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Use and abuse of correlation analyses in microbial ecology.

Carr A, Diener C, Baliga NS, Gibbons SM.

ISME J. 2019 Jun 28. doi: 10.1038/s41396-019-0459-z. [Epub ahead of print] Review.


Defining Microbiome Health through a Host Lens.

Gibbons SM.

mSystems. 2019 May 14;4(3). pii: e00155-19. doi: 10.1128/mSystems.00155-19.


Adaptive Evolution within Gut Microbiomes of Healthy People.

Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ.

Cell Host Microbe. 2019 May 8;25(5):656-667.e8. doi: 10.1016/j.chom.2019.03.007. Epub 2019 Apr 23.


The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities.

Rocca JD, Simonin M, Blaszczak JR, Ernakovich JG, Gibbons SM, Midani FS, Washburne AD.

Front Microbiol. 2019 Jan 10;9:3272. doi: 10.3389/fmicb.2018.03272. eCollection 2018.


Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort.

Gurry T; HST Microbiome Consortium*, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ.

Sci Rep. 2018 Aug 23;8(1):12699. doi: 10.1038/s41598-018-30783-1.


Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.

Kearney SM, Gibbons SM, Erdman SE, Alm EJ.

Cell Rep. 2018 Aug 14;24(7):1842-1851. doi: 10.1016/j.celrep.2018.07.032.


Systems biology approaches towards predictive microbial ecology.

Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS.

Environ Microbiol. 2018 Dec;20(12):4197-4209. doi: 10.1111/1462-2920.14378. Epub 2018 Oct 19.


Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota.

Kearney SM, Gibbons SM, Poyet M, Gurry T, Bullock K, Allegretti JR, Clish CB, Alm EJ.

ISME J. 2018 Oct;12(10):2403-2416. doi: 10.1038/s41396-018-0192-z. Epub 2018 Jun 13.


Correcting for batch effects in case-control microbiome studies.

Gibbons SM, Duvallet C, Alm EJ.

PLoS Comput Biol. 2018 Apr 23;14(4):e1006102. doi: 10.1371/journal.pcbi.1006102. eCollection 2018 Apr.


Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.

Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ.

Nat Commun. 2017 Dec 5;8(1):1784. doi: 10.1038/s41467-017-01973-8.


Designing synbiotics for improved human health.

Kearney SM, Gibbons SM.

Microb Biotechnol. 2018 Jan;11(1):141-144. doi: 10.1111/1751-7915.12885. Epub 2017 Dec 4. No abstract available.


Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment.

Pakpour S, Bhanvadia A, Zhu R, Amarnani A, Gibbons SM, Gurry T, Alm EJ, Martello LA.

Microbiome. 2017 Nov 13;5(1):148. doi: 10.1186/s40168-017-0368-1.


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.


Microbial community ecology: Function over phylogeny.

Gibbons SM.

Nat Ecol Evol. 2017 Jan 4;1(1):32. doi: 10.1038/s41559-016-0032. No abstract available.


Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.

mSystems. 2017 Jun 20;2(3). pii: e00016-17. doi: 10.1128/mSystems.00016-17. eCollection 2017 May-Jun.


Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.

Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA.

mSystems. 2017 Mar 7;2(2). pii: e00178-16. doi: 10.1128/mSystems.00178-16. eCollection 2017 Mar-Apr.


Two dynamic regimes in the human gut microbiome.

Gibbons SM, Kearney SM, Smillie CS, Alm EJ.

PLoS Comput Biol. 2017 Feb 21;13(2):e1005364. doi: 10.1371/journal.pcbi.1005364. eCollection 2017 Feb.


Metapopulation theory provides new insight into microbial biogeography.

Gibbons SM.

Environ Microbiol. 2017 Mar;19(3):849-850. doi: 10.1111/1462-2920.13702. Epub 2017 Mar 6. No abstract available.


Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.

Gibbons SM, Scholz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML.

MBio. 2016 Dec 20;7(6). pii: e01372-16. doi: 10.1128/mBio.01372-16.


The Built Environment Is a Microbial Wasteland.

