Biology @ The University of Miami includes an interactive community of six symbiosis | microbiome research groups. Our research represents a diverse set of systems and a wide range of approaches.  We share ideas, equipment, resources, lab meetings, and sometimes food!

Come and join us. We’re recruiting!

Our Work

Afkhami Lab

We study mutualisms and plant-microbial interactions at scales ranging from genes to ecosystems.

Silveira Lab

We study the molecular mechanisms and ecosystem outcomes of interactions between bacteriophages and bacteria in coral-associated microbiomes.

Wilson Lab

We work to elucidate the mechanisms of host/endosymbiont integration in insect models.

Dallman Lab

We study how microbes in the gut influence behavior in zebrafish models of autism spectrum disorder.

Traylor-Knowles Lab

We study the interaction between the cnidarian immune system and microbes. 

Rieger Lab

We are studying how nerves and skin cells interact with microbial communities to promote appendage regeneration.



David AS, Quintana-Ascencio PF, Menges ES, Thapa-Magar KB, Afkhami ME, Searcy CA (2019) Soil Microbiomes Underlie Population Persistence of an Endangered Plant Species. The American Naturalist, in press.

Feng H, Edwards N, Anderson CMH, Althaus M, Duncan RP, Hsu Y-C, Luetje CW, Price DRG, Wilson ACC, Thwaites DT (2019) Trading amino acids at the aphid–Buchnera symbiotic interface. Proceedings of the National Academy of Sciences, 116(32):16003–16011.

Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL (2019) Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes. Nature Communications, 10(1):502.

Traylor-Knowles N (2019) Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus. PeerJ, 7:e6510.

Traylor-Knowles N, Vandepas LE, Browne WE (2019) Still enigmatic: innate immunity in the ctenophore Mnemiopsis leidyi. Integrative and comparative biology,

James DM, Kozol RA, Kajiwara Y, Wahl AL, Storrs EC, Buxbaum JD, Klein M, Moshiree B, Dallman JE (2019) Intestinal dysmotility in a zebrafish (Danio rerio) shank3a;shank3b mutant model of autism. Molecular Autism, 10(1)

Mintz KJ, Mercado G, Zhou Y, Ji Y, Hettiarachchi SD, Liyanage PY, Pandey RR, Chusuei CC, Dallman J, Leblanc RM (2019) Tryptophan carbon dots and their ability to cross the blood-brain barrier. Colloids and surfaces. B, Biointerfaces, 176:488–493.


Palakurty SX, Stinchcombe JR, Afkhami ME (2018) Cooperation and coexpression: How coexpression networks shift in response to multiple mutualists. Molecular Ecology, 27(8):1860–1873.

Feng H, Wang L, Wuchty S, Wilson ACC (2018) microRNA regulation in an ancient obligate endosymbiosis. Molecular Ecology, 27(8):1777–1793.

David AS, Thapa-Magar KB, Afkhami ME (2018) Microbial mitigation–exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress. Ecology, 99(3):517–523.

Afkhami ME, Luke Mahler D, Burns JH, Weber MG, Wojciechowski MF, Sprent J, Strauss SY (2018) Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera. Ecology, 99(2):502–502.

Batstone RT, Carscadden KA, Afkhami ME, Frederickson ME (2018) Using niche breadth theory to explain generalization in mutualisms. Ecology, 99(5):1039–1050.

James EB, Feng H, Wilson ACC (2018) mTOR Complex 1 Implicated in Aphid/Buchnera Host/Symbiont Integration. G3, 8(9):3083–3091.

Nakajima R, Haas AF, Silveira CB, Kelly ELA, Smith JE, Sandin S, Kelly LW, Rohwer F, Nakatomi N, Kurihara H (2018) Release of dissolved and particulate organic matter by the soft coral Lobophytum and subsequent microbial degradation. Journal of experimental marine biology and ecology, 504:53–60.

Traylor-Knowles N (2018) In Situ Hybridization Techniques for Paraffin-Embedded Adult Coral Samples. Journal of visualized experiments: JoVE, (138)

Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N (2018) Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Scientific reports, 8(1):16134.

Cirrincione A, Rieger S (2018) Keratinocyte-specific mitochondrial H2O2 formation as possible cause of paclitaxel neurotoxicity. Journal of the peripheral nervous system, 23:389–390.

Waldron AL, Schroder PA, Bourgon KL, Bolduc JK, Miller JL, Pellegrini AD, Dubois AL, Blaszkiewicz M, Townsend KL, Rieger S (2018) Oxidative stress-dependent MMP-13 activity underlies glucose neurotoxicity. Journal of diabetes and its complications, 32(3):249–257.

