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Abundance-occupancy distributions to prioritize plant core microbiome membership.

Shade A, Stopnisek N.

Curr Opin Microbiol. 2019 Jun;49:50-58. doi: 10.1016/j.mib.2019.09.008. Epub 2019 Nov 10. Review.


Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops.

Grady KL, Sorensen JW, Stopnisek N, Guittar J, Shade A.

Nat Commun. 2019 Sep 12;10(1):4135. doi: 10.1038/s41467-019-11974-4.


Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop.

Shade A, Dunivin TK, Choi J, Teal TK, Howe AC.

mSystems. 2019 Aug 20;4(4). pii: e00297-19. doi: 10.1128/mSystems.00297-19.


A global survey of arsenic-related genes in soil microbiomes.

Dunivin TK, Yeh SY, Shade A.

BMC Biol. 2019 May 30;17(1):45. doi: 10.1186/s12915-019-0661-5.


16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil.

Bowsher AW, Kearns PJ, Shade A.

mSystems. 2019 Apr 2;4(2). pii: e00003-19. doi: 10.1128/mSystems.00003-19. eCollection 2019 Mar-Apr.


RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids.

Dunivin TK, Choi J, Howe A, Shade A.

mSystems. 2019 Feb 26;4(1). pii: e00349-18. doi: 10.1128/mSystems.00349-18. eCollection 2019 Jan-Feb.


No Evidence of Increased Chronic Traumatic Encephalopathy Pathology or Neurodegenerative Proteinopathy in Former Military Service Members: A Preliminary Study.

Tripathy A, Shade A, Erskine B, Bailey K, Grande A, deLong JJ, Perry G, Castellani RJ.

J Alzheimers Dis. 2019;67(4):1277-1289. doi: 10.3233/JAD-181039.


Trait-based community assembly and succession of the infant gut microbiome.

Guittar J, Shade A, Litchman E.

Nat Commun. 2019 Feb 1;10(1):512. doi: 10.1038/s41467-019-08377-w.


Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient.

Sorensen JW, Dunivin TK, Tobin TC, Shade A.

Nat Microbiol. 2019 Jan;4(1):55-61. doi: 10.1038/s41564-018-0276-6. Epub 2018 Nov 5.


Macroecology to Unite All Life, Large and Small.

Shade A, Dunn RR, Blowes SA, Keil P, Bohannan BJM, Herrmann M, Küsel K, Lennon JT, Sanders NJ, Storch D, Chase J.

Trends Ecol Evol. 2018 Oct;33(10):731-744. doi: 10.1016/j.tree.2018.08.005. Epub 2018 Sep 9.


Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession.

Kearns PJ, Shade A.

ISME J. 2018 Nov;12(11):2575-2581. doi: 10.1038/s41396-018-0194-x. Epub 2018 Jun 29. Review.


Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.).

Soltani A, MafiMoghaddam S, Oladzad-Abbasabadi A, Walter K, Kearns PJ, Vasquez-Guzman J, Mamidi S, Lee R, Shade AL, Jacobs JL, Chilivers MI, Lowry DB, McClean P, Osorno JM.

Front Plant Sci. 2018 Jun 6;9:767. doi: 10.3389/fpls.2018.00767. eCollection 2018.


A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class.

Tobin TC, Shade A.

FEMS Microbiol Lett. 2018 May 1;365(10). doi: 10.1093/femsle/fny104.


Understanding Microbiome Stability in a Changing World.

Shade A.

mSystems. 2018 Mar 20;3(2). pii: e00157-17. doi: 10.1128/mSystems.00157-17. eCollection 2018 Mar-Apr.


Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil.

Dunivin TK, Shade A.

FEMS Microbiol Ecol. 2018 Mar 1;94(3). doi: 10.1093/femsec/fiy016.


Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire.

Dunivin TK, Miller J, Shade A.

PLoS One. 2018 Jan 25;13(1):e0191893. doi: 10.1371/journal.pone.0191893. eCollection 2018.


