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Article

Eren, A. M.

and Delmont, T. O. (2024)
Bioprospecting marine microbial genomes to improve biotechnology ,

Nature, 633 (8029), pp. 287-288 .

doi:10.1038/d41586-024-02661-6 , hdl:10013/epic.ad870819-fb6b-4c2b-a8cc-b96827b9004c

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Article

Veseli, I.

, DeMers, M. A. , Cooper, Z. S. , Schechter, M. S. , Miller, S. , Weber, L. , Smith, C. B. , Rodriguez, L. T. , Schroer, W. F. , McIlvin, M. R. , Lopez, P. Z. , Saito, M. , Dyhrman, S. , Eren, A. M.

, Moran, M. A. and Braakman, R. (2024)
Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms ,

Scientific Data, 11 (1), p. 967 .

doi:10.1038/s41597-024-03778-z , hdl:10013/epic.9994689a-518e-4aec-adbf-f8956d4fd2fd

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Article

Eren, A. M.

and Banfield, J. F. (2024)
Modern microbiology: Embracing complexity through integration across scales ,

Cell, 187 (19), pp. 5151-5170 .

doi:10.1016/j.cell.2024.08.028 , hdl:10013/epic.e901267d-f643-40e6-9005-65387fa1447d

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Article

Peña-Montenegro, T. D. , Kleindienst, S. , Allen, A. E. , Eren, A. M.

, McCrow, J. P. , Arnold, J. and Joye, S. B. (2024)
Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant / Biddle, J. F. (editor) ,

Applied and Environmental Microbiology, 90 (8), e01083-e01024 .

doi:10.1128/aem.01083-24 , hdl:10013/epic.8718b808-07d7-41fe-9df9-eb8739e88856

Article

Peña-Montenegro, T. D. , Kleindienst, S. , Allen, A. E. , Eren, A. M.

, McCrow, J. P. , Arnold, J. and Joye, S. B. (2024)
Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant / Biddle, J. F. (editor) ,

Applied and Environmental Microbiology, 90 (8), e01083-e01024 .

doi:10.1128/aem.01083-24 , hdl:10013/epic.902cefee-8910-4712-83cf-8d384c67b765

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Article

Yang, M. , Zheng, X. , Fan, J. , Cheng, W. , Yan, T. , Lai, Y. , Zhang, N. , Lu, Y. , Qi, J. , Huo, Z. , Xu, Z. , Huang, J. , Jiao, Y. , Liu, B. , Pang, R. , Zhong, X. , Huang, S. , Luo, G. , Lee, G. , Jobin, C. , Eren, A. M.

, Chang, E. B. , Wei, H. , Pan, T. and Wang, X. (2024)
Antibiotic‐Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism ,

Advanced Science, 11 (28), p. 2307981 .

doi:10.1002/advs.202307981 , hdl:10013/epic.722df8f2-fdb0-4bb3-9a48-9be29405cf02

Article

Yang, M. , Zheng, X. , Fan, J. , Cheng, W. , Yan, T. , Lai, Y. , Zhang, N. , Lu, Y. , Qi, J. , Huo, Z. , Xu, Z. , Huang, J. , Jiao, Y. , Liu, B. , Pang, R. , Zhong, X. , Huang, S. , Luo, G. , Lee, G. , Jobin, C. , Eren, A. M.

, Chang, E. B. , Wei, H. , Pan, T. and Wang, X. (2024)
Antibiotic‐Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism ,

Advanced Science, 11 (28), p. 2307981 .

doi:10.1002/advs.202307981 , hdl:10013/epic.4e27fcd8-14d3-443b-8825-9c7e14e85921

[thumbnail of Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m<sup>6<sup>A Epitranscriptome via .pdf]

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Article

Möller, L. , Vainshtein, Y. , Meyer, B.

, Neidhardt, J. , Eren, A. M.

, Sohn, K. and Rabus, R. (2024)
Rich microbial and depolymerising diversity in Antarctic krill gut. / Kormas, K. A. (editor) ,

Microbiology Spectrum, e0403523-e0403523 .

doi:10.1128/spectrum.04035-23 , hdl:10013/epic.55ab403f-7f44-4f90-9f86-9524cbb23fbb

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Article

Yu, M. K. , Fogarty, E. C. and Eren, A. M.

(2024)
Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess ,

Nature Microbiology, 9 (3), pp. 830-847 .

doi:10.1038/s41564-024-01610-3 , hdl:10013/epic.7bb7e20d-bbea-458d-a284-c56f36b8927d

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Article

Fogarty, E. C. , Schechter, M. S. , Lolans, K. , Sheahan, M. L. , Veseli, I.

, Moore, R. M. , Kiefl, E. , Moody, T. , Rice, P. A. , Yu, M. K. , Mimee, M. , Chang, E. B. , Ruscheweyh, H. J. , Sunagawa, S. , Mclellan, S. L. , Willis, A. D. , Comstock, L. E. and Eren, A. M.

