Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

A core gut microbiome in obese and lean twins

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works

Enterotypes of the human gut microbiome

MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548 · see citing works

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works

Linking long-term dietary patterns with gut microbial enterotypes

Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works

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., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works

Revised Estimates for the Number of Human and Bacteria Cells in the Body

Sender, R., Fuchs, S., & Milo, R. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002533 · Cited by 5,425 · see citing works

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., & Jaffrey, S. R. (2012) · Cell · doi:10.1016/j.cell.2012.05.003 · Cited by 4,223 · see citing works

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

Woese, C. R., & Fox, G. E. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.11.5088 · Cited by 4,131 · see citing works

Duodenal Infusion of Donor Feces for Recurrent <i>Clostridium difficile</i>

van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708 · see citing works

Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis

Yano, J. M., Yu, K., Donaldson, G. P., Shastri, G. G., Ann, P., Ma, L., Nagler, C. R., Ismagilov, R. F., Mazmanian, S. K., & Hsiao, E. Y. (2015) · Cell · doi:10.1016/j.cell.2015.02.047 · Cited by 3,614 · see citing works

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2008.02.015 · Cited by 2,915 · see citing works

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

Wahlstrom, A. M., Sayin, S. I., Marschall, H., & Bäckhed, F. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.05.005 · Cited by 2,903 · see citing works

Mechanisms underlying the resistance to diet-induced obesity in germ-free mice

Bäckhed, F., Manchester, J. K., Semenkovich, C. F., & Gordon, J. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605374104 · Cited by 2,615 · see citing works

Metabolomics: the apogee of the omics trilogy

Patti, G. J., Yanes, Ó., & Siuzdak, G. E. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3314 · Cited by 2,605 · see citing works

Human nutrition, the gut microbiome and the immune system

Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588 · see citing works

MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT

Savage, D. C. (1977) · Annual Review of Microbiology · doi:10.1146/annurev.mi.31.100177.000543 · Cited by 2,436 · see citing works

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417 · see citing works

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

Zhao, L., Zhang, F., Ding, X., Wu, G., Lam, Y. Y., Wang, X., Fu, H., Xue, X., Lu, C., Ma, J., et al. (2018) · Science · doi:10.1126/science.aao5774 · Cited by 2,304 · see citing works

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

Sender, R., Fuchs, S., & Milo, R. (2016) · Cell · doi:10.1016/j.cell.2016.01.013 · Cited by 2,050 · see citing works

Best practices for analysing microbiomes

Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030 · see citing works

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., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988 · see citing works

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works

Extensive impact of non-antibiotic drugs on human gut bacteria

Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E. E., Brochado, A. R., Fernandez, K. C., Dose, H., Mori, H., et al. (2018) · Nature · doi:10.1038/nature25979 · Cited by 1,905 · see citing works

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415 · see citing works

Microbiota Transfer Therapy Alters Gut Ecosystem and Improves Gastrointestinal and Autism Symptoms: An Open-Label Study

Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0225-7 · Cited by 1,391 · see citing works

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works

Diet, gut microbiota and immune responses

Maslowski, K. M., & Mackay, C. R. (2011) · Nature Immunology · doi:10.1038/ni0111-5 · Cited by 1,261 · see citing works

Defining the human microbiome

Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255 · see citing works

Consumption of fermented milk product with probiotic modulates brain activity

Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., Guyonnet, D., Legrain–Raspaud, S., Trotin, B., Naliboff, B., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.02.043 · Cited by 1,192 · see citing works

GABA-modulating bacteria of the human gut microbiota

Strandwitz, P., Kim, K. H., Terekhova, D., Liu, J. K., Sharma, A., Levering, J., McDonald, D., Dietrich, D., Ramadhar, T. R., Lekbua, A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0307-3 · Cited by 1,170 · cited 1× · see citing works

Control of brain development, function, and behavior by the microbiome

Sampson, T. R., & Mazmanian, S. K. (2015) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2015.04.011 · Cited by 1,093 · see citing works

