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Volumn 10, Issue JUN, 2019, Pages

Micronutrient requirements and sharing capabilities of the human gut microbiome

Author keywords

16S; Comparative genomics; Gut microbiome; Metagenomics; Vitamin metabolism

Indexed keywords

BIOTIN; COENZYME A; PANTOTHENIC ACID; PREBIOTIC AGENT; RNA 16S; TRACE ELEMENT; VITAMIN B GROUP;

EID: 85069050675     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2019.01316     Document Type: Article
Times cited : (110)

References (75)
  • 1
    • 85032968165 scopus 로고    scopus 로고
    • Correcting for microbial blooms in fecal samples during room-temperature shipping
    • Amir, A., Mcdonald, D., Navas-Molina, J. A., Debelius, J., Morton, J. T., Hyde, E., et al. (2017). Correcting for microbial blooms in fecal samples during room-temperature shipping. mSystems 2:e00199-16. doi: 10.1128/mSystems.00199-16
    • (2017) mSystems , vol.2 , pp. e00199-e00216
    • Amir, A.1    Mcdonald, D.2    Navas-Molina, J.A.3    Debelius, J.4    Morton, J.T.5    Hyde, E.6
  • 2
    • 84959016595 scopus 로고    scopus 로고
    • Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
    • Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., et al. (2016). Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351:aad3311. doi: 10.1126/science.aad3311
    • (2016) Science , vol.351 , pp. aad3311
    • Blanton, L.V.1    Charbonneau, M.R.2    Salih, T.3    Barratt, M.J.4    Venkatesh, S.5    Ilkaveya, O.6
  • 5
    • 84860490976 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., et al. (2012). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40, D742–D753. doi: 10.1093/nar/gkr1014
    • (2012) Nucleic Acids Res , vol.40 , pp. D742-D753
    • Caspi, R.1    Altman, T.2    Dreher, K.3    Fulcher, C.A.4    Subhraveti, P.5    Keseler, I.M.6
  • 6
    • 84891787231 scopus 로고    scopus 로고
    • Ribosomal database project: Data and tools for high throughput rRNA analysis
    • Cole, J. R., Wang, Q., Fish, J. A., Chai, B., Mcgarrell, D. M., Sun, Y., et al. (2014). Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642. doi: 10.1093/nar/gkt1244
    • (2014) Nucleic Acids Res , vol.42 , pp. D633-D642
    • Cole, J.R.1    Wang, Q.2    Fish, J.A.3    Chai, B.4    Mcgarrell, D.M.5    Sun, Y.6
  • 7
    • 85020664861 scopus 로고    scopus 로고
    • Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota
    • Danchin, A., and Braham, S. (2017). Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota. Microb. Biotechnol. 10, 688–701. doi: 10.1111/1751-7915.12722
    • (2017) Microb. Biotechnol. , vol.10 , pp. 688-701
    • Danchin, A.1    Braham, S.2
  • 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
    • 34648840096 scopus 로고    scopus 로고
    • Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications
    • De Crecy-Lagard, V., Marck, C., Brochier-Armanet, C., and Grosjean, H. (2007). Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications. IUBMB Life 59, 634–658. doi: 10.1080/15216540701604632
    • (2007) IUBMB Life , vol.59 , pp. 634-658
    • De Crecy-Lagard, V.1    Marck, C.2    Brochier-Armanet, C.3    Grosjean, H.4
  • 10
    • 84910142845 scopus 로고    scopus 로고
    • Vitamin B12 as a modulator of gut microbial ecology
    • Degnan, P. H., Taga, M. E., and Goodman, A. L. (2014). Vitamin B12 as a modulator of gut microbial ecology. Cell Metab. 20, 769–778. doi: 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
  • 11
    • 13244255415 scopus 로고    scopus 로고
    • Muscle: A multiple sequence alignment method with reduced time and space complexity
