escherichia coli. J. Bacteriol. 188, 5266–5272. https://doi.org/10.1128/jb.01566-05 (2006).
Nocek, B. P., Gillner, D. M., Fan, Y., Holz, R. C. & Joachimiak, A. Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L, L-diaminopimelic acid desuccinylase. J. Mol. Biol. 397, 617–626. https://doi.org/10.1016/j.jmb.2010.01.062 (2010).
Ethapa, T. et al. Multiple factors modulate biofilm formation by the anaerobic pathogen Clostridium difficile. J. Bacteriol. 195, 545–555. https://doi.org/10.1128/jb.01980-12 (2013).
Donlan, R. M. Biofilms: microbial life on surfaces. Emerg. Infect. Dis. 8, 881–890. https://doi.org/10.3201/eid0809.020063 (2002).
Bottacini, F., Ventura, M., van Sinderen, D. & O’Connell Motherway, M. Diversity, ecology and intestinal function of bifidobacteria. Microbial Cell Fact. https://doi.org/10.1186/1475-2859-13-s1-s4 (2014).
Legrand-Defretin, V., Juste, C., Henry, R. & Corring, T. Ion-pair high-performance liquid chromatography of bile salt conjugates: Application to pig bile. Lipids 26, 578–583. https://doi.org/10.1007/bf02536421 (1991).
Sanchez, B. et al. Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: a proteomic and physiological approach. Appl. Environ. Microbiol. 73, 6757–6767. https://doi.org/10.1128/aem.00637-07 (2007).
Ruas-Madiedo, P., Hernandez-Barranco, A., Margolles, A. & de los Reyes-Gavilan, C. G. A bile salt-resistant derivative of Bifidobacterium animalis has an altered fermentation pattern when grown on glucose and maltose. Appl. Environ. Microbiol. 71, 6564–6570. https://doi.org/10.1128/aem.71.11.6564-6570.2005 (2005).
Ruiz, L. et al. The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment. Microbiology 155, 957–967. https://doi.org/10.1099/mic.0.024273-0 (2009).
Wang, G. et al. Functional role of oppA encoding an oligopeptide-binding protein from Lactobacillus salivarius Ren in bile tolerance. J. Ind. Microbiol. Biotechnol. 42, 1167–1174. https://doi.org/10.1007/s10295-015-1634-5 (2015).
Lebeer, S. et al. Impact of luxS and suppressor mutations on the gastrointestinal transit of Lactobacillus rhamnosus GG. Appl. Environ. Microbiol. 74, 4711–4718. https://doi.org/10.1128/aem.00133-08 (2008).
Wilson, C. M., Aggio, R. B., O’Toole, P. W., Villas-Boas, S. & Tannock, G. W. Transcriptional and metabolomic consequences of LuxS inactivation reveal a metabolic rather than quorum-sensing role for LuxS in Lactobacillus reuteri 100–23. J. Bacteriol. 194, 1743–1746. https://doi.org/10.1128/jb.06318-11 (2012).
Rezzonico, F. & Duffy, B. Lack of genomic evidence of AI-2 receptors suggests a non-quorum sensing role for luxS in most bacteria. BMC Microbiol. 8, 154. https://doi.org/10.1186/1471-2180-8-154 (2008).
Giddens, S. R. et al. Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proc. Natl. Acad. Sci. USA 104, 18247. https://doi.org/10.1073/pnas.0706739104 (2007).
Thompson, A. P. et al. Glycolysis and pyrimidine biosynthesis are required for replication of adherent–invasive Escherichia coli in macrophages. Microbiology 162, 954–965. https://doi.org/10.1099/mic.0.000289 (2016).
Sambrook, J. & Russell, D. Molecular Cloning: A Laboratory Manual 2001 Cold Spring Harbor (Cold Spring Harbor Laboratory Press, New York, 2001).
O’Riordan, K. & Fitzgerald, G. F. Molecular characterisation of a 575-kb cryptic plasmid from Bifidobacterium breve NCFB 2258 and determination of mode of replication. FEMS Microbiol. Lett. 174, 285–294. https://doi.org/10.1111/j.1574-6968.1999.tb13581.x (1999).
Alessandri, G. et al. Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota. Sci. Rep. 9, 5755–5755. https://doi.org/10.1038/s41598-019-42257-z (2019).
Duranti, S. et al. Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe-host co-evolution. Environ. Microbiol. 21, 3683–3695. https://doi.org/10.1111/1462-2920.14705 (2019).
Fredheim, E. G. et al. Biofilm formation by Staphylococcus haemolyticus. J Clin Microbiol 47, 1172–1180. https://doi.org/10.1128/jcm.01891-08 (2009).
Source: Ecology - nature.com