A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites.

Chodkowski JL, Shade A.

mSystems. 2017 Nov 14;2(6). pii: e00129-17. doi: 10.1128/mSystems.00129-17. eCollection 2017 Nov-Dec.


A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.


Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes".

Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD.

mSphere. 2017 Jul 19;2(4). pii: e00296-17. doi: 10.1128/mSphere.00296-17. eCollection 2017 Jul-Aug.


Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.

Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R, McMahon KD.

mSphere. 2017 Jun 28;2(3). pii: e00169-17. doi: 10.1128/mSphere.00169-17. eCollection 2017 May-Jun. Erratum in: mSphere. 2017 Jul 19;2(4):.


Ecological patterns of seed microbiome diversity, transmission, and assembly.

Shade A, Jacques MA, Barret M.

Curr Opin Microbiol. 2017 Jun;37:15-22. doi: 10.1016/j.mib.2017.03.010. Epub 2017 Apr 21. Review.


Corrigendum: Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau.

Zhang K, Shi Y, Jing X, He JS, Sun R, Yang Y, Shade A, Chu H.

Front Microbiol. 2017 Apr 18;8:667. doi: 10.3389/fmicb.2017.00667. eCollection 2017.


Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire.

Lee SH, Sorensen JW, Grady KL, Tobin TC, Shade A.

ISME J. 2017 Jun;11(6):1447-1459. doi: 10.1038/ismej.2017.1. Epub 2017 Mar 10.


Diversity is the question, not the answer.

Shade A.

ISME J. 2017 Jan;11(1):1-6. doi: 10.1038/ismej.2016.118. Epub 2016 Sep 16.


Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau.

Zhang K, Shi Y, Jing X, He JS, Sun R, Yang Y, Shade A, Chu H.

Front Microbiol. 2016 Jun 30;7:1032. doi: 10.3389/fmicb.2016.01032. eCollection 2016. Erratum in: Front Microbiol. 2017 Apr 18;8:667.


Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.

Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR.

ISME J. 2016 Jul;10(7):1589-601. doi: 10.1038/ismej.2015.241. Epub 2016 Jan 8.


Computing Workflows for Biologists: A Roadmap.

Shade A, Teal TK.

PLoS Biol. 2015 Nov 24;13(11):e1002303. doi: 10.1371/journal.pbio.1002303. eCollection 2015.


Temporal patterns of rarity provide a more complete view of microbial diversity.

Shade A, Gilbert JA.

Trends Microbiol. 2015 Jun;23(6):335-40. doi: 10.1016/j.tim.2015.01.007. Epub 2015 Feb 6.


When, where and how does microbial community composition matter?

Nemergut DR, Shade A, Violle C.

Front Microbiol. 2014 Sep 26;5:497. doi: 10.3389/fmicb.2014.00497. eCollection 2014. No abstract available.


Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA.

mBio. 2014 Jul 15;5(4):e01371-14. doi: 10.1128/mBio.01371-14.


The effect of simplified adhesives on the bond strength to dentin of dual-cure resin cements.

Shade AM, Wajdowicz MN, Bailey CW, Vandewalle KS.

Oper Dent. 2014 Nov-Dec;39(6):627-36. doi: 10.2341/13-319-L. Epub 2014 May 7.


Controls on soil microbial community stability under climate change.

de Vries FT, Shade A.

Front Microbiol. 2013 Sep 5;4:265. doi: 10.3389/fmicb.2013.00265. eCollection 2013.


Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil.

Shade A, Klimowicz AK, Spear RN, Linske M, Donato JJ, Hogan CS, McManus PS, Handelsman J.

Appl Environ Microbiol. 2013 Nov;79(21):6617-25. doi: 10.1128/AEM.02017-13. Epub 2013 Aug 23.


A meta-analysis of changes in bacterial and archaeal communities with time.

Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N.

ISME J. 2013 Aug;7(8):1493-506. doi: 10.1038/ismej.2013.54. Epub 2013 Apr 11.