    • Edgar, R. C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. doi: 10.1186/1471-2105-5-113
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 12
    • 84970021164 scopus 로고    scopus 로고
    • Gut microbiota as a target in the pathogenesis of metabolic disorders: A new approach to novel therapeutic agents
    • Ejtahed, H. S., Soroush, A. R., Angoorani, P., Larijani, B., and Hasani-Ranjbar, S. (2016). Gut microbiota as a target in the pathogenesis of metabolic disorders: a new approach to novel therapeutic agents. Horm. Metab. Res. 48, 349–358. doi: 10.1055/s-0042-107792
    • (2016) Horm. Metab. Res. , vol.48 , pp. 349-358
    • Ejtahed, H.S.1    Soroush, A.R.2    Angoorani, P.3    Larijani, B.4    Hasani-Ranjbar, S.5
  • 13
    • 84926030913 scopus 로고    scopus 로고
    • The STM4195 gene product (PanS) transports coenzyme a precursors in Salmonella enterica
    • Ernst, D. C., and Downs, D. M. (2015). The STM4195 gene product (PanS) transports coenzyme a precursors in Salmonella enterica. J. Bacteriol. 197, 1368–1377. doi: 10.1128/JB.02506-14
    • (2015) J. Bacteriol. , vol.197 , pp. 1368-1377
    • Ernst, D.C.1    Downs, D.M.2
  • 14
    • 84927945449 scopus 로고    scopus 로고
    • The queuine micronutrient: Charting a course from microbe to man
    • Fergus, C., Barnes, D., Alqasem, M. A., and Kelly, V. P. (2015). The queuine micronutrient: charting a course from microbe to man. Nutrients 7, 2897–2929. doi: 10.3390/nu7042897
    • (2015) Nutrients , vol.7 , pp. 2897-2929
    • Fergus, C.1    Barnes, D.2    Alqasem, M.A.3    Kelly, V.P.4
  • 15
    • 85069056249 scopus 로고    scopus 로고
    • Effects of microbiota-directed therapeutic foods in gnotobiotic mice, gnotobiotic piglets, and undernourished children
    • press
    • Gehrig, J. G., Venkatesh, S., Chang, H., Hibberd, M. C., Kung, V. L., Cheng, J., et al. (2019). Effects of microbiota-directed therapeutic foods in gnotobiotic mice, gnotobiotic piglets, and undernourished children. Science (in press). doi: 10.1126/science.aau4732
    • (2019) Science
    • Gehrig, J.G.1    Venkatesh, S.2    Chang, H.3    Hibberd, M.C.4    Kung, V.L.5    Cheng, J.6
  • 16
    • 82455188342 scopus 로고    scopus 로고
    • RibM from Streptomyces davawensis is a riboflavin/roseoflavin transporter and may be useful for the optimization of riboflavin production strains
    • Hemberger, S., Pedrolli, D. B., Stolz, J., Vogl, C., Lehmann, M., and Mack, M. (2011). RibM from Streptomyces davawensis is a riboflavin/roseoflavin transporter and may be useful for the optimization of riboflavin production strains. BMC Biotechnol. 11:119. doi: 10.1186/1472-6750-11-119
    • (2011) BMC Biotechnol , vol.11 , pp. 119
    • Hemberger, S.1    Pedrolli, D.B.2    Stolz, J.3    Vogl, C.4    Lehmann, M.5    Mack, M.6
  • 17
    • 85019419979 scopus 로고    scopus 로고
    • The effects of micronutrient deficiencies on bacterial species from the human gut microbiota
    • Hibberd, M. C., Wu, M., Rodionov, D. A., Li, X., Cheng, J., Griffin, N. W., et al. (2017). The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci. Transl. Med. 9:eaal4069. doi: 10.1126/scitranslmed.aal4069
    • (2017) Sci. Transl. Med. , vol.9
    • Hibberd, M.C.1    Wu, M.2    Rodionov, D.A.3    Li, X.4    Cheng, J.5    Griffin, N.W.6
  • 18
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214. doi: 10.1038/nature11234
    • (2012) Nature , vol.486 , pp. 207-214
  • 19
    • 84991759922 scopus 로고    scopus 로고
    • Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease
    • Imhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., et al. (2018). Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 67, 108–119. doi: 10.1136/gutjnl-2016-312135
