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Volumn 20, Issue 1, 2019, Pages

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Author keywords

B vitamins; Gut metabolism; Metagenomics; Metatranscriptomics; Vitamin consumers; Vitamin prototrophs

Indexed keywords

ENZYME; MENAQUINONE; VITAMIN B GROUP; BACTERIAL PROTEIN; VITAMIN;

EID: 85062822351     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-019-5591-7     Document Type: Article
Times cited : (87)

References (43)
  • 1
    • 0033010536 scopus 로고    scopus 로고
    • Intestinal absorption of vitamins
    • 1:CAS:528:DyaK1MXjt1Gjuro%3D
    • Said HM, Kumar C. Intestinal absorption of vitamins. Curr Opin Gastroenterol. 1999;15:172-6.
    • (1999) Curr Opin Gastroenterol , vol.15 , pp. 172-176
    • Said, H.M.1    Kumar, C.2
  • 2
    • 33745803057 scopus 로고    scopus 로고
    • Intestinal absorption of water-soluble vitamins: An update
    • Said HM, Mohammed ZM. Intestinal absorption of water-soluble vitamins: an update. Curr Opin Gastroenterol. 2006;22:140-6.
    • (2006) Curr Opin Gastroenterol , vol.22 , pp. 140-146
    • Said, H.M.1    Mohammed, Z.M.2
  • 3
    • 85061150065 scopus 로고    scopus 로고
    • Gastrointestinal Handling of Water-Soluble Vitamins
    • Said HM, Nexo E. Gastrointestinal Handling of Water-Soluble Vitamins. Compr Physiol. 2018;8:1291-311. https://doi.org/10.1002/cphy.c170054.
    • (2018) Compr Physiol , vol.8 , pp. 1291-1311
    • Said, H.M.1    Nexo, E.2
  • 4
    • 79952055276 scopus 로고    scopus 로고
    • Folate production by probiotic bacteria
    • Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients. 2011;3:118-34. https://doi.org/10.3390/nu3010118.
    • (2011) Nutrients. , vol.3 , pp. 118-134
    • Rossi, M.1    Amaretti, A.2    Raimondi, S.3
  • 5
    • 84910142845 scopus 로고    scopus 로고
    • Vitamin B12 as a modulator of gut microbial ecology
    • Degnan PH, Taga ME, Goodman AL. Vitamin B12 as a modulator of gut microbial ecology. Cell Metab. 2014;20:769-78. https://doi.org/10.1016/j.cmet.2014.10.002.
    • (2014) Cell Metab , vol.20 , pp. 769-778
    • Degnan, P.H.1    Taga, M.E.2    Goodman, A.L.3
  • 6
    • 85020293358 scopus 로고    scopus 로고
    • Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses
    • Serbus LR, et al. Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses. G3: Genes, Genomes, Genetics. 2017;7(6):1887-98.
    • (2017) G3: Genes, Genomes, Genetics , vol.7 , Issue.6 , pp. 1887-1898
    • Serbus, L.R.1
  • 7
    • 84927124979 scopus 로고    scopus 로고
    • Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
    • 148 10.3389/fgene.2015.00148 1:CAS:528:DC%2BC2MXht1KjsrbO 25941533 4403557
    • Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front Genet. 2015;6:148. https://doi.org/10.3389/fgene.2015.00148.
    • (2015) Front Genet , vol.6
    • Magnúsdóttir, S.1    Ravcheev, D.2    De Crécy-Lagard, V.3    Thiele, I.4
  • 8
    • 0018294555 scopus 로고
    • The differences of the metabolism related to vitamin B6-dependent enzymes among vitamin B6-deficient germ-free and conventional rats
    • Ikeda M, Hosotani T, Kurimoto K, Mori T, Ueda T, Kotake Y, et al. The differences of the metabolism related to vitamin B6-dependent enzymes among vitamin B6-deficient germ-free and conventional rats. J Nutr Sci Vitaminol. 1979;25(3):131-9. https://www.jstage.jst.go.jp/article/jnsv1973/25/3/25-3-131/-pdf.
    • (1979) J Nutr Sci Vitaminol , vol.25 , Issue.3 , pp. 131-139
    • Ikeda, M.1    Hosotani, T.2    Kurimoto, K.3    Mori, T.4    Ueda, T.5    Kotake, Y.6
  • 9
    • 0017758116 scopus 로고
    • Vitamin B-6 deficiency in germfree rats
    • Sumi Y, Miyakawa M, Kanzaki M, Kotake Y. Vitamin B-6 deficiency in germfree rats. J Nutr. 1977;107:1707-14. https://doi.org/10.1093/jn/107.9.1707.
    • (1977) J Nutr , vol.107 , pp. 1707-1714
    • Sumi, Y.1    Miyakawa, M.2    Kanzaki, M.3    Kotake, Y.4
