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Items: 24

1.

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP.

mSystems. 2019 Oct 8;4(5). pii: e00392-19. doi: 10.1128/mSystems.00392-19.

2.

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.

Arora-Williams K, Olesen SW, Scandella BP, Delwiche K, Spencer SJ, Myers EM, Abraham S, Sooklal A, Preheim SP.

Microbiome. 2018 Sep 18;6(1):165. doi: 10.1186/s40168-018-0556-7.

3.

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates.

Corzett CH, Elsherbini J, Chien DM, Hehemann JH, Henschel A, Preheim SP, Yu X, Alm EJ, Polz MF.

J Bacteriol. 2018 Jul 10;200(15). pii: e00020-18. doi: 10.1128/JB.00020-18. Print 2018 Aug 1.

4.

High resolution time series reveals cohesive but short-lived communities in coastal plankton.

Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, Polz MF.

Nat Commun. 2018 Jan 18;9(1):266. doi: 10.1038/s41467-017-02571-4.

5.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

King AJ, Preheim SP, Bailey KL, Robeson MS 2nd, Roy Chowdhury T, Crable BR, Hurt RA Jr, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin AP, Elias DA.

Environ Sci Technol. 2017 Mar 7;51(5):2879-2889. doi: 10.1021/acs.est.6b04751. Epub 2017 Feb 10.

6.

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes.

Hehemann JH, Arevalo P, Datta MS, Yu X, Corzett CH, Henschel A, Preheim SP, Timberlake S, Alm EJ, Polz MF.

Nat Commun. 2016 Sep 22;7:12860. doi: 10.1038/ncomms12860.

7.

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem.

Preheim SP, Olesen SW, Spencer SJ, Materna A, Varadharajan C, Blackburn M, Friedman J, Rodríguez J, Hemond H, Alm EJ.

Nat Microbiol. 2016 Aug 15;1(9):16130. doi: 10.1038/nmicrobiol.2016.130.

PMID:
27562262
8.

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Juhani Virta MP, Alm EJ.

ISME J. 2016 Feb;10(2):427-36. doi: 10.1038/ismej.2015.124. Epub 2015 Sep 22.

9.

Natural bacterial communities serve as quantitative geochemical biosensors.

Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC.

MBio. 2015 May 12;6(3):e00326-15. doi: 10.1128/mBio.00326-15.

10.

Computational methods for high-throughput comparative analyses of natural microbial communities.

Preheim SP, Perrotta AR, Friedman J, Smilie C, Brito I, Smith MB, Alm E.

Methods Enzymol. 2013;531:353-70. doi: 10.1016/B978-0-12-407863-5.00018-6.

PMID:
24060130
11.

Distribution-based clustering: using ecology to refine the operational taxonomic unit.

Preheim SP, Perrotta AR, Martin-Platero AM, Gupta A, Alm EJ.

Appl Environ Microbiol. 2013 Nov;79(21):6593-603. doi: 10.1128/AEM.00342-13. Epub 2013 Aug 23.

12.

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

Szabo G, Preheim SP, Kauffman KM, David LA, Shapiro J, Alm EJ, Polz MF.

ISME J. 2013 Mar;7(3):509-19. doi: 10.1038/ismej.2012.134. Epub 2012 Nov 22.

13.

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.

Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ.

PLoS One. 2012;7(6):e39242. doi: 10.1371/journal.pone.0039242. Epub 2012 Jun 29.

14.

Population genomics of early events in the ecological differentiation of bacteria.

Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ.

Science. 2012 Apr 6;336(6077):48-51. doi: 10.1126/science.1218198.

15.

Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion.

Wollenberg MS, Preheim SP, Polz MF, Ruby EG.

Environ Microbiol. 2012 Mar;14(3):655-68. doi: 10.1111/j.1462-2920.2011.02608.x. Epub 2011 Oct 9.

16.

Merging taxonomy with ecological population prediction in a case study of Vibrionaceae.

Preheim SP, Timberlake S, Polz MF.

Appl Environ Microbiol. 2011 Oct;77(20):7195-206. doi: 10.1128/AEM.00665-11. Epub 2011 Aug 26.

17.

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, Alm EJ, Polz MF.

Environ Microbiol. 2011 Jan;13(1):265-275. doi: 10.1111/j.1462-2920.2010.02328.x. Epub 2010 Sep 1.

PMID:
20819104
18.

O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates.

Wildschutte H, Preheim SP, Hernandez Y, Polz MF.

Environ Microbiol. 2010 Nov;12(11):2977-87. doi: 10.1111/j.1462-2920.2010.02274.x.

PMID:
20629700
19.

Transcriptome analyses of the Giardia lamblia life cycle.

Birkeland SR, Preheim SP, Davids BJ, Cipriano MJ, Palm D, Reiner DS, Svärd SG, Gillin FD, McArthur AG.

Mol Biochem Parasitol. 2010 Nov;174(1):62-5. doi: 10.1016/j.molbiopara.2010.05.010. Epub 2010 Jun 4.

20.

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.

21.

Protein phosphatase 2A plays a crucial role in Giardia lamblia differentiation.

Lauwaet T, Davids BJ, Torres-Escobar A, Birkeland SR, Cipriano MJ, Preheim SP, Palm D, Svärd SG, McArthur AG, Gillin FD.

Mol Biochem Parasitol. 2007 Mar;152(1):80-9. Epub 2006 Dec 22.

22.

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

Davids BJ, Reiner DS, Birkeland SR, Preheim SP, Cipriano MJ, McArthur AG, Gillin FD.

PLoS One. 2006 Dec 20;1:e44.

23.

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes.

Polz MF, Hunt DE, Preheim SP, Weinreich DM.

Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):2009-21. Review.

24.

Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data.

Marcelino LA, Backman V, Donaldson A, Steadman C, Thompson JR, Preheim SP, Lien C, Lim E, Veneziano D, Polz MF.

Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13629-34. Epub 2006 Sep 1. Erratum in: Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):20045.

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