    • (2018) Gut , vol.67 , pp. 108-119
    • Imhann, F.1    Vich Vila, A.2    Bonder, M.J.3    Fu, J.4    Gevers, D.5    Visschedijk, M.C.6
  • 20
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: Back to metabolism in KEGG
    • Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. (2014). Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205. doi: 10.1093/nar/gkt1076
    • (2014) Nucleic Acids Res , vol.42 , pp. D199-D205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Kawashima, M.4    Furumichi, M.5    Tanabe, M.6
  • 21
    • 0018200003 scopus 로고
    • Transport of vitamin B12 in Escherichia coli. Corrinoid specificity of the outer membrane receptor
    • Kenley, J. S., Leighton, M., and Bradbeer, C. (1978). Transport of vitamin B12 in Escherichia coli. corrinoid specificity of the outer membrane receptor. J. Biol. Chem. 253, 1341–1346.
    • (1978) J. Biol. Chem. , vol.253 , pp. 1341-1346
    • Kenley, J.S.1    Leighton, M.2    Bradbeer, C.3
  • 22
    • 84922941772 scopus 로고    scopus 로고
    • The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes
    • Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyotylainen, T., Hamalainen, A. M., et al. (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17, 260–273. doi: 10.1016/j.chom.2015.01.001
    • (2015) Cell Host Microbe , vol.17 , pp. 260-273
    • Kostic, A.D.1    Gevers, D.2    Siljander, H.3    Vatanen, T.4    Hyotylainen, T.5    Hamalainen, A.M.6
  • 23
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille, M. G., 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.1    Zaneveld, J.2    Caporaso, J.G.3    Mcdonald, D.4    Knights, D.5    Reyes, J.A.6
  • 24
    • 85014768147 scopus 로고    scopus 로고
    • Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees
    • Letunic, I., and Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245. doi: 10.1093/nar/gkw290
    • (2016) Nucleic Acids Res , vol.44 , pp. W242-W245
    • Letunic, I.1    Bork, P.2
  • 25
    • 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. (2014). An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841. doi: 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
  • 26
    • 84927124979 scopus 로고    scopus 로고
    • Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes
    • Magnusdottir, S., Ravcheev, D., De Crecy-Lagard, V., and Thiele, I. (2015). Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes. Front. Genet. 6:148. doi: 10.3389/fgene.2015.00148
    • (2015) Front. Genet. , vol.6 , pp. 148
    • Magnusdottir, S.1    Ravcheev, D.2    De Crecy-Lagard, V.3    Thiele, I.4
  • 27
    • 84861710931 scopus 로고    scopus 로고
    • Biosynthesis of biotin
    • eds L. N. Mander and H. Liu Kidlington: Elsevier Ltd
    • Marquet, A. (2010). “Biosynthesis of Biotin,” in Comprehensive Natural Products II: Chemistry and Biology, eds L. N. Mander and H. Liu (Kidlington: Elsevier Ltd), 161–180. doi: 10.1016/b978-008045382-8.00136-2
    • (2010) Comprehensive Natural Products II: Chemistry and Biology , pp. 161-180
    • Marquet, A.1
  • 28
    • 84922059063 scopus 로고    scopus 로고
    • YeeO from Escherichia coli exports flavins
    • McAnulty, M. J., and Wood, T. K. (2014). YeeO from Escherichia coli exports flavins. Bioengineered 5, 386–392. doi: 10.4161/21655979.2014.969173
    • (2014) Bioengineered , vol.5 , pp. 386-392
    • McAnulty, M.J.1    Wood, T.K.2
  • 29
    • 0345257922 scopus 로고    scopus 로고
    • Metabolism of vitamins in microbes and mammals
    • McCormick, D. B. (2003). Metabolism of vitamins in microbes and mammals. Biochem. Biophys. Res. Commun. 312, 97–101. doi: 10.1016/j.bbrc.2003.09.241