  • 10
    • 0019745997 scopus 로고
    • The germfree animal in nutritional studies
    • Wostmann BS. The germfree animal in nutritional studies. Annu Rev Nutr. 1981;1:257-79. https://doi.org/10.1146/annurev.nu.01.070181.001353.
    • (1981) Annu Rev Nutr , vol.1 , pp. 257-279
    • Wostmann, B.S.1
  • 11
    • 34249323673 scopus 로고
    • Antagonism between vitamins a and K in the germfree rat
    • Wostmann BS, Knight PL. Antagonism between vitamins a and K in the germfree rat. J Nutr. 1965;87:155-60. https://doi.org/10.1093/jn/87.2.155.
    • (1965) J Nutr , vol.87 , pp. 155-160
    • Wostmann, B.S.1    Knight, P.L.2
  • 12
    • 84866146940 scopus 로고    scopus 로고
    • Diversity, stability and resilience of the human gut microbiota
    • Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220-30. https://doi.org/10.1038/nature11550.
    • (2012) Nature. , vol.489 , pp. 220-230
    • Lozupone, C.A.1    Stombaugh, J.I.2    Gordon, J.I.3    Jansson, J.K.4    Knight, R.5
  • 13
    • 84867074831 scopus 로고    scopus 로고
    • A metagenome-wide association study of gut microbiota in type 2 diabetes
    • Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55-60. https://doi.org/10.1038/nature11450.
    • (2012) Nature. , vol.490 , pp. 55-60
    • Qin, J.1    Li, Y.2    Cai, Z.3    Li, S.4    Zhu, J.5    Zhang, F.6
  • 14
    • 85042225490 scopus 로고    scopus 로고
    • Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
    • Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3:337-46. https://doi.org/10.1038/s41564-017-0089-z.
    • (2018) Nat Microbiol , vol.3 , pp. 337-346
    • Schirmer, M.1    Franzosa, E.A.2    Lloyd-Price, J.3    McIver, L.J.4    Schwager, R.5    Poon, T.W.6
  • 16
    • 84921020525 scopus 로고    scopus 로고
    • Diversity of membrane transport proteins for vitamins in bacteria and archaea
    • Jaehme M, Slotboom DJ. Diversity of membrane transport proteins for vitamins in bacteria and archaea. Biochim Biophys Acta - Gen Subj. 2015;1850:565-76. https://doi.org/10.1016/J.BBAGEN.2014.05.006.
    • (2015) Biochim Biophys Acta - Gen Subj , vol.1850 , pp. 565-576
    • Jaehme, M.1    Slotboom, D.J.2
  • 18
    • 84924694174 scopus 로고    scopus 로고
    • Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum
    • 1:CAS:528:DC%2BC2MXjvFykurg%3D
    • Rodionova IA, Li X, Plymale AE, Motamedchaboki K, Konopka AE, Romine MF, et al. Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum. Environ Microbiol Rep. 2015;7:204-10.
    • (2015) Environ Microbiol Rep , vol.7 , pp. 204-210
    • Rodionova, I.A.1    Li, X.2    Plymale, A.E.3    Motamedchaboki, K.4    Konopka, A.E.5    Romine, M.F.6
  • 19
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65. https://doi.org/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
  • 20
    • 84905730165 scopus 로고    scopus 로고
    • An integrated catalog of reference genes in the human gut microbiome
    • Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32:834-41. https://doi.org/10.1038/nbt.2942.
    • (2014) Nat Biotechnol , vol.32 , pp. 834-841
    • Li, J.1    Jia, H.2    Cai, X.3    Zhong, H.4    Feng, Q.5    Sunagawa, S.6
  • 21
    • 33645962480 scopus 로고    scopus 로고
    • Rebuilding community ecology from functional traits
    • McGill BJ, Enquist BJ, Weiher E, Westoby M. Rebuilding community ecology from functional traits. Trends Ecol Evol. 2006;21:178-85. https://doi.org/10.1016/J.TREE.2006.02.002.
    • (2006) Trends Ecol Evol , vol.21 , pp. 178-185
    • McGill, B.J.1    Enquist, B.J.2    Weiher, E.3    Westoby, M.4
  • 22
    • 85027929693 scopus 로고    scopus 로고
    • Choosing and using multiple traits in functional diversity research
    • Lefcheck JS, Bastazini VAG, Griffin JN. Choosing and using multiple traits in functional diversity research. Environ Conserv. 2015;42:104-7. https://doi.org/10.1017/S0376892914000307.