Gibbons SM.

mSystems. 2016 Apr 19;1(2). pii: e00033-16. eCollection 2016 Mar-Apr.


Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau.

Xiang X, Gibbons SM, He JS, Wang C, He D, Li Q, Ni Y, Chu H.

PeerJ. 2016 Jul 12;4:e2226. doi: 10.7717/peerj.2226. eCollection 2016.


Spatial scale drives patterns in soil bacterial diversity.

O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA.

Environ Microbiol. 2016 Jun;18(6):2039-51. doi: 10.1111/1462-2920.13231. Epub 2016 Mar 21.


Microbial diversity--exploration of natural ecosystems and microbiomes.

Gibbons SM, Gilbert JA.

Curr Opin Genet Dev. 2015 Dec;35:66-72. doi: 10.1016/j.gde.2015.10.003. Epub 2015 Nov 18. Review.


Characterization of the salivary microbiome in patients with pancreatic cancer.

Torres PJ, Fletcher EM, Gibbons SM, Bouvet M, Doran KS, Kelley ST.

PeerJ. 2015 Nov 5;3:e1373. doi: 10.7717/peerj.1373. eCollection 2015.


The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis.

Fuller M, Priyadarshini M, Gibbons SM, Angueira AR, Brodsky M, Hayes MG, Kovatcheva-Datchary P, Bäckhed F, Gilbert JA, Lowe WL Jr, Layden BT.

Am J Physiol Endocrinol Metab. 2015 Nov 15;309(10):E840-51. doi: 10.1152/ajpendo.00171.2015. Epub 2015 Sep 22.


Athletic equipment microbiota are shaped by interactions with human skin.

Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT.

Microbiome. 2015 Jun 19;3:25. doi: 10.1186/s40168-015-0088-3. eCollection 2015.


Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management.

Van Bonn W, LaPointe A, Gibbons SM, Frazier A, Hampton-Marcell J, Gilbert J.

Zoo Biol. 2015 Jul-Aug;34(4):360-7. doi: 10.1002/zoo.21220. Epub 2015 May 28.


Forensic analysis of the microbiome of phones and shoes.

Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA.

Microbiome. 2015 May 12;3:21. doi: 10.1186/s40168-015-0082-9. eCollection 2015.


Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.

Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB.

Cell Host Microbe. 2015 May 13;17(5):681-9. doi: 10.1016/j.chom.2015.03.006. Epub 2015 Apr 16.


Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber.

Vitaglione P, Mennella I, Ferracane R, Rivellese AA, Giacco R, Ercolini D, Gibbons SM, La Storia A, Gilbert JA, Jonnalagadda S, Thielecke F, Gallo MA, Scalfi L, Fogliano V.

Am J Clin Nutr. 2015 Feb;101(2):251-61. doi: 10.3945/ajcn.114.088120. Epub 2014 Dec 3.


Bone-specific alkaline phosphatase by immunoassay or electrophoresis: their use in clinical practice.

Ahmed F, Gibbons SM.

J Clin Pathol. 2015 Mar;68(3):246-8. doi: 10.1136/jclinpath-2014-202766. Epub 2014 Dec 24. Erratum in: J Clin Pathol. 2015 Jul;68(7):e2.


Ecological succession and viability of human-associated microbiota on restroom surfaces.

Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST.

Appl Environ Microbiol. 2015 Jan;81(2):765-73. doi: 10.1128/AEM.03117-14. Epub 2014 Nov 14.


The role of macrobiota in structuring microbial communities along rocky shores.

Pfister CA, Gilbert JA, Gibbons SM.

PeerJ. 2014 Oct 16;2:e631. doi: 10.7717/peerj.631. eCollection 2014.


Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.


Longitudinal analysis of microbial interaction between humans and the indoor environment.

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA.

Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.


Understanding cultivar-specificity and soil determinants of the cannabis microbiome.

Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA, Hartsel JA, Kennedy SJ, Gibbons SM.

PLoS One. 2014 Jun 16;9(6):e99641. doi: 10.1371/journal.pone.0099641. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e107415. Hartsel, Josh [corrected to Hartsel, Joshua A].