    • (2003) Biochem. Biophys. Res. Commun. , vol.312 , pp. 97-101
    • McCormick, D.B.1
  • 30
    • 85090848405 scopus 로고    scopus 로고
    • American gut: An open platform for citizen science microbiome research
    • McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., et al. (2018). American gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. doi: 10.1128/mSystems.00031-18
    • (2018) mSystems , vol.3 , pp. e00031-e00118
    • McDonald, D.1    Hyde, E.2    Debelius, J.W.3    Morton, J.T.4    Gonzalez, A.5    Ackermann, G.6
  • 31
    • 84901049717 scopus 로고    scopus 로고
    • Syntrophic exchange in synthetic microbial communities
    • Mee, M. T., Collins, J. J., Church, G. M., and Wang, H. H. (2014). Syntrophic exchange in synthetic microbial communities. Proc. Natl. Acad. Sci. U.S.A. 111, E2149–E2156. doi: 10.1073/pnas.1405641111
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. E2149-E2156
    • Mee, M.T.1    Collins, J.J.2    Church, G.M.3    Wang, H.H.4
  • 32
    • 84886739636 scopus 로고    scopus 로고
    • RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
    • Novichkov, P. S., Kazakov, A. E., Ravcheev, D. A., Leyn, S. A., Kovaleva, G. Y., Sutormin, R. A., et al. (2013). RegPrecise 3.0–a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics 14:745. doi: 10.1186/1471-2164-14-745
    • (2013) BMC Genomics , vol.14 , pp. 745
    • Novichkov, P.S.1    Kazakov, A.E.2    Ravcheev, D.A.3    Leyn, S.A.4    Kovaleva, G.Y.5    Sutormin, R.A.6
  • 34
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: A comparative genomics approach
    • Osterman, A., and Overbeek, R. (2003). Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7, 238–251. doi: 10.1016/s1367-5931(03)00027-9
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 35
    • 73349120614 scopus 로고    scopus 로고
    • Genomic variations on a CoA biosynthetic theme
    • Osterman, A. L. (2009). Genomic variations on a CoA biosynthetic theme. Nat. Chem. Biol. 5, 871–872. doi: 10.1038/nchembio.267
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 871-872
    • Osterman, A.L.1
  • 36
    • 79958861315 scopus 로고    scopus 로고
    • The use of subsystems to encode biosynthesis of vitamins and cofactors
    • eds L. N. Mander and H. Liu Kidlington: Elsevier Ltd
    • Osterman, A. L., Overbeek, R., and Rodionov, D. A. (2010). “The Use of Subsystems to Encode Biosynthesis of Vitamins and Cofactors,” in Comprehensive Natural Products II: Chemistry and Biology, eds L. N. Mander and H. Liu (Kidlington: Elsevier Ltd), 141–159. doi: 10.1016/b978-008045382-8.00710-3
    • (2010) Comprehensive Natural Products II: Chemistry and Biology , pp. 141-159
    • Osterman, A.L.1    Overbeek, R.2    Rodionov, D.A.3
  • 37
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. Y., Cohoon, M., et al. (2005). The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702. doi: 10.1093/nar/gki866
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5    Cohoon, M.6
  • 38
    • 84891804612 scopus 로고    scopus 로고
    • The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)
    • Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., et al. (2014). The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42, D206–D214.
    • (2014) Nucleic Acids Res , vol.42 , pp. D206-D214
    • Overbeek, R.1    Olson, R.2    Pusch, G.D.3    Olsen, G.J.4    Davis, J.J.5    Disz, T.6
  • 39
    • 0016122081 scopus 로고
    • Active transport of biotin in Escherichia coli K-12
    • Prakash, O., and Eisenberg, M. A. (1974). Active transport of biotin in Escherichia coli K-12. J. Bacteriol. 120, 785–791.