Zhao H, Pullagura SRN, Rieger S, Lisse TS (2018) Vitamin D and MicroRNAs. Vitamin D, :245–267.

Bedell V, Buglo E, Marcato D, Pylatiuk C, Mikut R, Stegmaier J, Scudder W, Wray M, Züchner S, Strähle U, Peravali R, Dallman JE (2018) Zebrafish: A Pharmacogenetic Model for Anesthesia. Methods in enzymology, 602:189–209.


Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, Munster M van, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, Oosterhout C van, Swarbreck D, Hogenhout SA (2017) Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, 18(1):27.

Silveira CB, Cavalcanti GS, Walter JM, Silva-Lima AW, Dinsdale EA, Bourne DG, Thompson CC, Thompson FL (2017) Microbial processes driving coral reef organic carbon flow. FEMS microbiology reviews, 41(4):575–595.

Silveira CB, Gregoracci GB, Coutinho FH, Silva GGZ, Haggerty JM, Oliveira LS de, Cabral AS, Rezende CE, Thompson CC, Francini-Filho RB, Edwards RA, Dinsdale EA, Thompson FL (2017) Bacterial Community Associated with the Reef Coral Mussismilia braziliensis’s Momentum Boundary Layer over a Diel Cycle. Frontiers in microbiology, 8:784.

Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL (2017) Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nature communications, 8:15955.5.

Knowles B, Bailey B, Boling L, Breitbart M, Cobián-Güemes A, Del Campo J, Edwards R, Felts B, Grasis J, Haas AF, Katira P, Kelly LW, Luque A, Nulton J, Paul L, Peters G, Robinett N, Sandin S, Segall A, Silveira C, Youle M, Rohwer F (2017) Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature microbiology, 2:17064.

Traylor-Knowles N, Rose NH, Palumbi SR (2017) The cell specificity of gene expression in the response to heat stress in corals. The Journal of experimental biology, 220(Pt 10):1837–1845.

Traylor-Knowles N, Rose NH, Sheets EA, Palumbi SR (2017) Early Transcriptional Responses during Heat Stress in the Coral Acropora hyacinthus. The Biological bulletin, 232(2):91–100.

Rosental B, Kozhekbaeva Z, Fernhoff N, Tsai JM, Traylor-Knowles N (2017) Coral cell separation and isolation by fluorescence-activated cell sorting (FACS). BMC cell biology, 18(1):30.

Traylor-Knowles N, Connelly MT (2017) What Is Currently Known About the Effects of Climate Change on the Coral Immune Response. Current Climate Change Reports, 3(4):252–260.

Grover H, Rieger S (2017) Reactive oxygen species and neuroepithelial interactions during wound healing. Regenerative Engineering and Developmental Biology, :23–38.

Lisse TS, Rieger S (2017) IKKα regulates human keratinocyte migration through surveillance of the redox environment. Journal of cell science, 130(5):975–988.

Yan Q, Zhai L, Zhang B, Dallman JE (2017) Spatial patterning of excitatory and inhibitory neuropil territories during spinal circuit development. The Journal of comparative neurology, 525(7):1649–1667.

Hung CY, Volkmar B, Baker JD, Bauer JW, Gussoni E, Hainzl S, Klausegger A, Lorenzo J, Mihalek I, Rittinger O, Tekin M, Dallman JE, Bodamer OA (2017) A defect in the inner kinetochore protein CENPT causes a new syndrome of severe growth failure. PloS one, 12(12):e0189324.


Afkhami ME, Stinchcombe JR (2016) Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi. Molecular ecology, 25(19):4946–4962.

Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobián-Güemes AG, Coutinho FH, Dinsdale EA, Felts B, Furby KA, George EE, Green KT, Gregoracci GB, Haas AF, Haggerty JM, Hester ER, Hisakawa N, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, Oliveira LS de, Quistad SD, Robinett NL, Sala E, Salamon P, Sanchez SE, Sandin S, Silva GGZ, Smith J, Sullivan C, Thompson C, Vermeij MJA, Youle M, Young C, Zgliczynski B, Brainard R, Edwards RA, Nulton J, Thompson F, Rohwer F (2016) Corrigendum: Lytic to temperate switching of viral communities. Nature, 539(7627):123.

Silveira CB, Rohwer FL (2016) Piggyback-the-Winner in host-associated microbial communities. npj Biofilms and Microbiomes, 2(1)

Lu H-L, Chang C-C, Wilson ACC (2016) Amino acid transporters implicated in endocytosis of Buchnera during symbiont transmission in the pea aphid. EvoDevo, 7:24.

