Diversity of Bifidobacteria within the Infant Gut Microbiota
Tóm tắt
Từ khóa
Tài liệu tham khảo
VB Young, 2012, The intestinal microbiota in health and disease. Curr. Opin. Gastroenterol., 28, 63
F Backhed, 2005, Host-bacterial mutualism in the human intestine., Science, 307, 1915, 10.1126/science.1104816
J Xu, 2003, Honor thy symbionts. Proc Natl Acad Sci U S A., 100, 10452
CP Tamboli, 2004, Dysbiosis in inflammatory bowel disease. Gut., 53, 1
H Sokol, 2008, <italic>Faecalibacterium prausnitzii</italic> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A., 105, 16731
A Kassinen, 2007, The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology., 133, 24
J Parsonnet, 1991, <italic>Helicobacter pylori</italic> infection and the risk of gastric carcinoma. N. Engl. J. Med., 325, 1127
M Lecuit, 2004, Immunoproliferative small intestinal disease associated with <italic>Campylobacter jejuni</italic>. N. Engl.J. Med., 350, 239
PJ Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest. Nature., 444, 1027
NM Delzenne, 2011, Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat Rev Endocrinol., 7, 639
MF de la Cochetiere, 2004, Early intestinal bacterial colonization and necrotizing enterocolitis in premature infants: the putative role of <italic>Clostridium</italic>. Pediatr Res., 56, 366
MJ Claesson, 2011, Composition, variability, and temporal stability of the intestinal microbiota of the elderly., Proc Natl Acad Sci U S A., 108, 4586, 10.1073/pnas.1000097107
PB Eckburg, 2005, Diversity of the human intestinal microbial flora., Science, 308, 1635, 10.1126/science.1110591
F Turroni, 2009, Exploring the diversity of the bifidobacterial population in the human intestinal tract., Appl Environ Microbiol, 75, 1534, 10.1128/AEM.02216-08
J Tap, 2009, Towards the human intestinal microbiota phylogenetic core. Environ Microbiol., 11, 2574
C Palmer, 2007, Development of the human infant intestinal microbiota., PLoS Biol 5,, e177
C Roger L, 2010, Examination of faecal <italic>Bifidobacterium</italic> populations in breast- and formula-fed infants during the first 18 months of life., Microbiology, 156, 3329, 10.1099/mic.0.043224-0
JJ Werner, 2012, Impact of training sets on classification of high-throughput bacterial 16 S rRNA gene surveys. ISME J., 6, 94
JE Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome., Proc Natl Acad Sci U S A., 108, 4578, 10.1073/pnas.1000081107
S Fanaro, 2003, Fecal flora measurements of breastfed infants using an integrated transport and culturing system., Acta Paediatr, 92, 634, 10.1111/j.1651-2227.2003.tb02521.x
CF Favier, 2002, Molecular monitoring of succession of bacterial communities in human neonates., Appl Environ Microbiol, 68, 219, 10.1128/AEM.68.1.219-226.2002
F Turroni, 2011, Ability of <italic>Bifidobacterium breve</italic> to grow on different types of milk: exploring the metabolism of milk through genome analysis. Appl Environ Microbiol., 77, 7408
ES Klaassens, 2009, Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast- and formula-fed infants., Appl Environ Microbiol, 75, 2668, 10.1128/AEM.02492-08
EG Zoetendal, 2008, High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota., Nat Methods, 57, 1605
J Penders, 2006, Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics., 118, 511
AL Hart, 2004, Modulation of human dendritic cell phenotype and function by probiotic bacteria. Gut., 53, 1602
JH Apajalahti, 1998, Effective recovery of bacterial DNA and percent-guanine-plus-cytosine-based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl Environ Microbiol., 64, 4084
F Di Cello, 1996, A molecular strategy for the study of natural bacterial communities by PCR-based techniques. Minerva Biotecnologica., 8, 126
JG Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data. Nat Methods., 7, 335
J Reeder, 2010, Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods., 7, 668
JR Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141
RC Edgar, 2010, Search and clustering orders of magnitude faster than BLAST., Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461
P Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498
M Wang, 2005, Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16 S rRNA genes., FEMS Microbiol Ecol, 54, 219, 10.1016/j.femsec.2005.03.012
S Arboleya, 2011, Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbial. Ecolol., 79, 763
F Turroni, 2011, Genomics and ecological overview of the genus <italic>Bifidobacterium</italic>. Int J Food Microbiol., 149, 37
CR Woese, 1980, Secondary structure model for bacterial 16 S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res., 8, 2275
A Salonen, 2010, Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods., 81, 127
MJ Claesson, 2009, Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PloS One., 4, e6669
M Ventura, 2007, Genomics of <italic>Actinobacteria</italic>: tracing the evolutionary history of an ancient phylum., Microbiol Mol Biol Rev, 71, 495, 10.1128/MMBR.00005-07
C Lozupone, 2006, UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context., BMC Bioinformatics, 7, 371, 10.1186/1471-2105-7-371
EA Westerbeek, 2006, The intestinal bacterial colonisation in preterm infants: a review of the literature. Clin Nutr., 25, 361
L Stone, 1990, The checkerboard score and species distribution., Oecologia, 85, 74, 10.1007/BF00317345
JM Diamond, 1975, Assembly of species community., Ecology and Evolution of Communities, eds Cody ML, Diamond JM (Harvard Univ Press, Cambridge, MA),, 342–444
PA Vaishampayan, 2010, Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol., 2, 53
H Takahashi, 2010, Comparative analysis of the properties of bifidobacterial isolates from fecal samples of mother-infant pairs. J Pediatr Gastroenterol Nutr., 51, 653
J Jalanka-Tuovinen, 2011, Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS One., 6, e23035
F Turroni, 2009, Microbiomic analysis of the bifidobacterial population in the human distal gut., ISME J, 3, 745, 10.1038/ismej.2009.19
D Soergel, 2012, Selection of primers for optimal taxonomic classification of environmental 16 S rRNA gene sequences., ISME J, 1, 1
GR Gibson, 1995, Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics., J Nutr, 125, 1401, 10.1093/jn/125.6.1401
F Turroni, 2010, Genome analysis of <italic>Bifidobacterium bifidum</italic> PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc Natl Acad Sci U S A., 107, 19514
F Turroni, 2011, Genetic strategies for mucin metabolism in <italic>Bifidobacterium bifidum</italic> PRL2010: an example of possible human-microbe co-evolution. Gut Microbes., 2, 183
DA Sela, 2008, The genome sequence of <italic>Bifidobacterium longum</italic> subsp. <italic>infantis</italic> reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A., 105, 18964