(2024)
A cryptic plasmid is among the most numerous genetic elements in the human gut ,

Cell, 187 (5), 1206-1222.e16 .

doi:10.1016/j.cell.2024.01.039 , hdl:10013/epic.41f8282b-ce80-44a9-9f9f-b12ef8def8e7

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Article

Fiebig, A. , Schnizlein, M. K. , Pena-Rivera, S. , Trigodet, F. , Dubey, A. A. , Hennessy, M. K. , Basu, A. , Pott, S. , Dalal, S. , Rubin, D. , Sogin, M. L. , Eren, A. M.

, Chang, E. B. and Crosson, S. (2024)
Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient / Harwood, C. S. (editor) ,

mBio, 15 (1), e02830-e02823 .

doi:10.1128/mbio.02830-23 , hdl:10013/epic.74078163-500b-43e1-bd49-45c56b869034

[thumbnail of Bile acid fitness determinants of a iBacteroides fragilisi isolate from a human pouchitis patient.pdf]

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Article

Trouche, B. , Schrieke, H. , Duron, O. , Eren, A. M.

and Reveillaud, J. (2024)
Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms ,

ISME Communications, 4 (1), ycae078-ycae078 .

doi:10.1093/ismeco/ycae078 , hdl:10013/epic.ebe251c8-060c-499a-83d1-16db22e682b7

[thumbnail of iWolbachiai populations across organs of individual iCulex pipiensi highly conserved intra-individual core pangenome with in.pdf]

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Article

Little, A. S. , Younker, I. T. , Schechter, M. S. , Bernardino, P. N. , Méheust, R. , Stemczynski, J. , Scorza, K. , Mullowney, M. W. , Sharan, D. , Waligurski, E. , Smith, R. , Ramanswamy, R. , Leiter, W. , Moran, D. , McMillin, M. , Odenwald, M. A. , Iavarone, A. T. , Sidebottom, A. M. , Sundararajan, A. , Pamer, E. G. , Eren, A. M.

and Light, S. H. (2024)
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration ,

Nature Microbiology, 9 (1), pp. 55-69 .

doi:10.1038/s41564-023-01560-2 , hdl:10013/epic.fd7764ea-fe62-4960-89d0-23209161724f

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Article

Watson, A. R. , Füssel, J. , Veseli, I.

, DeLongchamp, J. Z. , Silva, M. , Trigodet, F. , Lolans, K. , Shaiber, A. , Fogarty, E. , Runde, J. M. , Quince, C. , Yu, M. K. , Söylev, A. , Morrison, H. G. , Lee, S. T. , Kao, D. , Rubin, D. T. , Jabri, B. , Louie, T. and Eren, A. M.

(2023)
Metabolic independence drives gut microbial colonization and resilience in health and disease ,

Genome Biology, 24 (1), p. 78 .

doi:10.1186/s13059-023-02924-x , hdl:10013/epic.5368cb4d-25eb-4bfc-ad2c-4244fb594980

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Peña-Montenegro, T. D. , Kleindienst, S. , Allen, A. E. , Eren, A. M.

, McCrow, J. P. , Sánchez-Calderón, J. D. , Arnold, J. and Joye, S. B. (2023)
Species-specific responses of marine bacteria to environmental perturbation ,

ISME Communications, 3 (1), p. 99 .

doi:10.1038/s43705-023-00310-z , hdl:10013/epic.f0808fea-cc98-4335-be7a-6fc0a2a05725

[thumbnail of 43705_2023_article_310.pdf]

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Article

Ghousein, A. , Tutagata, J. , Schrieke, H. , Etienne, M. , Chaumeau, V. , Boyer, S. , Pages, N. , Roiz, D. , Eren, A. M.

, Cambray, G. and Reveillaud, J. (2023)
pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes worldwide ,

ISME Communications, 3 (1), p. 40 .

doi:10.1038/s43705-023-00248-2 , hdl:10013/epic.bc8c1e4e-6723-4b01-b379-2cea7eafe048

[thumbnail of pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes w.pdf]

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Wu-Woods, N. J. , Barlow, J. T. , Trigodet, F. , Shaw, D. G. , Romano, A. E. , Jabri, B. , Eren, A. M.

and Ismagilov, R. F. (2023)
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples ,

Nature Methods, 20 (11), pp. 1672-1682 .

doi:10.1038/s41592-023-02025-4 , hdl:10013/epic.96fe2410-b2cc-4fd2-b31f-d2b23d4ddd0e

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Article

Veseli, I.

, Chen, Y. T. , Schechter, M. S. , Vanni, C. , Fogarty, E. C. , Watson, A. R. , Jabri, B. , Blekhman, R. , Willis, A. D. , Yu, M. K. , Fernàndez-Guerra, A. , Füssel, J. and Eren, A. M.

