Biology @ The University of Miami includes an interactive community of seven 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 interactions between viruses and bacteria in coral microbiomes.

Mueller Lab

We study the molecular mechanisms of plant interactions with symbiotic soil fungi.

Wilson Lab

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

Traylor-Knowles Lab

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

Dallman Lab

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

Rieger Lab

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



Silveira CB, Coutinho FH, Cavalcanti GS, Benler S, Doane MP, Dinsdale EA, Edwards RA, Francini-Filho RB, Thompson CC, Luque A, Rohwer FL, Thompson F (2020) Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics, 21(1):126.

Roach TNF, Little M, Arts MGI, Huckeba J, Haas AF, George EE, Quinn RA, Cobián-Güemes AG, Naliboff DS, Silveira CB, Vermeij MJA, Kelly LW, Dorrestein PC, Rohwer F (2020) A multiomic analysis of in situ coral-turf algal interactions. Proceedings of the National Academy of Sciences of the United States of America, 117(24):13588–13595.

Cortese A, Inherited Neuropathy Consortium, Zhu Y, Rebelo AP, Negri S, Courel S, Abreu L, Bacon CJ, Bai Y, Bis-Brewer DM, Bugiardini E, Buglo E, Danzi MC, Feely SME, Athanasiou-Fragkouli A, Haridy NA, Isasi R, Khan A, Laurà M, Magri S, Pipis M, Pisciotta C, Powell E, Rossor AM, Saveri P, Sowden JE, Tozza S, Vandrovcova J, Dallman J, Grignani E, Marchioni E, Scherer SS, Tang B, Lin Z, Al-Ajmi A, Schüle R, Synofzik M, Maisonobe T, Stojkovic T, Auer-Grumbach M, Abdelhamed MA, Hamed SA, Zhang R, Manganelli F, Santoro L, Taroni F, Pareyson D, Houlden H, Herrmann DN, Reilly MM, Shy ME, Grace Zhai R, Zuchner S (2020) Author Correction: Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes. Nature Genetics, 52(6):640–640.

Müller LM, Campos-Soriano L, Levesque-Tremblay V, Bravo A, Daniels DA, Pathak S, Park H-J, Harrison MJ Constitutive overexpression of RAM1 increases arbuscule density during arbuscular mycorrhizal symbiosis in Brachypodium distachyon.

Walters BM, Connelly MT, Young B, Traylor-Knowles N (2020) The Complicated Evolutionary Diversification of the Mpeg-1/Perforin-2 Family in Cnidarians. Frontiers in immunology, 11:1690.

Connelly MT, McRae CJ, Liu P-J, Traylor-Knowles N (2020) Lipopolysaccharide treatment stimulates Pocillopora coral genotype-specific immune responses but does not alter coral-associated bacteria communities. Developmental and comparative immunology, 109:103717.

Snyder GA, Browne WE, Traylor-Knowles N*, Rosental B* (2020) Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations. Journal of Visualized Experiments, (159) *Co-senior authors

David AS, Thapa-Magar KB, Menges ES, Searcy CA, Afkhami ME (2020) Do plant-microbe interactions support the Stress Gradient Hypothesis? Ecology, 101(8):e03081.

Afkhami ME, Almeida BK, Hernandez DJ, Kiesewetter KN, Revillini DP (2020) Tripartite mutualisms as models for understanding plant–microbial interactions. Current Opinion in Plant Biology, 56:28–36.

Rudgers JA, Afkhami ME, Bell-Dereske L, Anny Chung Y, Crawford KM, Kivlin SN, Mann MA, Nuñez MA (2020) Climate Disruption of Plant-Microbe Interactions. Annual Review of Ecology, Evolution, and Systematics, 51(1)

Carscadden KA, Emery NC, Arnillas CA, Cadotte MW, Afkhami ME, Gravel D, Livingstone SW, Wiens JJ (2020) Niche Breadth: Causes and Consequences for Ecology, Evolution, and Conservation. The Quarterly Review of Biology, 95(3):179–214.

Almeida BK, Garg M, Kubat M, Afkhami ME (2020) Not that kind of tree: Assessing the potential for decision tree-based plant identification using trait databases. Applications in plant sciences, 8(7):e11379.

Hernandez D, Kiesewetter KN, Palakurty S, Stinchcombe JR, Afkhami ME (2020) Synergism and symbioses: unpacking complex mutualistic species interactions using transcriptomic approaches. The Model Legume Medicago truncatula, :1045–1054.

Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK (2020) Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biological reviews of the Cambridge Philosophical Society, 95(2):409–433.

Buglo E, Sarmiento E, Martuscelli NB, Sant DW, Danzi MC, Abrams AJ, Dallman JE, Züchner S (2020) Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease. PloS one, 15(3):e0230566.


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. *Co-senior authors

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.

Silveira CB, Luque A, Roach TN, Villela H, Barno A, Green K, Reyes B, Rubio-Portillo E, Le T, Mead S, Hatay M, Vermeij MJ, Takeshita Y, Haas A, Bailey B, Rohwer F (2019) Biophysical and physiological processes causing oxygen loss from coral reefs. eLife, 8 *Article featured in an eLife Digest.

Müller LM, Harrison MJ (2019) Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis. Current opinion in plant biology, 50:132–139.

Müller LM, Flokova K, Schnabel E, Sun X, Fei Z, Frugoli J, Bouwmeester HJ, Harrison MJ (2019) A CLE–SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza. Nature Plants, 5(9):933–939.

Rosales SM, Miller MW, Williams DE, Traylor-Knowles N, Young B, Serrano XM (2019) Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays. Scientific reports, 9(1):18279.


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.

Floss DS, Gomez SK, Park H-J, MacLean AM, Müller LM, Bhattarai KK, Lévesque-Tremblay V, Maldonado-Mendoza IE, Harrison MJ (2017) A Transcriptional Program for Arbuscule Degeneration during AM Symbiosis Is Regulated by MYB1. Current biology: CB, 27(8):1206–1212.


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]

Mueller – LMM357 [at]

Rieger – srieger [at]

Silveira – cynthiasilveira [at]

Traylor-Knowles – ntraylorknowles [at]

Wilson – acwilson [at]

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