Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Cell Host & Microbe - Tập 20 - Trang 515-526 - 2016
María X. Maldonado-Gómez1, Inés Martínez1,2,3, Francesca Bottacini4, Amy O’Callaghan4, Marco Ventura5, Douwe van Sinderen4, Benjamin Hillmann6, Pajau Vangay7, Dan Knights6,7,8, Robert W. Hutkins1, Jens Walter1,2,3
1Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
2Department of Agricultural, Nutritional and Food Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
3Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada
4APC Microbiome Institute & School of Microbiology, University College Cork, Cork T12 YN60, Ireland
5Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma 43124, Italy
6Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455 USA
7Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
8Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108-6106, USA

Tài liệu tham khảo

Alander, 2001, Effect of galacto-oligosaccharide supplementation on human faecal microflora and on survival and persistence of Bifidobacterium lactis Bb-12 in the gastrointestinal tract, Int. Dairy J., 11, 817, 10.1016/S0958-6946(01)00100-5 Biavati, 2012, Genus I. Bifidobacterium, Volume 5, 171 Boto, 2010, Horizontal gene transfer in evolution: facts and challenges, Proc. Biol. Sci., 277, 819, 10.1098/rspb.2009.1679 Caporaso, 2011, QIIME allows analysis of high-throughput community sequencing data, NIH Public Access, 7, 335 Ceapa, 2013, Influence of fermented milk products, prebiotics and probiotics on microbiota composition and health, Best Pract. Res. Clin. Gastroenterol., 27, 139, 10.1016/j.bpg.2013.04.004 Chaplin, 2015, Intraspecies genomic diversity and long-term persistence of Bifidobacterium longum, PLoS ONE, 10, e0135658, 10.1371/journal.pone.0135658 Charbonneau, 2013, Fecal excretion of Bifidobacterium infantis 35624 and changes in fecal microbiota after eight weeks of oral supplementation with encapsulated probiotic, Gut Microbes, 4, 201, 10.4161/gmic.24196 Costello, 2012, The application of ecological theory toward an understanding of the human microbiome, Science, 336, 1255, 10.1126/science.1224203 Darwin, 1859 Davis, 2000, Eight ways to be a colonizer; Two ways to be an invader: A proposed nomenclature scheme for invasion ecology, Bull. Ecol. Soc. Am., 81, 226 Davis, 2011, Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans, PLoS ONE, 6, e25200, 10.1371/journal.pone.0025200 De Roy, 2013, Environmental conditions and community evenness determine the outcome of biological invasion, Nat. Commun., 4, 1383, 10.1038/ncomms2392 Díaz, 2001, Vive la différence: plant functional diversity matters to ecosystem processes, Trends Ecol. Evol., 16, 646, 10.1016/S0169-5347(01)02283-2 Dictionaries, 2014 Elton, 1958 Eren, 2015, Anvi’o: an advanced analysis and visualization platform for 'omics data, PeerJ, 3, e1319, 10.7717/peerj.1319 Firmesse, 2008, Lactobacillus rhamnosus R11 consumed in a food supplement survived human digestive transit without modifying microbiota equilibrium as assessed by real-time polymerase chain reaction, J. Mol. Microbiol. Biotechnol., 14, 90, 10.1159/000106087 Frese, 2012, Comparison of the colonization ability of autochthonous and allochthonous strains of Lactobacilli in the human gastrointestinal tract, Adv. Microbiol., 2, 399, 10.4236/aim.2012.23051 Fujiwara, 2001, Intestinal transit of an orally administered streptomycin-rifampicin-resistant variant of Bifidobacterium longum SBT2928: its long-term survival and effect on the intestinal microflora and metabolism, J. Appl. Microbiol., 90, 43, 10.1046/j.1365-2672.2001.01205.x Fukuda, 2011, Bifidobacteria can protect from enteropathogenic infection through production of acetate, Nature, 469, 543, 10.1038/nature09646 Guo, 2015, A unified approach for quantifying invasibility and degree of invasion, Ecology, 96, 2613, 10.1890/14-2172.1 Hardin, 1960, The competitive exclusion principle, Science, 131, 1292, 10.1126/science.131.3409.1292 Hill, 2014, Expert consensus document. 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, 10.1038/nrgastro.2014.66 Kennedy, 2002, Biodiversity as a barrier to ecological invasion, Nature, 417, 636, 10.1038/nature00776 Kneitel, 2007, Disturbance-induced changes in community composition increase species invasion success, Community Ecol., 7, 245, 10.1556/ComEc.7.2006.2.11 Knights, 2011, Supervised classification of human microbiota, FEMS Microbiol. Rev., 35, 343, 10.1111/j.1574-6976.2010.00251.x Kolida, 2011, Synbiotics in health and disease, Annu. Rev. Food Sci. Technol., 2, 373, 10.1146/annurev-food-022510-133739 Kristensen, 2016, Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials, Genome Med., 8, 52, 10.1186/s13073-016-0300-5 Krumbeck, 2015, In vivo selection to identify bacterial strains with enhanced ecological performance in synbiotic applications, Appl. Environ. Microbiol., 81, 2455, 