Chemical transformation of xenobiotics by the human gut microbiota

Koppel, N., Maini Rekdal, V., & Balskus, E. P. (2017) · Science · doi:10.1126/science.aag2770 · Cited by 1,080 · see citing works

Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition

Kootte, R. S., Levin, E., Salojärvi, J., Smits, L. P., Hartstra, A. V., Udayappan, S. D., Hermes, G., Bouter, K. E., Koopen, A. M., Holst, J. J., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.09.008 · Cited by 1,039 · see citing works

Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics

Brindle, J. T., Antti, H., Holmes, E. C., Tranter, G. E., Nicholson, J. K., Bethell, H., Clarke, S., Schofield, P. M., McKilligin, E., Mosedale, D. E., et al. (2002) · Nature Medicine · doi:10.1038/nm1202-802 · Cited by 1,031 · see citing works

Counting absolute numbers of molecules using unique molecular identifiers

Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., & Taipale, J. (2012) · Nature Methods · doi:10.1038/nmeth.1778 · Cited by 1,010 · see citing works

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling

Caesar, R., Tremaroli, V., Kovatcheva-Datchary, P., Cani, P. D., & Bäckhed, F. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.026 · Cited by 960 · see citing works

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) · Science · doi:10.1126/science.1220671 · Cited by 923 · see citing works

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

Langdon, A. E., Crook, N., & Dantas, G. A. (2016) · Genome Medicine · doi:10.1186/s13073-016-0294-z · Cited by 917 · see citing works

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaiss, C. A., Levy, M., Korem, T., Dohnalová, L., Shapiro, H., Jaitin, D. A., David, E., Winter, D. R., Gury-BenAri, M., Tatirovsky, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.003 · Cited by 870 · see citing works

Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity

Cani, P. D., Osto, M., Geurts, L., & Everard, A. (2012) · Gut Microbes · doi:10.4161/gmic.19625 · Cited by 864 · see citing works

Nascent transcript sequencing visualizes transcription at nucleotide resolution

Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823 · see citing works

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

Greenblum, S., Turnbaugh, P. J., & Borenstein, E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116053109 · Cited by 821 · see citing works

The host shapes the gut microbiota via fecal microRNA

Liu, S., da Cunha, A. P., Rezende, R. M., Cialic, R., Wei, Z., Bry, L., Comstock, L. E., Gandhi, R., & Weiner, H. L. (2016) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2015.12.005 · Cited by 808 · see citing works

Lysine propionylation and butyrylation are novel post-translational modifications in histones

Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S. C., Falck, J. R., Peng, J., Gu, W., & Zhao, Y. (2007) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m700021-mcp200 · Cited by 764 · see citing works

Xanthomonas citri MinC Oscillates from Pole to Pole to Ensure Proper Cell Division and Shape

Lorenzoni, A. S. G., Dantas, G. C., Bergsma, T., Ferreira, H., & Scheffers, D. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01352 · Cited by 727 · see citing works

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

Franzosa, E. A., Hsu, T. Y., Sirota‐Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3451 · Cited by 725 · see citing works

Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes

Cai, L., Sutter, B. M., Li, B., & Tu, B. P. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.004 · Cited by 701 · see citing works

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Down, T. A., Rakyan, V. K., Turner, D., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, E. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1414 · Cited by 651 · see citing works

Innate immune recognition of the microbiota promotes host-microbial symbiosis

Chu, H., & Mazmanian, S. K. (2013) · Nature Immunology · doi:10.1038/ni.2635 · Cited by 630 · see citing works

Epigenetics: a molecular link between environmental factors and type 2 diabetes

Ling, C., & Groop, L. (2009) · Diabetes · doi:10.2337/db09-1003 · Cited by 617 · see citing works

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

Krautkramer, K. A., Kreznar, J. H., Romano, K. A., Vivas, E. I., Barrett-Wilt, G. A., Rabaglia, M. E., Keller, M. P., Attie, A. D., Rey, F. E., & Denu, J. M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.025 · Cited by 607 · see citing works