Duncan RP, Feng H, Nguyen DM, Wilson ACC (2016) Gene Family Expansions in Aphids Maintained by Endosymbiotic and Nonsymbiotic Traits. Genome biology and evolution, 8(3):753–764.

Lu H-L, Price DRG, Wikramanayake A, Chang C-C, Wilson ACC (2016) Ontogenetic differences in localization of glutamine transporter ApGLNT1 in the pea aphid demonstrate that mechanisms of host/symbiont integration are not similar in the maternal versus embryonic bacteriome. EvoDevo, 7(1):1.

Afkhami ME, Strauss SY (2016) Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales. Ecology, 97(5):1159–1169.

Haas AF, Fairoz MFM, Kelly LW, Nelson CE, Dinsdale EA, Edwards RA, Giles S, Hatay M, Hisakawa N, Knowles B, Lim YW, Maughan H, Pantos O, Roach TNF, Sanchez SE, Silveira CB, Sandin S, Smith JE, Rohwer F (2016) Global microbialization of coral reefs. Nature Microbiology, 1(6)

Somera TM, Bailey B, Barott K, Grasis J, Hatay M, Hilton BJ, Hisakawa N, Nosrat B, Nulton J, Silveira CB, Sullivan C, Brainard RE, Rohwer F (2016) Energetic differences between bacterioplankton trophic groups and coral reef resistance. Proceedings of the Royal Society B: Biological Sciences, 283(1829):20160467.

Quistad SD, Traylor-Knowles N (2016) Precambrian origins of the TNFR superfamily. Cell death discovery, 2:16058.

Traylor-Knowles N (2016) Distinctive wound-healing characteristics in the corals Pocillopora damicornis and Acropora hyacinthus found in two different temperature regimes. Marine biology, 163(11):231.

Zhao H, Rieger S, Abe K, Hewison M, Lisse TS (2016) DNA Damage-Inducible Transcript 4 Is an Innate Surveillant of Hair Follicular Stress in Vitamin D Receptor Knockout Mice and a Regulator of Wound Re-Epithelialization. International journal of molecular sciences, 17(12)

Lisse TS, Middleton LJ, Pellegrini AD, Martin PB, Spaulding EL, Lopes O, Brochu EA, Carter EV, Waldron A, Rieger S (2016) Paclitaxel-induced epithelial damage and ectopic MMP-13 expression promotes neurotoxicity in zebrafish. Proceedings of the National Academy of Sciences of the United States of America, 113(15):E2189–98.

Lisse TS, King BL, Rieger S (2016) Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing. Scientific Reports, 6(1)

Coffman JA, Rieger S, Rogers AN, Updike DL, Yin VP (2016) Comparative biology of tissue repair, regeneration and aging. Npj Regenerative Medicine, 1:16003.

Rebelo AP, Abrams AJ, Cottenie E, Horga A, Gonzalez M, Bis DM, Sanchez-Mejias A, Pinto M, Buglo E, Markel K, Prince J, Laura M, Houlden H, Blake J, Woodward C, Sweeney MG, Holton JL, Hanna M, Dallman JE, Auer-Grumbach M, Reilly MM, Zuchner S (2016) Cryptic Amyloidogenic Elements in the 3′ UTRs of Neurofilament Genes Trigger Axonal Neuropathy. American journal of human genetics, 98(4):597–614.

Kozol RA, Abrams AJ, James DM, Buglo E, Yan Q, Dallman JE (2016) Function Over Form: Modeling Groups of Inherited Neurological Conditions in Zebrafish. Frontiers in molecular neuroscience, 9:55.

Li S, Skromne I, Peng Z, Dallman J, Al-Youbi AO, Bashammakh AS, El-Shahawi MS, Leblanc RM (2016) “Dark” carbon dots specifically “light-up” calcified zebrafish bones. Journal of Materials Chemistry B, 4(46):7398–7405.

Prince JS, Dallman J, Miyazaki S, Wen R (2016) Ultrastructural Analysis of Zebra Fish (Daniorerio) DHDDS Retinitis Pigmentosa Disease Model Functionally Links DHDDS to Mitochondrial and Membrane Dysfunction. American International Journal of Biology, 4(2)


Afkhami – michelle.afkhami [at]

Dallman – j.dallman [at]

Rieger – srieger [at]

Silveira – cynthiasilveira [at]

Traylor-Knowles – ntraylorknowles [at]

Wilson – acwilson [at]

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