메뉴 건너뛰기




Volumn 7, Issue MAY, 2016, Pages

Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of prevotella and megasphaera in Indian subjects

Author keywords

16S rRNA amplicon; Indian subjects; Prevotella and Megasphaera; QPCR

Indexed keywords

GLYCAN;

EID: 84973472722     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.00660     Document Type: Article
Times cited : (97)

References (50)
  • 1
    • 79958265126 scopus 로고    scopus 로고
    • Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads
    • Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno-Hagelsieb, G., and Neufeld, J. D. (2011). Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl. Environ. Microbiol. 77, 3846-3852. doi: 10.1128/AEM.02772-10
    • (2011) Appl. Environ. Microbiol , vol.77 , pp. 3846-3852
    • Bartram, A.K.1    Lynch, M.D.J.2    Stearns, J.C.3    Moreno-Hagelsieb, G.4    Neufeld, J.D.5
  • 2
    • 10744228209 scopus 로고    scopus 로고
    • Ethnic India: a genomic view, with special reference to peopling and structure
    • Basu, A., Mukherjee, N., Roy, S., Sengupta, S., Banerjee, S., Chakraborty, M., et al. (2003). Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res. 13, 2277-2290. doi: 10.1101/gr.1413403
    • (2003) Genome Res , vol.13 , pp. 2277-2290
    • Basu, A.1    Mukherjee, N.2    Roy, S.3    Sengupta, S.4    Banerjee, S.5    Chakraborty, M.6
  • 3
    • 84890363776 scopus 로고    scopus 로고
    • Therapeutic faecal microbiota transplantation: current status and future developments
    • Borody, T. J., Brandt, L. J., and Paramsothy, S. (2014). Therapeutic faecal microbiota transplantation: current status and future developments. Curr. Opin. Gastroenterol. 30, 97-105. doi: 10.1097/MOG.0000000000000027
    • (2014) Curr. Opin. Gastroenterol , vol.30 , pp. 97-105
    • Borody, T.J.1    Brandt, L.J.2    Paramsothy, S.3
  • 4
    • 33745628389 scopus 로고    scopus 로고
    • Probiotic use in clinical practice: what are the risks?
    • Boyle, R. J., Robins-browne, R. M., and Tang, M. L. K. (2006). Probiotic use in clinical practice: what are the risks? Am. J. Clin. Nutr. 1-3, 1256-1264.
    • (2006) Am. J. Clin. Nutr , vol.1-3 , pp. 1256-1264
    • Boyle, R.J.1    Robins-browne, R.M.2    Tang, M.L.K.3
  • 5
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data intensity normalization improves color calling in SOLiD sequencing
    • Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data intensity normalization improves color calling in SOLiD sequencing. Nat. Methods 7, 335-336. doi: 10.1038/nmeth.f.303
    • (2010) Nat. Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3    Bittinger, K.4    Bushman, F.D.5    Costello, E.K.6
  • 6
    • 84858439578 scopus 로고    scopus 로고
    • The human microbiome: at the interface of health and disease
    • Cho, I., and Blaser, M. J. (2012). The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260-270. doi: 10.1038/nrg3182
    • (2012) Nat. Rev. Genet , vol.13 , pp. 260-270
    • Cho, I.1    Blaser, M.J.2
  • 7
    • 84862637797 scopus 로고    scopus 로고
    • Gut immune maturation depends on colonization with a host-specific microbiota
    • Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., et al. (2012). Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149, 1578-1593. doi: 10.1016/j.cell.2012.04.037
    • (2012) Cell , vol.149 , pp. 1578-1593
    • Chung, H.1    Pamp, S.J.2    Hill, J.A.3    Surana, N.K.4    Edelman, S.M.5    Troy, E.B.6
  • 8
    • 84892828465 scopus 로고    scopus 로고
    • Diet rapidly and reproducibly alters the human gut microbiome
    • David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563. doi: 10.1038/nature12820
    • (2014) Nature , vol.505 , pp. 559-563
    • David, L.A.1    Maurice, C.F.2    Carmody, R.N.3    Gootenberg, D.B.4    Button, J.E.5    Wolfe, B.E.6
  • 9
    • 77957075815 scopus 로고    scopus 로고
    • Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
    • De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., et al. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107, 14691-14696. doi: 10.1073/pnas.1005963107