Genetic Control of MHC Class II Expression

Ting, J. P.-Y., & Trowsdale, J. (2002) · Cell · doi:10.1016/s0092-8674(02)00696-7 · Cited by 583 · see citing works

Specialized metabolites from the microbiome in health and disease

Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.10.016 · Cited by 544 · see citing works

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

Groussin, M., Mazel, F., Sanders, J. G., Smillie, C. S., Lavergne, S., Thuiller, W., & Alm, E. J. (2017) · Nature Communications · doi:10.1038/ncomms14319 · Cited by 491 · see citing works

Analytical strategies for LC–MS-based targeted metabolomics

Lu, W., Bennett, B. D., & Rabinowitz, J. D. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.04.031 · Cited by 489 · see citing works

Fecal microbiota transplantation: in perspective

Gupta, S., Allen‐Vercoe, E., & Petrof, E. O. (2015) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x15607414 · Cited by 484 · see citing works

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

Petersen, J. M., Kemper, A., Gruber‐Vodicka, H. R., Cardini, U., van der Geest, M., Kleiner, M., Bulgheresi, S., Mußmann, M., Herbold, C. W., Seah, B. K. B., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.195 · Cited by 467 · see citing works

Use of Lactobacillus to prevent infection by pathogenic bacteria

Reid, G., & Burton, J. P. (2002) · Microbes and Infection · doi:10.1016/s1286-4579(02)01544-7 · Cited by 445 · see citing works

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

Gilbert, J. A., Field, D., Huang, Y., Edwards, R. A., Li, W., Gilna, P., & Joint, I. R. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003042 · Cited by 403 · see citing works

Signaling Kinase AMPK Activates Stress-Promoted Transcription via Histone H2B Phosphorylation

Bungard, D., Fuerth, B. J., Zeng, P.-Y., Faubert, B., Maas, N. L., Viollet, B., Carling, D., Thompson, C. B., Jones, R. G., & Berger, S. L. (2010) · Science · doi:10.1126/science.1191241 · Cited by 372 · see citing works

Correction: Corrigendum: Effect of TREM-1 blockade and single nucleotide variants in experimental renal injury and kidney transplantation

Tammaro, A., Kers, J., Emal, D., Stroo, I., Teske, G. J. D., Butter, L. M., Claessen, N., Damman, J. J., Derive, M., Navis, G. J., et al. (2017) · Scientific Reports · doi:10.1038/srep44163 · Cited by 368 · see citing works

Gut microbiota, probiotics and diabetes

Gomes, A. C., Bueno, A. A., de Souza, R. G. M., & Mota, J. F. (2014) · Nutrition Journal · doi:10.1186/1475-2891-13-60 · Cited by 363 · see citing works

Human-origin probiotic cocktail increases short-chain fatty acid production via modulation of mice and human gut microbiome

Nagpal, R., Wang, S., Ahmadi, S., Hayes, J., Gagliano, J., Subashchandrabose, S., Kitzman, D. W., Becton, T., Read, R., & Yadav, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-30114-4 · Cited by 355 · see citing works

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial

Reijnders, D., Goossens, G. H., Hermes, G. D. A., Neis, E. P. J. G., van der Beek, C. M., Most, J., Holst, J. J., Lenaerts, K., Kootte, R. S., Nieuwdorp, M., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.06.016 · Cited by 351 · see citing works

Segmented Filamentous Bacteria Are Indigenous Intestinal Bacteria That Activate Intraepithelial Lymphocytes and Induce MHC Class II Molecules and Fucosyl Asialo GM1 Glycolipids on the Small Intestinal Epithelial Cells in the Ex‐Germ‐Free Mouse

Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A., & Setoyama, H. (1995) · Microbiology and Immunology · doi:10.1111/j.1348-0421.1995.tb02242.x · Cited by 346 · see citing works

Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain

Menni, C., Jackson, M. A., Pallister, T., Steves, C. J., Spector, T. D., & Valdes, A. M. (2017) · International Journal of Obesity · doi:10.1038/ijo.2017.66 · Cited by 343 · see citing works

Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

Greninger, A. L., Messacar, K., Dunnebacke, T. H., Naccache, S. N., Federman, S., Bouquet, J., Mirsky, D. M., Nomura, Y., Yagi, S., Glaser, C. A., et al. (2016) · Genome Medicine · doi:10.1186/s13073-015-0257-9 · Cited by 333 · see citing works

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

Heintz-Buschart, A., May, P., Laczny, C. C., Lebrun, L. A., Bellora, C., Krishna, A., Wampach, L., Schneider, J. G., Hogan, A., de Beaufort, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.180 · Cited by 316 · see citing works

Hanbury-Brown and Twiss exchange and non-equilibrium-induced correlations in disordered, four-terminal graphene-ribbon conductor

Tan, Z., Elo, T., Puska, A., Sarkar, J., Lähteenmäki, P., Duerr, F., Gould, C., Molenkamp, L. W., Nagaev, K. E., & Hakonen, P. J. (2018) · Scientific Reports · doi:10.1038/s41598-018-32777-5 · Cited by 316 · see citing works

Connecting threads: epigenetics and metabolism

Katada, S., Imhof, A., & Sassone-Corsi, P. (2012) · Cell · doi:10.1016/j.cell.2012.01.001 · Cited by 315 · see citing works

Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases

Paul, B., Barnes, S., Demark-Wahnefried, W., Morrow, C., Salvador, C., Skibola, C., & Tollefsbol, T. O. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0144-7 · Cited by 306 · see citing works

History and Current Use of Antimicrobial Drugs in Veterinary Medicine

Prescott, J. F. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.arba-0002-2017 · Cited by 297 · see citing works

Correction: Corrigendum: 14-3-3ζ regulates the mitochondrial respiratory reserve linked to platelet phosphatidylserine exposure and procoagulant function

Schoenwaelder, S. M., Darbousset, R., Cranmer, S. L., Ramshaw, H. S., Orive, S. L., Sturgeon, S. A., Yuan, Y., Yao, Y., Krycer, J. R., Woodcock, J. M., et al. (2017) · Nature Communications · doi:10.1038/ncomms16125 · Cited by 293 · see citing works

Nutritional Epigenetics: Impact of Folate Deficiency on DNA Methylation and Colon Cancer Susceptibility

Kim, Y. (2005) · Journal of Nutrition · doi:10.1093/jn/135.11.2703 · Cited by 265 · see citing works

The Human Gut Phage Community and Its Implications for Health and Disease

Manrique, P., Dills, M., & Young, M. (2017) · Viruses · doi:10.3390/v9060141 · Cited by 253 · see citing works

Secretory Leukoprotease Inhibitor (Slpi) Expression Is Required for Educating Murine Dendritic Cells Inflammatory Response Following Quercetin Exposure

Santis, S. D., Galleggiante, V., Scandiffio, L., Liso, M., Sommella, E., Sobolewski, A., Spilotro, V., Pinto, A., Campiglia, P., Serino, G., et al. (2017) · Nutrients · doi:10.3390/nu9070706 · Cited by 252 · see citing works

A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology

Williamson, I., Arnold, J. W., Samsa, L. A., Gaynor, L. T., DiSalvo, M., Cocchiaro, J. L., Carroll, I. M., Azcárate-Peril, M. A., Rawls, J. F., Allbritton, N. L., et al. (2018) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2018.05.004 · Cited by 248 · see citing works

Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders to caloric restriction

Bouchard, L., RABASA-LHORET, R. P. R., Faraj, M., Lavoie, M.-È., Mill, J. S., Përusse, L., & Vohl, M. (2009) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.2009.28085 · Cited by 244 · see citing works