    • (2015) Environ Conserv , vol.42 , pp. 104-107
    • Lefcheck, J.S.1    Bastazini, V.A.G.2    Griffin, J.N.3
  • 23
    • 77955556848 scopus 로고    scopus 로고
    • Towards an assessment of multiple ecosystem processes and services via functional traits
    • de Bello F, Lavorel S, Díaz S, Harrington R, Cornelissen JHC, Bardgett RD, et al. Towards an assessment of multiple ecosystem processes and services via functional traits. Biodivers Conserv. 2010;19:2873-93. https://doi.org/10.1007/s10531-010-9850-9.
    • (2010) Biodivers Conserv , vol.19 , pp. 2873-2893
    • De Bello, F.1    Lavorel, S.2    Díaz, S.3    Harrington, R.4    Cornelissen, J.H.C.5    Bardgett, R.D.6
  • 24
    • 0031915196 scopus 로고    scopus 로고
    • Conversion of dietary Phylloquinone to tissue Menaquinone-4 in rats is not dependent on gut Bacteria
    • Davidson RT, Foley AL, Engelke JA, Suttie JW. Conversion of dietary Phylloquinone to tissue Menaquinone-4 in rats is not dependent on gut Bacteria. J Nutr. 1998;128:220-3. https://doi.org/10.1093/jn/128.2.220.
    • (1998) J Nutr , vol.128 , pp. 220-223
    • Davidson, R.T.1    Foley, A.L.2    Engelke, J.A.3    Suttie, J.W.4
  • 26
    • 84864037467 scopus 로고    scopus 로고
    • Metabolic reconstruction for metagenomic data and its application to the human microbiome
    • e1002358 10.1371/journal.pcbi.1002358 1:CAS:528:DC%2BC38Xpt1Gnu7k%3D 22719234 3374609
    • Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8:e1002358. https://doi.org/10.1371/journal.pcbi.1002358.
    • (2012) PLoS Comput Biol , vol.8
    • Abubucker, S.1    Segata, N.2    Goll, J.3    Schubert, A.M.4    Izard, J.5    Cantarel, B.L.6
  • 27
    • 0024347425 scopus 로고
    • Vitamin status in patients with inflammatory bowel disease
    • Accessed 27 Nov 2018
    • Fernandez-Banares F, Abad-Lacruz A, Xiol X, Gine JJ, Dolz C, Cabre E, et al. Vitamin status in patients with inflammatory bowel disease. Am J Gastroenterol 1989;84:744-748. https://europepmc.org/abstract/med/2500847. Accessed 27 Nov 2018.
    • (1989) Am J Gastroenterol , vol.84 , pp. 744-748
    • Fernandez-Banares, F.1    Abad-Lacruz, A.2    Xiol, X.3    Gine, J.J.4    Dolz, C.5    Cabre, E.6
  • 28
    • 85012996162 scopus 로고    scopus 로고
    • Status of serum vitamin B12 and folate in patients with inflammatory bowel disease in China
    • Huang S, Ma J, Zhu M, Ran Z. Status of serum vitamin B12 and folate in patients with inflammatory bowel disease in China. Intest Res. 2017;15:103-8. https://doi.org/10.5217/ir.2017.15.1.103.
    • (2017) Intest Res , vol.15 , pp. 103-108
    • Huang, S.1    Ma, J.2    Zhu, M.3    Ran, Z.4
  • 29
    • 84866426985 scopus 로고    scopus 로고
    • Micronutrient deficiencies in inflammatory bowel disease: From a to zinc
    • Hwang C, Ross V, Mahadevan U. Micronutrient deficiencies in inflammatory bowel disease: from a to zinc. Inflamm Bowel Dis. 2012;18:1961-81. https://doi.org/10.1002/ibd.22906.
    • (2012) Inflamm Bowel Dis , vol.18 , pp. 1961-1981
    • Hwang, C.1    Ross, V.2    Mahadevan, U.3
  • 30
    • 85044953063 scopus 로고    scopus 로고
    • In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
    • e0195161 10.1371/journal.pone.0195161 1:CAS:528:DC%2BC1cXhslenurbJ 29601608 5877883
    • Das P, Ji B, Kovatcheva-Datchary P, Bäckhed F, Nielsen J. In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis. PLoS One. 2018;13:e0195161. https://doi.org/10.1371/journal.pone.0195161.
    • (2018) PLoS One , vol.13
    • Das, P.1    Ji, B.2    Kovatcheva-Datchary, P.3    Bäckhed, F.4    Nielsen, J.5
  • 31
    • 84861557084 scopus 로고    scopus 로고
    • Species interactions Alter evolutionary responses to a novel environment
    • e1001330 10.1371/journal.pbio.1001330 1:CAS:528:DC%2BC38XnslyhsLc%3D 22615541 3352820
    • Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, et al. Species interactions Alter evolutionary responses to a novel environment. PLoS Biol. 2012;10:e1001330. https://doi.org/10.1371/journal.pbio.1001330.