Unexpected diversity during community succession in the apple flower microbiome.

Shade A, McManus PS, Handelsman J.

mBio. 2013 Feb 26;4(2). pii: e00602-12. doi: 10.1128/mBio.00602-12.


Fundamentals of microbial community resistance and resilience.

Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JB, Matulich KL, Schmidt TM, Handelsman J.

Front Microbiol. 2012 Dec 19;3:417. doi: 10.3389/fmicb.2012.00417. eCollection 2012.


Lineage-specific responses of microbial communities to environmental change.

Youngblut ND, Shade A, Read JS, McMahon KD, Whitaker RJ.

Appl Environ Microbiol. 2013 Jan;79(1):39-47. doi: 10.1128/AEM.02226-12. Epub 2012 Oct 12.


Culturing captures members of the soil rare biosphere.

Shade A, Hogan CS, Klimowicz AK, Linske M, McManus PS, Handelsman J.

Environ Microbiol. 2012 Sep;14(9):2247-52. doi: 10.1111/j.1462-2920.2012.02817.x. Epub 2012 Jul 13.


Lake microbial communities are resilient after a whole-ecosystem disturbance.

Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J, Whitaker RJ, Wu CH, McMahon KD.

ISME J. 2012 Dec;6(12):2153-67. doi: 10.1038/ismej.2012.56. Epub 2012 Jun 28.


Characterizing microbial communities through space and time.

Gonzalez A, King A, Robeson MS 2nd, Song S, Shade A, Metcalf JL, Knight R.

Curr Opin Biotechnol. 2012 Jun;23(3):431-6. doi: 10.1016/j.copbio.2011.11.017. Epub 2011 Dec 7. Review.


Beyond the Venn diagram: the hunt for a core microbiome.

Shade A, Handelsman J.

Environ Microbiol. 2012 Jan;14(1):4-12. doi: 10.1111/j.1462-2920.2011.02585.x. Epub 2011 Oct 18. Review.


Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance.

Shade A, Read JS, Welkie DG, Kratz TK, Wu CH, McMahon KD.

Environ Microbiol. 2011 Oct;13(10):2752-67. doi: 10.1111/j.1462-2920.2011.02546.x. Epub 2011 Aug 30.


Our microbial selves: what ecology can teach us.

Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R.

EMBO Rep. 2011 Jul 1;12(8):775-84. doi: 10.1038/embor.2011.137. Review.


Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.

Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R.

Stand Genomic Sci. 2010 Dec 25;3(3):243-8. doi: 10.4056/sigs.1433550.


Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment.

Shade A, Chiu CY, McMahon KD.

Environ Microbiol. 2010 Feb;12(2):455-66. doi: 10.1111/j.1462-2920.2009.02087.x. Epub 2009 Oct 29.


Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics.

Shade A, Chiu CY, McMahon KD.

Microb Ecol. 2010 Apr;59(3):546-54. doi: 10.1007/s00248-009-9589-6. Epub 2009 Sep 18.


Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

Shade A, Carey CC, Kara E, Bertilsson S, McMahon KD, Smith MC.

ISME J. 2009 Aug;3(8):881-8. doi: 10.1038/ismej.2009.56. Epub 2009 May 21. Review.


Temporal dynamics of South End tidal creek (Sapelo Island, Georgia) bacterial communities.

Kara E, Shade A.

Appl Environ Microbiol. 2009 Feb;75(4):1058-64. doi: 10.1128/AEM.01725-08. Epub 2008 Dec 29.


The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics.

Shade A, Jones SE, McMahon KD.

Environ Microbiol. 2008 Apr;10(4):1057-67. doi: 10.1111/j.1462-2920.2007.01527.x. Epub 2008 Jan 23.


Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective.

Jones SE, Shade AL, McMahon KD, Kent AD.

Appl Environ Microbiol. 2007 Jan;73(2):659-62. Epub 2006 Nov 22.

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