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

Staley, C. M., Kaiser, T., Beura, L. K., Hamilton, M. J., Weingarden, A. R., Bobr, A., Kang, J., Masopust, D., Sadowsky, M. J., & Khoruts, A. (2017) · Microbiome · doi:10.1186/s40168-017-0306-2 · Cited by 236 · see citing works

Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals

Bhat, M. I., & Kapila, R. (2017) · Nutrition Reviews · doi:10.1093/nutrit/nux001 · Cited by 227 · see citing works

Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption

Romano, K. A., Martinez-del Campo, A., Kasahara, K., Chittim, C. L., Vivas, E. I., Amador-Noguez, D., Balskus, E. P., & Rey, F. E. (2017) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2017.07.021 · Cited by 224 · see citing works

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

Booth, M. J., Marsico, G., Bachman, M., Beraldi, D., & Balasubramanian, S. (2014) · Nature Chemistry · doi:10.1038/nchem.1893 · Cited by 214 · see citing works

Hypermethylation of the TGF-β target, ABCA1 is associated with poor prognosis in ovarian cancer patients

Chou, J.-L., Huang, R., Shay, J., Chen, L.-Y., Lin, S.-J., Yan, P. S., Chao, W., Lai, Y.-H., Lai, Y.-L., Chao, T., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-014-0036-2 · Cited by 207 · see citing works

Diet, the Gut Microbiome, and Epigenetics

Hullar, M. A. J., & Fu, B. C. (2014) · The Cancer Journal · doi:10.1097/ppo.0000000000000053 · Cited by 205 · see citing works

The development of the ventral prefrontal cortex and social flexibility

Nelson, E. E., & Guyer, A. E. (2011) · Developmental Cognitive Neuroscience · doi:10.1016/j.dcn.2011.01.002 · Cited by 201 · see citing works

Humans as holobionts: implications for prevention and therapy

van de Guchte, M., Blottière, H. M., & Dore, J. M. (2018) · Microbiome · doi:10.1186/s40168-018-0466-8 · Cited by 192 · see citing works

Induction of innate immune memory via microRNA targeting of chromatin remodelling factors

Seeley, J. J., Baker, R. G., Ghait, M., Bruns, T., Hayden, M. S., Deshmukh, S. D., Freedberg, D. E., & Ghosh, S. (2018) · Nature · doi:10.1038/s41586-018-0253-5 · Cited by 188 · see citing works

TET family dioxygenases and DNA demethylation in stem cells and cancers

An, J., Rao, A., & Ko, M. (2017) · Experimental & Molecular Medicine · doi:10.1038/emm.2017.5 · Cited by 187 · see citing works

From Stool Transplants to Next-Generation Microbiota Therapeutics

Petrof, E. O., & Khoruts, A. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.004 · Cited by 184 · see citing works

The Metabolic Impact on Histone Acetylation and Transcription in Ageing

Peleg, S., Feller, C., Ladurner, A. G., & Imhof, A. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.05.008 · Cited by 178 · see citing works

Diet, Gut Microbiome and Epigenetics: Emerging Links with Inflammatory Bowel Diseases and Prospects for Management and Prevention

Aleksandrova, K., Romero-Mosquera, B., & Hernández, V. (2017) · Nutrients · doi:10.3390/nu9090962 · Cited by 169 · see citing works

Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics

Brindle, J. T., Antti, H., Holmes, E. C., et al. (2002) · Nature Medicine · doi:10.1038/nm802 · Cited by 167 · see citing works

Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome

Ussar, S., Fujisaka, S., & Kahn, C. R. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.07.004 · Cited by 157 · see citing works

Inactivation of Rheb by PRAK-mediated phosphorylation is essential for energy-depletion-induced suppression of mTORC1

Zheng, M., Wang, Y., Wu, X., Wu, S., Lu, B.-J., Dong, M., Zhang, H., Sun, P., Lin, S., Guan, K., et al. (2011) · Nature Cell Biology · doi:10.1038/ncb2168 · Cited by 137 · see citing works

Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry

Sidoli, S., Cheng, L., & Jensen, O. N. (2012) · Journal of Proteomics · doi:10.1016/j.jprot.2011.12.029 · Cited by 125 · see citing works