    • (1974) J. Bacteriol. , vol.120 , pp. 785-791
    • Prakash, O.1    Eisenberg, M.A.2
  • 40
    • 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
  • 41
    • 84927692256 scopus 로고    scopus 로고
    • The first 1000 cultured species of the human gastrointestinal microbiota
    • Rajilic-Stojanovic, M., and de Vos, W. M. (2014). The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol. Rev. 38, 996–1047. doi: 10.1111/1574-6976.12075
    • (2014) FEMS Microbiol. Rev. , vol.38 , pp. 996-1047
    • Rajilic-Stojanovic, M.1    De Vos, W.M.2
  • 43
    • 85011968948 scopus 로고    scopus 로고
    • A novel transcriptional regulator related to thiamine phosphate synthase controls thiamine metabolism genes in archaea
    • Rodionov, D. A., Leyn, S. A., Li, X., and Rodionova, I. A. (2017). A novel transcriptional regulator related to thiamine phosphate synthase controls thiamine metabolism genes in archaea. J. Bacteriol. 199:e00743-16. doi: 10.1128/JB.00743-16
    • (2017) J. Bacteriol. , vol.199 , pp. e00743-e00816
    • Rodionov, D.A.1    Leyn, S.A.2    Li, X.3    Rodionova, I.A.4
  • 44
    • 0036797992 scopus 로고    scopus 로고
    • Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea
    • Rodionov, D. A., Mironov, A. A., and Gelfand, M. S. (2002a). Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res. 12, 1507–1516. doi: 10.1101/gr.314502
    • (2002) Genome Res , vol.12 , pp. 1507-1516
    • Rodionov, D.A.1    Mironov, A.A.2    Gelfand, M.S.3
  • 45
    • 2242446202 scopus 로고    scopus 로고
    • Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms
    • Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., and Gelfand, M. S. (2002b). Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277, 48949–48959. doi: 10.1074/jbc.m208965200
    • (2002) J. Biol. Chem. , vol.277 , pp. 48949-48959
    • Rodionov, D.A.1    Vitreschak, A.G.2    Mironov, A.A.3    Gelfand, M.S.4
  • 46
    • 0142071742 scopus 로고    scopus 로고
    • Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes
    • Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., and Gelfand, M. S. (2003). Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem. 278, 41148–41159. doi: 10.1074/jbc.m305837200
    • (2003) J. Biol. Chem. , vol.278 , pp. 41148-41159
    • Rodionov, D.A.1    Vitreschak, A.G.2    Mironov, A.A.3    Gelfand, M.S.4
  • 47
    • 85019140967 scopus 로고    scopus 로고
    • A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea
    • Rodionova, I. A., Vetting, M. W., Li, X., Almo, S. C., Osterman, A. L., and Rodionov, D. A. (2017). A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res. 45, 3785–3799. doi: 10.1093/nar/gkw1331
    • (2017) Nucleic Acids Res , vol.45 , pp. 3785-3799
    • Rodionova, I.A.1    Vetting, M.W.2    Li, X.3    Almo, S.C.4    Osterman, A.L.5    Rodionov, D.A.6
  • 48
    • 85012195235 scopus 로고    scopus 로고
    • Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities
    • Romine, M. F., Rodionov, D. A., Maezato, Y., Osterman, A. L., and Nelson, W. C. (2017). Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities. ISME J. 11, 1434–1446. doi: 10.1038/ismej.2017.2
    • (2017) ISME J , vol.11 , pp. 1434-1446
    • Romine, M.F.1    Rodionov, D.A.2    Maezato, Y.3    Osterman, A.L.4    Nelson, W.C.5
  • 49
    • 0034704158 scopus 로고    scopus 로고
    • The Enigma of Cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway
    • Roper, J. M., Raux, E., Brindley, A. A., Schubert, H. L., Gharbia, S. E., Shah, H. N., et al. (2000). The Enigma of Cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. identification and characterization of a functional corrin pathway. J. Biol. Chem. 275, 40316–40323. doi: 10.1074/jbc.M007146200
    • (2000) J. Biol. Chem. , vol.275 , pp. 40316-40323
    • Roper, J.M.1    Raux, E.2    Brindley, A.A.3    Schubert, H.L.4    Gharbia, S.E.5    Shah, H.N.6
  • 50
    • 0022294772 scopus 로고
    • Nicotinic acid transport in Escherichia coli
    • Rowe, J. J., Lemmon, R. D., and Tritz, G. J. (1985). Nicotinic acid transport in Escherichia coli. Microbios 44, 169–184.
