Human gut microbiome viewed across age and geography
Tóm tắt
Từ khóa
Tài liệu tham khảo
Mueller, S. et al. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl. Environ. Microbiol. 72, 1027–1033 (2006)
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010)
Li, M. et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl Acad. Sci. USA 105, 2117–2122 (2008)
Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169–181 (2007)
Koenig, J. E. et al. Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108 (suppl. 1). 4578–4585 (2011)
Favier, C. F., Vaughan, E. E., De Vos, W. M. & Akkermans, A. D. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68, 219–226 (2002)
Tannock, G. W. What immunologists should know about bacterial communities of the human bowel. Semin. Immunol. 19, 94–105 (2007)
Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl Acad. Sci. USA 107, 11971–11975 (2010)
Blaser, M. J. & Falkow, S. What are the consequences of the disappearing human microbiota? Nature Rev. Microbiol. 7, 887–894 (2009)
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010)
De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010)
Peach, S., Fernandez, F., Johnson, K. & Drasar, B. S. The non-sporing anaerobic bacteria in human faeces. J. Med. Microbiol. 7, 213–221 (1974)
Mackie, R. I., Sghir, A. & Gaskins, H. R. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69, 1035S–1045S (1999)
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007)
Penders, J. et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511–521 (2006)
Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005)
Knights, D., Costello, E. K. & Knight, R. Supervised classification of human microbiota. FEMS Microbiol. Rev. 35, 343–359 (2011)
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011)
Kristiansson, E., Hugenholtz, P. & Dalevi, D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25, 2737–2738 (2009)
Monsen, A. L., Refsum, H., Markestad, T. & Ueland, P. M. Cobalamin status and its biochemical markers methylmalonic acid and homocysteine in different age groups from 4 days to 19 years. Clin. Chem. 49, 2067–2075 (2003)
Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447–457 (2008)
Hooper, L. V., Xu, J., Falk, P. G., Midtvedt, T. & Gordon, J. I. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl Acad. Sci. USA 96, 9833–9838 (1999)
Harzer, G., Franzke, V. & Bindels, J. G. Human milk nonprotein nitrogen components: changing patterns of free amino acids and urea in the course of early lactation. Am. J. Clin. Nutr. 40, 303–309 (1984)
Metges, C. C. et al. Incorporation of urea and ammonia nitrogen into ileal and fecal microbial proteins and plasma free amino acids in normal men and ileostomates. Am. J. Clin. Nutr. 70, 1046–1058 (1999)
Millward, D. J. et al. The transfer of 15N from urea to lysine in the human infant. Br. J. Nutr. 83, 505–512 (2000)
Meakins, T. S. & Jackson, A. A. Salvage of exogenous urea nitrogen enhances nitrogen balance in normal men consuming marginally inadequate protein diets. Clin. Sci. (Lond.) 90, 215–225 (1996)
Langran, M., Moran, B. J., Murphy, J. L. & Jackson, A. A. Adaptation to a diet low in protein: effect of complex carbohydrate upon urea kinetics in normal man. Clin. Sci. (Lond.) 82, 191–198 (1992)
Mora, D. et al. Characterization of urease genes cluster of Streptococcus thermophilus. J. Appl. Microbiol. 96, 209–219 (2004)
Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011)
Kaufman, L. & Rousseeuw, P. J. Finding Groups in Data: an Introduction to Cluster Analysis Ch. 2 68–125 (Wiley, 1990)
Rousseeuw, P. J. Silhouettes — a graphical aid to the interpretation and validation of cluster-analysis. J. Comput. Appl. Math. 20, 53–65 (1987)
Tibshirani, R. & Walther, G. Cluster validation by prediction strength. J. Comput. Graph. Statist. 14, 511–528 (2005)
Teal, T. K. & Schmidt, T. M. Identifying and removing artificial replicates from 454 pyrosequencing data. Cold Spring Harb. Protoc. 2010, pdb.prot5409 (2010)
R Development Core Team. . R: A Language and Envirnoment for Statistical Compuiting (R Foundation for Statistical Computing, 2010)
Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002)