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway

Robertson, K. A., Hsieh, W. Y., Forster, T., Blanc, M., Lu, H., Crick, P. J., Yutuc, E., Watterson, S., Martin, K., Griffiths, S. J., et al. (2016) · PLoS Biology · doi:10.1371/journal.pbio.1002364 · Cited by 122 · see citing works

Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns

Pamer, E. G. (2014) · Mucosal Immunology · doi:10.1038/mi.2013.117 · Cited by 109 · see citing works

The Role of AMP-Activated Protein Kinase in Obesity

Kola, B., Grossman, A. B., & Korbonits, M. (2008) · KARGER eBooks · doi:10.1159/000115366 · Cited by 99 · see citing works

Engineering Diagnostic and Therapeutic Gut Bacteria

Landry, B. P., & Tabor, J. J. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.bad-0020-2017 · Cited by 95 · see citing works

The human microbiome in hematopoiesis and hematologic disorders

Manzo, V. E., & Bhatt, A. S. (2015) · Blood · doi:10.1182/blood-2015-04-574392 · Cited by 93 · see citing works

Blood determinations of S-adenosylmethionine, S-adenosylhomocysteine, and homocysteine: correlations with diet.

Poirier, L. A., Wise, C., Delongchamp, R. R., & Sinha, R. (2001) · PubMed · Cited by 92 · see citing works

Superorganisms and Holobionts

Gordon, J. I., Youle, M., Knowlton­, N., Rohwer, F. L., & Relman, D. A. (2013) · Microbe Magazine · doi:10.1128/microbe.8.152.1 · Cited by 92 · see citing works

Fiber-derived butyrate and the prevention of colon cancer

Hassig, C. A., Tong, J. K., & Schreiber, S. L. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90111-3 · Cited by 87 · see citing works

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A., & Li, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr668 · Cited by 87 · see citing works

The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire

Carrier, T. J., & Reitzel, A. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00802 · Cited by 78 · see citing works

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis

Watanabe, K., Gilchrist, C. A., Uddin, M. J., Burgess, S. L., Abhyankar, M. M., Moonah, S. N., Noor, Z., Donowitz, J. R., Schneider, B. N., Arju, T., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006513 · Cited by 76 · see citing works

Chemical signaling between gut microbiota and host chromatin: What is your gut really saying?

Krautkramer, K. A., Rey, F. E., & Denu, J. M. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.r116.761577 · Cited by 70 · see citing works

Epigenetic Metabolite Acetate Inhibits Class I/II Histone Deacetylases, Promotes Histone Acetylation, and Increases HIV-1 Integration in CD4+T Cells

Bolduc, J.-F., Hany, L., Barat, C., Ouellet, M., & Tremblay, M. J. (2017) · Journal of Virology · doi:10.1128/jvi.01943-16 · Cited by 65 · see citing works

Human seroreactivity to gut microbiota antigens

Christmann, B. S., Abrahamsson, T., Bernstein, C. N., Duck, L. W., Mannon, P., Berg, G. E., Björkstén, B., Jenmalm, M. C., & Elson, C. O. (2015) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2015.03.036 · Cited by 64 · see citing works

Epigenetics and obesity: the devil is in the details

Franks, P. W., & Ling, C. (2010) · BMC Medicine · doi:10.1186/1741-7015-8-88 · Cited by 62 · see citing works

Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans

Laker, R. C., Garde, C., CAMERA, D. M., Smiles, W. J., Zierath, J. R., Hawley, J. A., & Barrès, R. (2017) · Scientific Reports · doi:10.1038/s41598-017-15420-7 · Cited by 58 · see citing works

Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration

Ojeda, E. F. C., Andrade, A. S., Mellors, J. W., Kuritzkes, D. R., Perelson, A. S., & Ribeiro, R. M. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006478 · Cited by 56 · see citing works

