A. Murat Eren

Assistant Professor
Websites
Research Summary
From the human gut and oral cavity to sewage and marine ecosystems, me and my group use our expertise in microbiology and computation to study the ecology and evolution of environmental microbial populations through cultivation and genome-resolved metagenomic strategies. We also are the primary developers of anvi'o (http://merenlab.org/software/anvio).
Keywords
Metagenomics, Metatranscriptomics, metapangenomics, phylogenomics, anvi'o, microbial ecology, microbial evolution, human microbiome, microbial symbioses
Biosciences Graduate Program Association
Publications
  1. Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. The Wolbachia mobilome in Culex pipiens includes a putative plasmid. Nat Commun. 2019 03 05; 10(1):1051. View in: PubMed

  2. McKay LJ, Dlakic M, Fields MW, Delmont TO, Eren AM, Jay ZJ, Klingelsmith KB, Rusch DB, Inskeep WP. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat Microbiol. 2019 04; 4(4):614-622. View in: PubMed

  3. Wang X, Li Y, Chen W, Shi H, Eren AM, Morozov A, He C, Luo GZ, Pan T. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 Feb; 29(2):167-170. View in: PubMed

  4. Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun. 2018 12 17; 9(1):5353. View in: PubMed

  5. Roguet A, Eren AM, Newton RJ, McLellan SL. Fecal source identification using random forest. Microbiome. 2018 10 18; 6(1):185. View in: PubMed

  6. Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018 Aug; 3(8):963. View in: PubMed

  7. Miyoshi J, Leone V, Nobutani K, Musch MW, Martinez-Guryn K, Wang Y, Miyoshi S, Bobe AM, Eren AM, Chang EB. Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome. PeerJ. 2018; 6:e5166. View in: PubMed

  8. Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018 07; 3(7):804-813. View in: PubMed

  9. McIntosh CM, Chen L, Shaiber A, Eren AM, Alegre ML. Gut microbes contribute to variation in solid organ transplant outcomes in mice. Microbiome. 2018 05 25; 6(1):96. View in: PubMed

  10. Meisel M, Hinterleitner R, Pacis A, Chen L, Earley ZM, Mayassi T, Pierre JF, Ernest JD, Galipeau HJ, Thuille N, Bouziat R, Buscarlet M, Ringus DL, Wang Y, Li Y, Dinh V, Kim SM, McDonald BD, Zurenski MA, Musch MW, Furtado GC, Lira SA, Baier G, Chang EB, Eren AM, Weber CR, Busque L, Godley LA, Verdú EF, Barreiro LB, Jabri B. Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host. Nature. 2018 05; 557(7706):580-584. View in: PubMed

  11. Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ. 2018; 6:e4320. View in: PubMed

  12. Courtine D, Alain K, Georges M, Bienvenu N, Morrison HG, Eren AM, Maignien L. Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N. Genome Announc. 2017 Dec 14; 5(50). View in: PubMed

  13. Delmont TO, Eren AM. Simulations predict microbial responses in the environment? This environment disagrees retrospectively. Proc Natl Acad Sci U S A. 2017 10 24; 114(43):E8947-E8949. View in: PubMed

  14. Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun. 2017 10 24; 8(1):1114. View in: PubMed

  15. Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM. DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biol. 2017 09 21; 18(1):181. View in: PubMed

  16. Miyoshi J, Bobe AM, Miyoshi S, Huang Y, Hubert N, Delmont TO, Eren AM, Leone V, Chang EB. Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring. Cell Rep. 2017 07 11; 20(2):491-504. View in: PubMed

  17. Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM. Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics. Microbiome. 2017 05 04; 5(1):50. View in: PubMed

  18. Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D. A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment. Front Microbiol. 2017; 8:264. View in: PubMed

  19. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 Feb 13. View in: PubMed

  20. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB. Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflamm Bowel Dis. 2017 03; 23(3):366-378. View in: PubMed

  21. Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML. Patient-Specific Bacteroides Genome Variants in Pouchitis. MBio. 2016 11 15; 7(6). View in: PubMed

