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Items: 29

1.

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.

Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K.

Front Microbiol. 2018 Jul 23;9:1635. doi: 10.3389/fmicb.2018.01635. eCollection 2018.

2.

Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Aug;3(8):963. doi: 10.1038/s41564-018-0209-4.

PMID:
30042441
3.

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes.

Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM.

Nat Microbiol. 2018 Jul;3(7):804-813. doi: 10.1038/s41564-018-0176-9. Epub 2018 Jun 11. Erratum in: Nat Microbiol. 2018 Aug;3(8):963.

PMID:
29891866
4.

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.

Delmont TO, Eren AM.

PeerJ. 2018 Jan 25;6:e4320. doi: 10.7717/peerj.4320. eCollection 2018.

5.

Simulations predict microbial responses in the environment? This environment disagrees retrospectively.

Delmont TO, Eren AM.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E8947-E8949. doi: 10.1073/pnas.1712186114. Epub 2017 Oct 10. No abstract available.

6.

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.

Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA.

Nat Commun. 2017 Oct 24;8(1):1114. doi: 10.1038/s41467-017-01228-6.

7.

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Quince C, Delmont TO, Raguideau S, Alneberg J, Darling AE, Collins G, Eren AM.

Genome Biol. 2017 Sep 21;18(1):181. doi: 10.1186/s13059-017-1309-9.

8.

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring.

Miyoshi J, Bobe AM, Miyoshi S, Huang Y, Hubert N, Delmont TO, Eren AM, Leone V, Chang EB.

Cell Rep. 2017 Jul 11;20(2):491-504. doi: 10.1016/j.celrep.2017.06.060.

9.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM.

Microbiome. 2017 May 4;5(1):50. doi: 10.1186/s40168-017-0270-x.

10.

Patient-Specific Bacteroides Genome Variants in Pouchitis.

Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML.

MBio. 2016 Nov 15;7(6). pii: e01713-16. doi: 10.1128/mBio.01713-16.

11.
12.

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree.

Finkel OM, Delmont TO, Post AF, Belkin S.

Appl Environ Microbiol. 2016 Apr 18;82(9):2854-2861. doi: 10.1128/AEM.00483-16. Print 2016 May.

13.

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica.

Delmont TO, Eren AM, Vineis JH, Post AF.

Front Microbiol. 2015 Oct 26;6:1090. doi: 10.3389/fmicb.2015.01090. eCollection 2015.

14.

Anvi'o: an advanced analysis and visualization platform for 'omics data.

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO.

PeerJ. 2015 Oct 8;3:e1319. doi: 10.7717/peerj.1319. eCollection 2015.

15.

Functional Basis of Microorganism Classification.

Zhu C, Delmont TO, Vogel TM, Bromberg Y.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004472. doi: 10.1371/journal.pcbi.1004472. eCollection 2015 Aug.

16.

Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.

Bertrand EM, McCrow JP, Moustafa A, Zheng H, McQuaid JB, Delmont TO, Post AF, Sipler RE, Spackeen JL, Xu K, Bronk DA, Hutchins DA, Allen AE.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):9938-43. doi: 10.1073/pnas.1501615112. Epub 2015 Jul 28.

17.

Integron diversity in marine environments.

Abella J, Bielen A, Huang L, Delmont TO, Vujaklija D, Duran R, Cagnon C.

Environ Sci Pollut Res Int. 2015 Oct;22(20):15360-9. doi: 10.1007/s11356-015-5085-3. Epub 2015 Jul 28. Review.

PMID:
26213132
18.

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.

Delmont TO, Eren AM, Maccario L, Prestat E, Esen ÖC, Pelletier E, Le Paslier D, Simonet P, Vogel TM.

Front Microbiol. 2015 Apr 30;6:358. doi: 10.3389/fmicb.2015.00358. eCollection 2015.

19.

Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya.

Delmont TO, Hammar KM, Ducklow HW, Yager PL, Post AF.

Front Microbiol. 2014 Dec 19;5:646. doi: 10.3389/fmicb.2014.00646. eCollection 2014.

20.

Large-scale metagenomic-based study of antibiotic resistance in the environment.

Nesme J, Cécillon S, Delmont TO, Monier JM, Vogel TM, Simonet P.

Curr Biol. 2014 May 19;24(10):1096-100. doi: 10.1016/j.cub.2014.03.036. Epub 2014 May 8.

21.

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

Jacquiod S, Demanèche S, Franqueville L, Ausec L, Xu Z, Delmont TO, Dunon V, Cagnon C, Mandic-Mulec I, Vogel TM, Simonet P.

J Biotechnol. 2014 Nov 20;190:18-29. doi: 10.1016/j.jbiotec.2014.03.036. Epub 2014 Apr 8.

PMID:
24721211
22.

Life on human surfaces: skin metagenomics.

Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R, Simonet P.

PLoS One. 2013 Jun 12;8(6):e65288. doi: 10.1371/journal.pone.0065288. Print 2013.

23.

Mastering methodological pitfalls for surviving the metagenomic jungle.

Delmont TO, Simonet P, Vogel TM.

Bioessays. 2013 Aug;35(8):744-54. doi: 10.1002/bies.201200155. Epub 2013 Jun 11.

PMID:
23757040
24.

Describing microbial communities and performing global comparisons in the 'omic era.

Delmont TO, Simonet P, Vogel TM.

ISME J. 2012 Sep;6(9):1625-8. doi: 10.1038/ismej.2012.55. Epub 2012 Jun 21. No abstract available.

25.

Structure, fluctuation and magnitude of a natural grassland soil metagenome.

Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM.

ISME J. 2012 Sep;6(9):1677-87. doi: 10.1038/ismej.2011.197. Epub 2012 Feb 2.

26.

Metagenomic comparison of direct and indirect soil DNA extraction approaches.

Delmont TO, Robe P, Clark I, Simonet P, Vogel TM.

J Microbiol Methods. 2011 Sep;86(3):397-400. doi: 10.1016/j.mimet.2011.06.013. Epub 2011 Jun 25.

PMID:
21723887
27.

Metagenomic exploration of antibiotic resistance in soil.

Monier JM, Demanèche S, Delmont TO, Mathieu A, Vogel TM, Simonet P.

Curr Opin Microbiol. 2011 Jun;14(3):229-35. doi: 10.1016/j.mib.2011.04.010. Epub 2011 May 23. Review.

PMID:
21601510
28.

Metagenomic mining for microbiologists.

Delmont TO, Malandain C, Prestat E, Larose C, Monier JM, Simonet P, Vogel TM.

ISME J. 2011 Dec;5(12):1837-43. doi: 10.1038/ismej.2011.61. Epub 2011 May 19.

29.

Accessing the soil metagenome for studies of microbial diversity.

Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR, Vogel TM.

Appl Environ Microbiol. 2011 Feb;77(4):1315-24. doi: 10.1128/AEM.01526-10. Epub 2010 Dec 23.

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