Nutritional “Omics” Technologies for Elucidating the Role(s) of Bioactive Food Components in Colon Cancer Prevention

Davis, C. D., & Hord, N. G. (2005) · Journal of Nutrition · doi:10.1093/jn/135.11.2694 · Cited by 47 · see citing works

Anti-HIV-1 ADCC Antibodies following Latency Reversal and Treatment Interruption

Lee, W. S., Kristensen, A. B., Rasmussen, T. A., Tolstrup, M., Østergaard, L. J., Søgaard, O. S., Wines, B. D., Hogarth, P. M., Reynaldi, A., Davenport, M. P., et al. (2017) · Journal of Virology · doi:10.1128/jvi.00603-17 · Cited by 40 · see citing works

Chemical and Physiological Features of Mitochondrial Acylation

Ringel, A. E., Tucker, S. A., & Haigis, M. C. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.023 · Cited by 40 · see citing works

Effective Detection of Porcine Cytomegalovirus Using Non-Invasively Taken Samples from Piglets

Morozov, V. A., Heinrichs, G., & Denner, J. (2017) · Viruses · doi:10.3390/v9010009 · Cited by 35 · see citing works

Gut Microbiota, Probiotics, and Sport

Pane, M., Amoruso, A., Deidda, F., Graziano, T., Allesina, S., & Mogna, L. (2018) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0000000000001058 · Cited by 33 · see citing works

In situ detection of histone variants and modifications in mouse brain using imaging mass spectrometry

Lahiri, S., Sun, N., Solis‐Mezarino, V., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500345 · Cited by 21 · see citing works

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

Gilbert, J. A., Field, D., Huang, Y., et al. (2011) · doi:10.1002/9781118010549.ch27 · Cited by 5 · see citing works

Are we home yet?

Seradjeh, B. (2011) · Nature · doi:10.1038/nj7328-1 · Cited by 4 · see citing works

Probiotics and the microbiota-gut-brain axis: Focus on psychiatry

Mörkl, S., Butler, M. I., Holl, A., Cryan, J. F., & Dinan, T. G. (2020) · Current Nutrition Reports · doi:10.1007/s13668-020-00313-5 · Cited by 337 · see citing works

Food Addiction and Psychosocial Adversity: Biological Embedding, Contextual Factors, and Public Health Implications

Wiss, D. A., Avena, N., & Gold, M. (2020) · Nutrients · doi:10.3390/nu12113521 · Cited by 66 · see citing works

Epigenetic mechanisms in irritable bowel syndrome

Mahurkar-Joshi, S., & Chang, L. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.00805 · Cited by 59 · see citing works

Interaction between gut microbiota metabolites and dietary components in lipid metabolism and metabolic diseases

Basnet, T. B., Srijana, G. C., Basnet, R., Fatima, S., Safdar, M., Sehar, B., Alsubaie, A. S. R., & Zeb, F. (2023) · Access Microbiology · doi:10.1099/acmi.0.000403 · Cited by 16 · see citing works

Metabolic Fingerprint of Dimethyl Sulfone (DMSO2) in Microbial–Mammalian Co-metabolism

He, X., & Slupsky, C. M. (2014) · Journal of Proteome Research · doi:10.1021/pr500629t · Cited by 86 · see citing works

Microbial Metabolism of Reduced Phosphorus Compounds

White, A. K., & Metcalf, W. W. (2007) · Annual Review of Microbiology · doi:10.1146/annurev.micro.61.080706.093357 · Cited by 315 · see citing works

Diet modulates host health through gut microbiota derived extracellular vesicles: A short review

Feng, X., Luo, C., & Che, J. (2023) · Aceh Journal of Animal Science · doi:10.13170/ajas.8.2.32030 · Cited by 1 · see citing works

PBK Model‐Based Prediction of Intestinal Microbial and Host Metabolism of Zearalenone and Consequences for its Estrogenicity

Catala, D. M. M., Wang, Q., & Rietjens, I. M. C. M. (2021) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202100443 · Cited by 22 · see citing works