    • (1985) Microbios , vol.44 , pp. 169-184
    • Rowe, J.J.1    Lemmon, R.D.2    Tritz, G.J.3
  • 51
    • 84891779616 scopus 로고    scopus 로고
    • The transporter classification database
    • Saier, M. H. Jr., Reddy, V. S., Tamang, D. G., and Vastermark, A. (2014). The transporter classification database. Nucleic Acids Res. 42, D251–D258. doi: 10.1093/nar/gkt1097
    • (2014) Nucleic Acids Res , vol.42 , pp. D251-D258
    • Saier, M.H.1    Reddy, V.S.2    Tamang, D.G.3    Vastermark, A.4
  • 52
    • 85051055503 scopus 로고    scopus 로고
    • Functional and structural characterization of an ECF-type ABC transporter for vitamin B12
    • Santos, J. A., Rempel, S., Mous, S. T., Pereira, C. T., Ter Beek, J., De Gier, J. W., et al. (2018). Functional and structural characterization of an ECF-type ABC transporter for vitamin B12. eLife 7:e35828. doi: 10.7554/eLife.35828
    • (2018) eLife , vol.7
    • Santos, J.A.1    Rempel, S.2    Mous, S.T.3    Pereira, C.T.4    Ter Beek, J.5    De Gier, J.W.6
  • 53
    • 44249113090 scopus 로고    scopus 로고
    • High-Level Folate Production in Fermented Foods by the B12 Producer Lactobacillus reuteri JCM1112
    • Santos, F., Wegkamp, A., de Vos, W. M., Smid, E. J., and Hugenholtz, J. (2008). High-Level Folate Production in Fermented Foods by the B12 Producer Lactobacillus reuteri JCM1112. Appl. Environ. Microbiol. 74, 3291–3294. doi: 10.1128/AEM.02719-07
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 3291-3294
    • Santos, F.1    Wegkamp, A.2    De Vos, W.M.3    Smid, E.J.4    Hugenholtz, J.5
  • 55
    • 85017249254 scopus 로고    scopus 로고
    • Linking dietary patterns with gut microbial composition and function
    • Sheflin, A. M., Melby, C. L., Carbonero, F., and Weir, T. L. (2017). Linking dietary patterns with gut microbial composition and function. Gut Microbes 8, 113–129. doi: 10.1080/19490976.2016.1270809
    • (2017) Gut Microbes , vol.8 , pp. 113-129
    • Sheflin, A.M.1    Melby, C.L.2    Carbonero, F.3    Weir, T.L.4
  • 56
    • 84874249804 scopus 로고    scopus 로고
    • Common folds and transport mechanisms of secondary active transporters
    • Shi, Y. (2013). Common folds and transport mechanisms of secondary active transporters. Annu. Rev. Biophys. 42, 51–72. doi: 10.1146/annurev-biophys-083012-130429
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 51-72
    • Shi, Y.1
  • 57
    • 84873642708 scopus 로고    scopus 로고
    • Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci
    • Sorci, L., Blaby, I. K., Rodionova, I. A., De Ingeniis, J., Tkachenko, S., De Crecy-Lagard, V., et al. (2013). Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci. J. Bacteriol. 195, 726–732. doi: 10.1128/JB.02002-12
    • (2013) J. Bacteriol. , vol.195 , pp. 726-732
    • Sorci, L.1    Blaby, I.K.2    Rodionova, I.A.3    De Ingeniis, J.4    Tkachenko, S.5    De Crecy-Lagard, V.6
  • 58
  • 59
    • 85005808154 scopus 로고    scopus 로고
    • Using RAxML to infer phylogenies
    • Stamatakis, A. (2015). Using RAxML to infer phylogenies. Curr. Protoc. Bioinform. 51, 11–14.