    • (2010) Proc. Natl. Acad. Sci. U.S.A , vol.107 , pp. 14691-14696
    • De Filippo, C.1    Cavalieri, D.2    Di Paola, M.3    Ramazzotti, M.4    Poullet, J.B.5    Massart, S.6
  • 10
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2462. doi: 10.1093/bioinformatics/btq461
    • (2010) Bioinformatics , vol.26 , pp. 2460-2462
    • Edgar, R.C.1
  • 11
    • 0000803388 scopus 로고
    • The population frequencies of species and the estimation of population parameters
    • Good (1953). The population frequencies of species and the estimation of population parameters. Biometrika 40, 237-264. doi: 10.1093/biomet/40.3-4.237
    • (1953) Biometrika , vol.40 , pp. 237-264
  • 12
    • 84894118144 scopus 로고    scopus 로고
    • Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders
    • Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., et al. (2013). Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155, 1451-1463. doi: 10.1016/j.cell.2013.11.024
    • (2013) Cell , vol.155 , pp. 1451-1463
    • Hsiao, E.Y.1    McBride, S.W.2    Hsien, S.3    Sharon, G.4    Hyde, E.R.5    McCue, T.6
  • 13
    • 84862173705 scopus 로고    scopus 로고
    • A core human microbiome as viewed through 16S rRNA sequence clusters
    • Huse, S. M., Ye, Y., Zhou, Y., and Fodor, A. A. (2012). A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7:e34242. doi: 10.1371/journal.pone.0034242
    • (2012) PLoS ONE , vol.7
    • Huse, S.M.1    Ye, Y.2    Zhou, Y.3    Fodor, A.A.4
  • 14
    • 79251625980 scopus 로고    scopus 로고
    • Supervised classification of human microbiota
    • Knights, D., Costello, E. K., and Knight, R. (2011). Supervised classification of human microbiota. FEMS Microbiol. Rev. 35, 343-359. doi: 10.1111/j.1574-6976.2010.00251.x
    • (2011) FEMS Microbiol. Rev , vol.35 , pp. 343-359
    • Knights, D.1    Costello, E.K.2    Knight, R.3
  • 16
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821. doi: 10.1038/nbt.2676
    • (2013) Nat. Biotechnol , vol.31 , pp. 814-821
    • Langille, M.G.I.1    Zaneveld, J.2    Caporaso, J.G.3    McDonald, D.4    Knights, D.5    Reyes, J.A.6
  • 17
    • 84907803675 scopus 로고    scopus 로고
    • Ancient human genomes suggest three ancestral populations for present-day Europeans
    • Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., et al. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-413. doi: 10.1038/nature13673
    • (2014) Nature , vol.513 , pp. 409-413
    • Lazaridis, I.1    Patterson, N.2    Mittnik, A.3    Renaud, G.4    Mallick, S.5    Kirsanow, K.6
  • 19
    • 32944466887 scopus 로고    scopus 로고
    • Ecological and evolutionary forces shaping microbial diversity in the human intestine
    • Ley, R. E., Peterson, D. A., and Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837-848. doi: 10.1016/j.cell.2006.02.017
    • (2006) Cell , vol.124 , pp. 837-848
    • Ley, R.E.1    Peterson, D.A.2    Gordon, J.I.3
  • 20
    • 84872825519 scopus 로고    scopus 로고
    • Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States
    • Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., et al. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS ONE 8:e53838. doi: 10.1371/journal.pone.0053838
    • (2013) PLoS ONE , vol.8
    • Lin, A.1    Bik, E.M.2    Costello, E.K.3    Dethlefsen, L.4    Haque, R.5    Relman, D.A.6
  • 22
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: a new phylogenetic method for comparing microbial communities
    • Lozupone, C., and Knight, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235. doi: 10.1128/AEM.71.12.8228-8235.2005
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 23
    • 78751575501 scopus 로고    scopus 로고
    • UniFrac: an effective distance metric for microbial community comparison
    • Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., and Knight, R. (2011). UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169-1172. doi: 10.1038/ismej.2010.133
    • (2011) ISME J , vol.5 , pp. 169-1172