10.1128/AEM.03903-14 Lee, 2013, Bacterial colonization factors control specificity and stability of the gut microbiota, Nature, 501, 426, 10.1038/nature12447 Li, 2015, The effects of phylogenetic relatedness on invasion success and impact: deconstructing Darwin’s naturalisation conundrum, Ecol. Lett., 18, 1285, 10.1111/ele.12522 Li, 2016, Durable coexistence of donor and recipient strains after fecal microbiota transplantation, Science, 352, 586, 10.1126/science.aad8852 Mächler, 2012, Interaction of species traits and environmental disturbance predicts invasion success of aquatic microorganisms, PLoS ONE, 7, e45400, 10.1371/journal.pone.0045400 Malinen, 2002, PCR-ELISA II: Analysis of Bifidobacterium populations in human faecal samples from a consumption trial with Bifidobacterium lactis Bb-12 and a galacto-oligosaccharide preparation, Syst. Appl. Microbiol., 25, 249 Mallon, 2015, Microbial invasions: the process, patterns, and mechanisms, Trends Microbiol., 23, 719, 10.1016/j.tim.2015.07.013 Martínez, 2013, Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species, PLoS ONE, 8, e69621, 10.1371/journal.pone.0069621 Mayfield, 2010, Opposing effects of competitive exclusion on the phylogenetic structure of communities, Ecol. Lett., 13, 1085, 10.1111/j.1461-0248.2010.01509.x Miller, 2005 O’Callaghan, 2015, Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems, BMC Genomics, 16, 832, 10.1186/s12864-015-1968-4 O’Connell, 2013, Metabolism of four α-glycosidic linkage-containing oligosaccharides by Bifidobacterium breve UCC2003, Appl. Environ. Microbiol., 79, 6280, 10.1128/AEM.01775-13 O’Connell, 2014, Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators, Appl. Environ. Microbiol., 80, 3604, 10.1128/AEM.00130-14 O’Connell Motherway, 2011, Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003, Microb. Biotechnol., 4, 403, 10.1111/j.1751-7915.2010.00218.x Olle, 2013, Medicines from microbiota, Nat. Biotechnol., 31, 309, 10.1038/nbt.2548 Olyarnik, 2009, Ecological factors affecting community invasibility, 215 Proches, 2008, Searching for phylogenetic pattern in biological invasions, Glob. Ecol. Biogeogr., 17, 5 Rattanaprasert, 2014, Quantitative evaluation of synbiotic strategies to improve persistence and metabolic activity of Lactobacillus reuteri DSM 17938 in the human gastrointestinal tract, J. Funct. Foods, 10, 85, 10.1016/j.jff.2014.05.017 Rochet, 2008, Modulation of Lactobacillus casei in ileal and fecal samples from healthy volunteers after consumption of a fermented milk containing Lactobacillus casei DN-114 001Rif, Can. J. Microbiol., 54, 660, 10.1139/W08-050 Round, 2009, The gut microbiota shapes intestinal immune responses during health and disease, Nat. Rev. Immunol., 9, 313, 10.1038/nri2515 Sanders, 2013, An update on the use and investigation of probiotics in health and disease, Gut, 62, 787, 10.1136/gutjnl-2012-302504 Schloissnig, 2013, Genomic variation landscape of the human gut microbiome, Nature, 493, 45, 10.1038/nature11711 Shafquat, 2014, Functional and phylogenetic assembly of microbial communities in the human microbiome, Trends Microbiol., 22, 261, 10.1016/j.tim.2014.01.011 Shea, 2002, Community ecology theory as a framework for biological invasions, Trends Ecol. Evol., 17, 170, 10.1016/S0169-5347(02)02495-3 Simberloff, 2013, Impacts of biological invasions: what’s what and the way forward, Trends Ecol. Evol., 28, 58, 10.1016/j.tree.2012.07.013 Stecher, 2010, Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria, PLoS Pathog., 6, e1000711, 10.1371/journal.ppat.1000711 Thuiller, 2010, Resolving Darwin’s naturalization conundrum: A quest for evidence, Divers. Distrib., 16, 461, 10.1111/j.1472-4642.2010.00645.x Tilman, 2004, Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly, Proc. Natl. Acad. Sci. USA, 101, 10854, 10.1073/pnas.0403458101 Turroni, 2009, Exploring the diversity of the bifidobacterial population in the human intestinal tract, Appl. Environ. Microbiol., 75, 1534, 10.1128/AEM.02216-08 Violle, 2011, Phylogenetic limiting similarity and competitive exclusion, Ecol. Lett., 14, 782, 10.1111/j.1461-0248.2011.01644.x Walker, 2013, Therapeutic modulation of intestinal dysbiosis, Pharmacol. Res., 69, 75, 10.1016/j.phrs.2012.09.008 Walter, 2008, Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research, Appl. Environ. Microbiol., 74, 4985, 10.1128/AEM.00753-08 Walter, 2011, The human gut microbiome: ecology and recent evolutionary changes, Annu. Rev. Microbiol., 65, 411, 10.1146/annurev-micro-090110-102830 Wittebolle, 2009, Initial community evenness favours functionality under selective stress, Nature, 458, 623, 10.1038/nature07840 Zhang, 2016, Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes, ISME J., 10, 2235, 10.1038/ismej.2016.13 Zhu, 2015, Inter-individual differences in the gene content of human gut bacterial species, Genome Biol., 16, 82, 10.1186/s13059-015-0646-9