    • (2015) Curr. Protoc. Bioinform. , vol.51 , pp. 11-14
    • Stamatakis, A.1
  • 60
    • 84941140948 scopus 로고    scopus 로고
    • RrnDB: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
    • Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R., and Schmidt, T. M. (2015). rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 43, D593–D598. doi: 10.1093/nar/gku1201
    • (2015) Nucleic Acids Res , vol.43 , pp. D593-D598
    • Stoddard, S.F.1    Smith, B.J.2    Hein, R.3    Roller, B.R.4    Schmidt, T.M.5
  • 61
    • 77956629209 scopus 로고    scopus 로고
    • Biocatalytic production of coenzyme a analogues
    • Strauss, E., De Villiers, M., and Rootman, I. (2010). Biocatalytic production of coenzyme a analogues. ChemCatChem 2, 929–937. doi: 10.1021/jacs.5b12252
    • (2010) ChemCatChem , vol.2 , pp. 929-937
    • Strauss, E.1    De Villiers, M.2    Rootman, I.3
  • 62
    • 84903134830 scopus 로고    scopus 로고
    • Persistent gut microbiota immaturity in malnourished Bangladeshi children
    • Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M. A., et al. (2014). Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417–421. doi: 10.1038/nature13421
    • (2014) Nature , vol.510 , pp. 417-421
    • Subramanian, S.1    Huq, S.2    Yatsunenko, T.3    Haque, R.4    Mahfuz, M.5    Alam, M.A.6
  • 63
    • 85047915410 scopus 로고    scopus 로고
    • Description of Mediterraneibacter massiliensis, gen. Nov., sp. Nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. Nov., Mediterraneibacter lactaris comb. Nov., Mediterraneibacter torques comb. Nov., Mediterraneibacter gnavus comb. Nov. And Mediterraneibacter glycyrrhizinilyticus comb. Nov
    • Togo, A. H., Diop, A., Bittar, F., Maraninchi, M., Valero, R., Armstrong, N., et al. (2018). Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. Antonie Van Leeuwenhoek 111, 2107–2128. doi: 10.1007/s10482-018-1104-y
    • (2018) Antonie Van Leeuwenhoek , vol.111 , pp. 2107-2128
    • Togo, A.H.1    Diop, A.2    Bittar, F.3    Maraninchi, M.4    Valero, R.5    Armstrong, N.6
  • 64
    • 0037100667 scopus 로고    scopus 로고
    • Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation
    • Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., and Gelfand, M. S. (2002). Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30, 3141–3151. doi: 10.1093/nar/gkf433
    • (2002) Nucleic Acids Res , vol.30 , pp. 3141-3151
    • Vitreschak, A.G.1    Rodionov, D.A.2    Mironov, A.A.3    Gelfand, M.S.4
  • 65
    • 72149110077 scopus 로고    scopus 로고
    • Development of a minimal growth medium for Lactobacillus plantarum
    • Wegkamp, A., Teusink, B., de Vos, W. M., and Smid, E. J. (2010). Development of a minimal growth medium for Lactobacillus plantarum. Lett. Appl. Microbiol. 50, 57–64. doi: 10.1111/j.1472-765X.2009.02752.x
    • (2010) Lett. Appl. Microbiol. , vol.50 , pp. 57-64
    • Wegkamp, A.1    Teusink, B.2    De Vos, W.M.3    Smid, E.J.4
  • 66
    • 85016046470 scopus 로고    scopus 로고
    • Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center
    • Wattam, A. R., Davis, J. J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., et al. (2017). Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res. 45, D535–D542. doi: 10.1093/nar/gkw1017