    • Lozupone, C.1    Lladser, M.E.2    Knights, D.3    Stombaugh, J.4    Knight, R.5
  • 24
    • 20844445609 scopus 로고    scopus 로고
    • Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes
    • Macaulay, V., Hill, C., Achilli, A., Rengo, C., Clarke, D., Meehan, W., et al. (2005). Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308, 1034-1036. doi: 10.1126/science.1109792
    • (2005) Science , vol.308 , pp. 1034-1036
    • Macaulay, V.1    Hill, C.2    Achilli, A.3    Rengo, C.4    Clarke, D.5    Meehan, W.6
  • 25
    • 84866565238 scopus 로고    scopus 로고
    • Changes in human gut flora with age: an Indian familial study
    • Marathe, N., Shetty, S., Lanjekar, V., Ranade, D., and Shouche, Y. (2012). Changes in human gut flora with age: an Indian familial study. BMC Microbiol. 12:222. doi: 10.1186/1471-2180-12-222
    • (2012) BMC Microbiol , vol.12 , pp. 222
    • Marathe, N.1    Shetty, S.2    Lanjekar, V.3    Ranade, D.4    Shouche, Y.5
  • 26
    • 69949094849 scopus 로고    scopus 로고
    • Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm
    • Martens, E. C., Koropatkin, N. M., Smith, T. J., and Gordon, J. I. (2009). Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284, 24673-24677. doi: 10.1074/jbc.R109.022848
    • (2009) J. Biol. Chem , vol.284 , pp. 24673-24677
    • Martens, E.C.1    Koropatkin, N.M.2    Smith, T.J.3    Gordon, J.I.4
  • 27
    • 84872535919 scopus 로고    scopus 로고
    • Xenobiotics shape the physiology and gene expression of the active human gut microbiome
    • Maurice, C. F., Haiser, H. J., and Turnbaugh, P. J. (2013). Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50. doi: 10.1016/j.cell.2012.10.052
    • (2013) Cell , vol.152 , pp. 39-50
    • Maurice, C.F.1    Haiser, H.J.2    Turnbaugh, P.J.3
  • 28
    • 84879512750 scopus 로고    scopus 로고
    • Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
    • Mellars, P., Gori, K. C., Carr, M., Soares, P. A., and Richards, M. B. (2013). Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc. Natl. Acad. Sci. U.S.A. 110, 10699-10704. doi: 10.1073/pnas.1306043110
    • (2013) Proc. Natl. Acad. Sci. U.S.A , vol.110 , pp. 10699-10704
    • Mellars, P.1    Gori, K.C.2    Carr, M.3    Soares, P.A.4    Richards, M.B.5
  • 29
    • 79956301905 scopus 로고    scopus 로고
    • Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
    • Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., et al. (2011). Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974. doi: 10.1126/science.1198719
    • (2011) Science , vol.332 , pp. 970-974
    • Muegge, B.D.1    Kuczynski, J.2    Knights, D.3    Clemente, J.C.4    González, A.5    Fontana, L.6
  • 30
    • 33144460422 scopus 로고    scopus 로고
    • Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study
    • Mueller, S., Saunier, K., Hanisch, C., Norin, E., Alm, L., Midtvedt, T., et al. (2006). 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. doi: 10.1128/AEM.72.2.1027-1033.2006
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 1027-1033
    • Mueller, S.1    Saunier, K.2    Hanisch, C.3    Norin, E.4    Alm, L.5    Midtvedt, T.6
  • 31
    • 79960904343 scopus 로고    scopus 로고
    • Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing
    • Nam, Y.-D., Jung, M.-J., Roh, S. W., Kim, M.-S., and Bae, J.-W. (2011). Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS ONE 6:e22109. doi: 10.1371/journal.pone.0022109
    • (2011) PLoS ONE , vol.6
    • Nam, Y.-D.1    Jung, M.-J.2    Roh, S.W.3    Kim, M.-S.4    Bae, J.-W.5
  • 32
    • 79960878444 scopus 로고    scopus 로고
    • The active human gut microbiota differs from the total microbiota
    • Peris-Bondia, F., Latorre, A., Artacho, A., Moya, A., and D'Auria, G. (2011). The active human gut microbiota differs from the total microbiota. PLoS ONE 6:e22448. doi: 10.1371/journal.pone.0022448
    • (2011) PLoS ONE , vol.6
    • Peris-Bondia, F.1    Latorre, A.2    Artacho, A.3    Moya, A.4    D'Auria, G.5
  • 33
    • 81755161339 scopus 로고    scopus 로고