Human and environmental impacts on river sediment microbial communities.

Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA.

PLoS One. 2014 May 19;9(5):e97435. doi: 10.1371/journal.pone.0097435. eCollection 2014.


Chylothorax diagnosis: can the clinical chemistry laboratory do more?

Gibbons SM, Ahmed F.

Ann Clin Biochem. 2015 Jan;52(Pt 1):173-6. doi: 10.1177/0004563214530677. Epub 2014 Apr 8.


Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns?

Lekberg Y, Gibbons SM, Rosendahl S.

New Phytol. 2014 Jun;202(4):1101-4. doi: 10.1111/nph.12758. Epub 2014 Feb 27. No abstract available.


Characterizing changes in soil bacterial community structure in response to short-term warming.

Xiong J, Sun H, Peng F, Zhang H, Xue X, Gibbons SM, Gilbert JA, Chu H.

FEMS Microbiol Ecol. 2014 Aug;89(2):281-92. doi: 10.1111/1574-6941.12289. Epub 2014 Feb 18.


Investigating the impact of storage conditions on microbial community composition in soil samples.

Rubin BE, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA.

PLoS One. 2013 Jul 31;8(7):e70460. doi: 10.1371/journal.pone.0070460. Print 2013.


Heavy metal tolerance genes alter cellular thermodynamics in Pseudomonas putida and river Pseudomonas spp. and influence amebal predation.

McTee MR, Gibbons SM, Feris K, Gordon NS, Gannon JE, Ramsey PW.

FEMS Microbiol Lett. 2013 Oct;347(2):97-106. doi: 10.1111/1574-6968.12226. Epub 2013 Aug 14.


Evidence for a persistent microbial seed bank throughout the global ocean.

Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA.

Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4651-5. doi: 10.1073/pnas.1217767110. Epub 2013 Mar 4.


Severe plant invasions can increase mycorrhizal fungal abundance and diversity.

Lekberg Y, Gibbons SM, Rosendahl S, Ramsey PW.

ISME J. 2013 Jul;7(7):1424-33. doi: 10.1038/ismej.2013.41. Epub 2013 Mar 14.


Modeling microbial community structure and functional diversity across time and space.

Larsen PE, Gibbons SM, Gilbert JA.

FEMS Microbiol Lett. 2012 Jul;332(2):91-8. doi: 10.1111/j.1574-6968.2012.02588.x. Epub 2012 May 28. Review.


Use of microcalorimetry to determine the costs and benefits to Pseudomonas putida strain KT2440 of harboring cadmium efflux genes.

Gibbons SM, Feris K, McGuirl MA, Morales SE, Hynninen A, Ramsey PW, Gannon JE.

Appl Environ Microbiol. 2011 Jan;77(1):108-13. doi: 10.1128/AEM.01187-10. Epub 2010 Nov 5.


Hyporheic microbial community development is a sensitive indicator of metal contamination.

Feris KP, Ramsey PW, Gibbons SM, Frazar C, Rillig MC, Moore JN, Gannon JE, Holben WE.

Environ Sci Technol. 2009 Aug 15;43(16):6158-63.


Regulating biobanks: a twelve-point typological tool.

Gibbons SM.

Med Law Rev. 2009 Autumn;17(3):313-46. doi: 10.1093/medlaw/fwp016. Epub 2009 Aug 11. No abstract available.



Gibbons SM, Kaye J.

Kings Law J. 2007;18(2):ukpmcpa1468.


Adaptation to altitude as a vehicle for experiential learning of physiology by university undergraduates.

Weigle DS, Buben A, Burke CC, Carroll ND, Cook BM, Davis BS, Dubowitz G, Fisher RE, Freeman TC, Gibbons SM, Hansen HA, Heys KA, Hopkins B, Jordan BL, McElwain KL, Powell FL, Reinhart KE, Robbins CD, Summers CC, Walker JD, Weber SS, Weinheimer CJ.

Adv Physiol Educ. 2007 Sep;31(3):270-8.

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