    • (2012) PLoS Biol , vol.10
    • Lawrence, D.1    Fiegna, F.2    Behrends, V.3    Bundy, J.G.4    Phillimore, A.B.5    Bell, T.6
  • 32
    • 84953208457 scopus 로고    scopus 로고
    • Fortification and health: Challenges and opportunities
    • Dwyer JT, Wiemer KL, Dary O, Keen CL, King JC, Miller KB, et al. Fortification and health: challenges and opportunities. Adv Nutr. 2015;6:124-31. https://doi.org/10.3945/an.114.007443.
    • (2015) Adv Nutr , vol.6 , pp. 124-131
    • Dwyer, J.T.1    Wiemer, K.L.2    Dary, O.3    Keen, C.L.4    King, J.C.5    Miller, K.B.6
  • 33
    • 85027927719 scopus 로고    scopus 로고
    • Enterotypes of the human gut microbiome
    • Arumugam M, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174-80. https://doi.org/10.1038/nature09944.
    • (2011) Nature. , vol.473 , pp. 174-180
    • Arumugam, M.1
  • 34
    • 85062955462 scopus 로고    scopus 로고
    • Richness of human gut microbiome correlates with metabolic markers
    • 28 10.1038/nature12506 1:CAS:528:DC%2BC3sXhtlCgtbnF
    • Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. Richness of human gut microbiome correlates with metabolic markers. Karine Clément. 2013;13:28. https://doi.org/10.1038/nature12506.
    • (2013) Karine Clément , vol.13
    • Le Chatelier, E.1    Nielsen, T.2    Qin, J.3    Prifti, E.4    Hildebrand, F.5    Falony, G.6
  • 35
    • 84907686349 scopus 로고    scopus 로고
    • The integrative human microbiome project: Dynamic analysis of microbiome-host omics profiles during periods of human health and disease
    • The Integrative HMP Research Network Consortium
    • The Integrative HMP Research Network Consortium. The integrative human microbiome project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014;16:276-89.
    • (2014) Cell Host Microbe , vol.16 , pp. 276-289
  • 36
    • 84990828229 scopus 로고    scopus 로고
    • FMAP: Functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies
    • 420 10.1186/s12859-016-1278-0 1:CAS:528:DC%2BC1cXptlGrsg%3D%3D
    • Kim J, Kim MS, Koh AY, Xie Y, Zhan X. FMAP: functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. BMC Bioinforma. 2016;17:420. https://doi.org/10.1186/s12859-016-1278-0.
    • (2016) BMC Bioinforma , vol.17
    • Kim, J.1    Kim, M.S.2    Koh, A.Y.3    Xie, Y.4    Zhan, X.5
  • 37
    • 84925021592 scopus 로고    scopus 로고
    • Fast and sensitive protein alignment using DIAMOND
    • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59-60. https://doi.org/10.1038/nmeth.3176.
    • (2015) Nat Methods , vol.12 , pp. 59-60
    • Buchfink, B.1    Xie, C.2    Huson, D.H.3
  • 39
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011;40:D109-14.
    • (2011) Nucleic Acids Res , vol.40 , pp. D109-D114
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 40
    • 84905454882 scopus 로고    scopus 로고
    • Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue
    • e1003706 10.1371/journal.pcbi.1003706 1:CAS:528:DC%2BC2cXhs1amsb7E 25010449 4091689
    • Karlsson FH, Nookaew I, Nielsen J, Ribeca P, Berger S. Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue. PLoS Comput Biol. 2014;10:e1003706. https://doi.org/10.1371/journal.pcbi.1003706.
    • (2014) PLoS Comput Biol , vol.10
    • Karlsson, F.H.1    Nookaew, I.2    Nielsen, J.3    Ribeca, P.4    Berger, S.5
  • 41
    • 85051385729 scopus 로고    scopus 로고
    • Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling
    • Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, et al. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: lessons from genome-scale metabolic modeling. Metab Eng. 2018;49.
    • (2018) Metab Eng , vol.49
    • Kumar, M.1    Ji, B.2    Babaei, P.3    Das, P.4    Lappa, D.5    Ramakrishnan, G.6


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