    • Abdominal obesity, an independent cardiovascular risk factor in Indian subcontinent: a clinico epidemiological evidence summary
    • Prasad, D. S., Kabir, Z., Dash, A. K., and Das, B. C. (2011). Abdominal obesity, an independent cardiovascular risk factor in Indian subcontinent: a clinico epidemiological evidence summary. J. Cardiovasc. Dis. Res. 2, 199-205. doi: 10.4103/0975-3583.89803
    • (2011) J. Cardiovasc. Dis. Res , vol.2 , pp. 199-205
    • Prasad, D.S.1    Kabir, Z.2    Dash, A.K.3    Das, B.C.4
  • 34
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi: 10.1038/nature08821
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5    Manichanh, C.6
  • 36
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. doi: 10.1128/AEM.01541-09
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5    Hollister, E.B.6
  • 37
    • 84870266477 scopus 로고    scopus 로고
    • The evolution of mutualism in gut microbiota via host epithelial selection
    • Schluter, J., and Foster, K. R. (2012). The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol. 10:e1001424. doi: 10.1371/journal.pbio.1001424
    • (2012) PLoS Biol , vol.10
    • Schluter, J.1    Foster, K.R.2
  • 39
    • 84894133363 scopus 로고    scopus 로고
    • Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut
    • Shetty, S. A., Marathe, N. P., Lanjekar, V., Ranade, D., and Shouche, Y. S. (2013). Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut. PLoS ONE 8:e79353. doi: 10.1371/journal.pone.0079353
    • (2013) PLoS ONE , vol.8
    • Shetty, S.A.1    Marathe, N.P.2    Lanjekar, V.3    Ranade, D.4    Shouche, Y.S.5
  • 40
    • 0036837971 scopus 로고    scopus 로고
    • Descriptive epidemiology of body mass index of an urban adult population in western India
    • Shukla, H. C., Gupta, P. C., Mehta, H. C., and Hebert, J. R. (2002). Descriptive epidemiology of body mass index of an urban adult population in western India. J. Epidemiol. Commun. Health 56, 876-880. doi: 10.1136/jech.56.11.876
    • (2002) J. Epidemiol. Commun. Health , vol.56 , pp. 876-880
    • Shukla, H.C.1    Gupta, P.C.2    Mehta, H.C.3    Hebert, J.R.4
  • 41
    • 34548263593 scopus 로고    scopus 로고
    • Income inequality and the double burden of under-and overnutrition in India
    • Subramanian, S. V., Kawachi, I., and Smith, G. D. (2007). Income inequality and the double burden of under-and overnutrition in India. J. Epidemiol. Commun. Health 61, 802-809. doi: 10.1136/jech.2006.053801
    • (2007) J. Epidemiol. Commun. Health , vol.61 , pp. 802-809
    • Subramanian, S.V.1    Kawachi, I.2    Smith, G.D.3
  • 43
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., and Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031. doi: 10.1038/nature05414
    • (2006) Nature , vol.444 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6
  • 44
    • 84927695047 scopus 로고    scopus 로고
    • Influence of the microbiota on vaccine effectiveness
    • Valdez, Y., Brown, E. M., and Finlay, B. B. (2014). Influence of the microbiota on vaccine effectiveness. Trends Immunol. 35, 526-537. doi: 10.1016/j.it.2014.07.003
    • (2014) Trends Immunol , vol.35 , pp. 526-537
    • Valdez, Y.1    Brown, E.M.2    Finlay, B.B.3
  • 46
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 47
    • 78549275442 scopus 로고    scopus 로고
    • Genetic diversity in India and the inference of Eurasian population expansion
    • Xing, J., Watkins, W. S., Hu, Y., Huff, C. D., Sabo, A., Muzny, D. M., et al. (2010). Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol. 11:R113. doi: 10.1186/gb-2010-11-11-r113
    • (2010) Genome Biol , vol.11
    • Xing, J.1    Watkins, W.S.2    Hu, Y.3    Huff, C.D.4    Sabo, A.5    Muzny, D.M.6
  • 48
    • 85027944984 scopus 로고    scopus 로고
    • Dietary effects on human gut microbiome diversity
    • Xu, Z., and Knight, R. (2014). Dietary effects on human gut microbiome diversity. Br. J. Nutr. 113, S1-S5. doi: 10.1017/S0007114514004127
    • (2014) Br. J. Nutr , vol.113 , pp. S1-S5
    • Xu, Z.1    Knight, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.