(2023)
Microbes with higher metabolic independence are enriched in human gut microbiomes under stress ,

eLife, 4 (06-07), 2023.05.10.540289-2023.05.10.540289 .

doi:10.7554/eLife.89862 , hdl:10013/epic.5812ff84-0c32-4a74-a9ad-84081f35ed61

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Article

Runde, J. , Veseli, I.

, Fogarty, E. C. , Watson, A. R. , Clayssen, Q. , Yosef, M. , Shaiber, A. , Verma, R. , Quince, C. , Gerasimidis, K. , Rubin, D. T. and Eren, A. M.

(2023)
Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn’s Disease ,

Journal of Crohn's and Colitis, 17 (7), pp. 1103-1113 .

doi:10.1093/ecco-jcc/jjad031 , hdl:10013/epic.54ce949d-75b3-4362-abd9-2e03d6612b2e

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Kiefl, E. , Esen, O. C. , Miller, S. E. , Kroll, K. L. , Willis, A. D. , Rappé, M. S. , Pan, T. and Eren, A. M.

(2023)
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution ,

Science Advances, 9 (8), eabq4632-eabq4632 .

doi:10.1126/sciadv.abq4632 , hdl:10013/epic.167e267e-8d86-4ae4-8d24-f7ceeea90ba0

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Chitale, P. , Lemenze, A. D. , Fogarty, E. C. , Shah, A. , Grady, C. , Odom-Mabey, A. R. , Johnson, W. E. , Yang, J. H. , Eren, A. M.

, Brosch, R. , Kumar, P. and Alland, D. (2022)
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome ,

Nature Communications, 13 (1), p. 7068 .

doi:10.1038/s41467-022-34853-x , hdl:10013/epic.76519194-808b-46e8-a905-5b60a5707f1f

[thumbnail of A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.pdf]

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Article

Paul, B. G. and Eren, A. M.

(2022)
Eco-evolutionary significance of domesticated retroelements in microbial genomes ,

Mobile DNA, 13 (1), p. 6 .

doi:10.1186/s13100-022-00262-6 , hdl:10013/epic.6ea61470-bda8-441b-b961-b365c7ad848e

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Article

Roguet, A. , Newton, R. J. , Eren, A. M.

and McLellan, S. L. (2022)
Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure / Allard, S. M. (editor) ,

mSystems, 7 (4), e00118-e00122 .

doi:10.1128/msystems.00118-22 , hdl:10013/epic.6f9848dc-c2f9-4aff-83b6-4f567e570f3b

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Article

Delmont, T. O. , Gaia, M. , Hinsinger, D. D. , Frémont, P. , Vanni, C. , Fernandez-Guerra, A. , Eren, A. M.

, Kourlaiev, A. , d'Agata, L. , Clayssen, Q. , Villar, E. , Labadie, K. , Cruaud, C. , Poulain, J. , Da Silva, C. , Wessner, M. , Noel, B. , Aury, J. M. , Coordinators, T. O. , Sunagawa, S. , Acinas, S. G. , Bork, P. , Karsenti, E. , Bowler, C. , Sardet, C. , Stemmann, L. , de Vargas, C. , Wincker, P. , Lescot, M. , Babin, M. , Gorsky, G. , Grimsley, N. , Guidi, L. , Hingamp, P. , Jaillon, O. , Kandels, S. , Iudicone, D. , Ogata, H. , Pesant, S. , Sullivan, M. B. , Not, F. , Lee, K. B. , Boss, E. , Cochrane, G. , Follows, M. , Poulton, N. , Raes, J. , Sieracki, M. , Speich, S. , de Vargas, C. , Bowler, C. , Karsenti, E. , Pelletier, E. , Wincker, P. and Jaillon, O. (2022)
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean ,

Cell Genomics, 2 (5), p. 100123 .

doi:10.1016/j.xgen.2022.100123 , hdl:10013/epic.676c1c10-b538-48e1-bdd8-345c4bf32b73

[thumbnail of 1-s2.0-S2666979X22000477-main.pdf]

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Moran, M. A. , Kujawinski, E. B. , Schroer, W. F. , Amin, S. A. , Bates, N. R. , Bertrand, E. M. , Braakman, R. , Brown, C. T. , Covert, M. W. , Doney, S. C. , Dyhrman, S. T. , Edison, A. S. , Eren, A. M.

, Levine, N. M. , Li, L. , Ross, A. C. , Saito, M. A. , Santoro, A. E. , Segrè, D. , Shade, A. , Sullivan, M. B. and Vardi, A. (2022)
Microbial metabolites in the marine carbon cycle ,

Nature Microbiology, 7 (4), pp. 508-523 .

doi:10.1038/s41564-022-01090-3 , hdl:10013/epic.3addec45-98a0-4f62-b3a4-0ae87fc2a3cf

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