  22. Eren AM, Sogin ML, Maignien L. Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation. Front Microbiol. 2016; 7:1318. View in: PubMed

  23. Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev. 2016 09; 40(5):686-700. View in: PubMed

  24. Zozaya M, Ferris MJ, Siren JD, Lillis R, Myers L, Nsuami MJ, Eren AM, Brown J, Taylor CM, Martin DH. Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis. Microbiome. 2016 Apr 19; 4:16. View in: PubMed

  25. Delmont TO, Eren AM. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ. 2016; 4:e1839. View in: PubMed

  26. Delmont TO, Eren AM, Vineis JH, Post AF. Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Front Microbiol. 2015; 6:1090. View in: PubMed

  27. Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, Bertz M, Blaut M, Hansen R, McGrogan P, Russell RK, Edwards CA, Gerasimidis K. Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition. Am J Gastroenterol. 2015 Dec; 110(12):1718-29; quiz 1730. View in: PubMed

  28. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ. 2015; 3:e1319. View in: PubMed

  29. Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL. Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups. Appl Environ Microbiol. 2015 Oct; 81(20):7023-33. View in: PubMed

  30. Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol. 2015; 6:358. View in: PubMed

  31. Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, Walter J. The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015 Apr 28; 11(4):527-38. View in: PubMed

  32. Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML. Sewage reflects the microbiomes of human populations. MBio. 2015 Feb 24; 6(2):e02574. View in: PubMed

  33. Mark Welch JL, Utter DR, Rossetti BJ, Mark Welch DB, Eren AM, Borisy GG. Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Front Microbiol. 2014; 5:568. View in: PubMed

  34. Koskey AM, Fisher JC, Eren AM, Ponce-Terashima R, Reis MG, Blanton RE, McLellan SL. Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters. Environ Microbiol Rep. 2014 Dec; 6(6):696-704. View in: PubMed

  35. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2015 Mar 17; 9(4):968-79. View in: PubMed

  36. McLellan SL, Eren AM. Discovering new indicators of fecal pollution. Trends Microbiol. 2014 Dec; 22(12):697-706. View in: PubMed

  37. Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci U S A. 2014 Jul 15; 111(28):E2875-84. View in: PubMed

  38. Eren AM, Sogin ML, Morrison HG, Vineis JH, Fisher JC, Newton RJ, McLellan SL. A single genus in the gut microbiome reflects host preference and specificity. ISME J. 2015 Jan; 9(1):90-100. View in: PubMed

  39. Fischer AH, Mozzherin D, Eren AM, Lans KD, Wilson N, Cosentino C, Smith J. SeaBase: a multispecies transcriptomic resource and platform for gene network inference. Integr Comp Biol. 2014 Jul; 54(2):250-63. View in: PubMed

  40. Apprill A, Robbins J, Eren AM, Pack AA, Reveillaud J, Mattila D, Moore M, Niemeyer M, Moore KM, Mincer TJ. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? PLoS One. 2014; 9(3):e90785. View in: PubMed

  41. Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML. VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics. 2014 Feb 05; 15:41. View in: PubMed

  42. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 2013 Mar 04; 1(1):9. View in: PubMed

  43. Maignien L, DeForce EA, Chafee ME, Eren AM, Simmons SL. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio. 2014 Jan 21; 5(1):e00682-13. View in: PubMed

  44. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 2013 Dec 01; 4(12). View in: PubMed

  45. Eren AM, Vineis JH, Morrison HG, Sogin ML. A filtering method to generate high quality short reads using illumina paired-end technology. PLoS One. 2013; 8(6):e66643. View in: PubMed

  46. Eren AM, Morrison HG, Huse SM, Sogin ML. DRISEE overestimates errors in metagenomic sequencing data. Brief Bioinform. 2014 Sep; 15(5):783-7. View in: PubMed

  47. McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML. Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol. 2013 Aug; 15(8):2213-27. View in: PubMed

  48. Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ. Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. PLoS One. 2011; 6(10):e26732. View in: PubMed