    • (2017) Nucleic Acids Res , vol.45 , pp. D535-D542
    • Wattam, A.R.1    Davis, J.J.2    Assaf, R.3    Boisvert, S.4    Brettin, T.5    Bun, C.6
  • 67
  • 68
    • 84947983159 scopus 로고    scopus 로고
    • Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides
    • Wu, M., Mcnulty, N. P., Rodionov, D. A., Khoroshkin, M. S., Griffin, N. W., Cheng, J., et al. (2015). Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 350:aac5992. doi: 10.1126/science.aac5992
    • (2015) Science , vol.350 , pp. aac5992
    • Wu, M.1    Mcnulty, N.P.2    Rodionov, D.A.3    Khoroshkin, M.S.4    Griffin, N.W.5    Cheng, J.6
  • 70
    • 70049085269 scopus 로고    scopus 로고
    • A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    • Ye, Y., and Doak, T. G. (2009). A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput. Biol. 5:e1000465. doi: 10.1371/journal.pcbi.1000465
    • (2009) PLoS Comput. Biol. , vol.5
    • Ye, Y.1    Doak, T.G.2
  • 71
    • 27144524216 scopus 로고    scopus 로고
    • Automatic detection of subsystem/pathway variants in genome analysis
    • Ye, Y., Osterman, A., Overbeek, R., and Godzik, A. (2005). Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics 21(Suppl. 1), i478–i486. doi: 10.1093/bioinformatics/bti1052
    • (2005) Bioinformatics , vol.21 , pp. i478-i486
    • Ye, Y.1    Osterman, A.2    Overbeek, R.3    Godzik, A.4
  • 72
    • 85012298637 scopus 로고    scopus 로고
    • The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ(0)) Transport
    • Zallot, R., Yuan, Y., and De Crecy-Lagard, V. (2017). The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ(0)) Transport. Biomolecules 7:E12. doi: 10.3390/biom7010012
    • (2017) Biomolecules , vol.7 , pp. E12
    • Zallot, R.1    Yuan, Y.2    De Crecy-Lagard, V.3
  • 73
    • 84924026956 scopus 로고    scopus 로고
    • Potential of fecal microbiota for early-stage detection of colorectal cancer
    • Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., et al. (2014). Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol. 10:766. doi: 10.15252/msb.20145645
    • (2014) Mol. Syst. Biol. , vol.10 , pp. 766
    • Zeller, G.1    Tap, J.2    Voigt, A.Y.3    Sunagawa, S.4    Kultima, J.R.5    Costea, P.I.6
  • 74
    • 84901056709 scopus 로고    scopus 로고
    • Mongolians core gut microbiota and its correlation with seasonal dietary changes
    • Zhang, J., Guo, Z., Lim, A. A., Zheng, Y., Koh, E. Y., Ho, D., et al. (2014). Mongolians core gut microbiota and its correlation with seasonal dietary changes. Sci. Rep. 4:5001. doi: 10.1038/srep05001
    • (2014) Sci. Rep. , vol.4 , pp. 5001
    • Zhang, J.1    Guo, Z.2    Lim, A.A.3    Zheng, Y.4    Koh, E.Y.5    Ho, D.6
  • 75
    • 64849111600 scopus 로고    scopus 로고
    • Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
    • Zhang, Y., Rodionov, D. A., Gelfand, M. S., and Gladyshev, V. N. (2009). Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 10:78. doi: 10.1186/1471-2164-10-78
    • (2009) BMC Genomics , vol.10 , pp. 78
    • Zhang, Y.1    Rodionov, D.A.2    Gelfand, M.S.3    Gladyshev, V.N.4


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