Amanda M.V. Brown

Research Interests

Dr. Brown's lab explores how innovation emerges from microbial symbiosis, using high throughput genome and transcriptome sequencing, bioinformatics, population and comparative genomics, confocal microscopy, phylogenomics, and microevolutionary analysis.

The lab examines several systems, with a focus on agriculture and disease: (1) bacteria in plant-parasitic nematodes (2) bacteria in hemipteran insects (3) multi-trophic communities in the rhizosphere (involving plants, plant-pests, fungi, viruses, and bacteria) (4) beneficial microbes associated with plant and tree leaves, and (5) other microbes associated with humans and mosquitos.

This work centers on “big data" analysis, and includes shotgun metagenomics, de novo assembly, annotation, comparative pathway enrichment analysis, and detection of selection. Her research also extends to software development to implement algorithms to aid in biological discovery from these complex datasets.

Why?

Microbes are ubiquitous, occurring in every habitat on earth. Stable, mutually beneficial interactions have evolved in all major groups across the tree of life. Microbe-host interactions have evolved to serve biochemically fundamental processes independently many times. Examples include organelles such as mitochondria and chloroplasts, obligate intracellular endosymbionts such as bacteria within insect bacteriomes, and beneficial microbes that make up the human microbiome.

Despite the importance of host-associated microbes, key questions remain unanswered. Using cutting-edge techniques, Dr. Brown's lab investigates the following questions:

Origins?   How do microbial partnerships originate and what is the role of horizontal gene transfer?

Maintenance?   How are microbial partnerships maintained in the face of evolutionary and ecological pressure? How do host and microbe regulate their biochemical interactions?

Disruption?   How can disruption of these partnerships lead to species invasions, or disease outbreaks? What do models predict about stability of microbial mutualism?

Complexity?   What are the costs of complexity and opposing selection at different levels, and how do hosts and microbes overcome this?

Impact?   What role do microbial partnerships have in the evolution of adaptive innovation, disease resistance, biomass production, and ecosystem stability?

Articles Submitted or In Review:

2022 Weyandt N, Aghdam SA, Brown AMV. Discovery of early-branching Wolbachia reveals functional enrichment on horizontally transferred genes. Frontiers in Microbiology published Apr. 25. https://www.frontiersin.org/articles/10.3389/fmicb.2022.867392/full

2021 Hill BM, Bisht K, Atkins GR, Gomez AA, RumbaughKP, WakemanCA, BrownAMV. Lysis-Hi-C as a method to study polymicrobial communities and eDNA. Molecular Ecology Resources 22(3):1029-1042. https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13535
                                 
2021 Salazar MM, Pupo MT, Brown AMV. Co-occurrence of viruses, plant pathogens, and symbionts in an underexplored hemipteran clade.  Frontiers in Cellular and Infection Microbiology 11:715998. https://www.frontiersin.org/articles/10.3389/fcimb.2021.715998/full

2021 Ivanova M, Oh B, Khan IUH, Nightingale K, Bugarel M, Brown AMV, Loneragan GH. Draft genome assemblies of two Campylobacter novaezeelandiae and four unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water. Microbiology Resource Announcements 10(17): e00249-21. https://journals.asm.org/doi/full/10.1128/MRA.00249-21

2021 Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. Environmental Microbiome 16:6. https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-021-00375-0

2021 Myers KN, Conn D, Brown AMV. Essential amino acid enrichment and positive selection highlight endosymbiont's role in a global virus-vectoring pest. mSystems 6: e01048-20. https://journals.asm.org/doi/full/10.1128/mSystems.01048-20

2019 Wasala SK, Brown AMV, Kang J, Howe DK, Peetz AB, Zasada IA, Denver DR. Variable abundance and distribution of Wolbachia and Cardinium endosymbionts in plant-parasitic nematode field populations. Frontiers in Microbiology 10:964. https://www.frontiersin.org/articles/10.3389/fmicb.2019.00964/full

2018 Howe DK, Smith M, Tom D, Brown AMV, Peetz AB, Zasada IA, Denver DR. Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates. Nematology 21(5): 533–546. https://brill.com/view/journals/nemy/21/5/article-p533_9.xml

2018 BrownAMV, WasalaSK, HoweDK, PeetzAB, ZasadaIA, Denver DR. Comparative genomics ofWolbachia-Cardinium dual endosymbiosis in a plant-parasitic nematode. Frontiers in Microbiology 9:2482. https://www.frontiersin.org/articles/10.3389/fmicb.2018.02482/full

2018 Brown AMV. Endosymbionts of plant-parasitic nematodes. Annual Review of Phytopathology 56:225-242. https://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-080417-045824?journalCode=phyto

2017 Phillips WS, Howe DK, Brown AMV, Eves-van Den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA. The draft genome of Globodera ellingtonae. Journal of Nematology 42(2):127-128. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507130/

2016 Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Scientific Reports 6: 34955. https://www.nature.com/articles/srep34955

2016 Phillips WS, Brown AMV, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 17:706. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3047-x

2016 Denver DR, Brown AMV, Howe DK, Peetz AB, Zasada IA. Genome skimming: a rapid approach to gaining diverse biological insights into multicellular pathogens. PLoS Pathogens 12(8): e1005713. https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005713

2015 Brown AMV, Howe DK, Peetz AB, Wasala SK, Zasada IA, Denver DR. Comparative genomics of an endosymbiont in a plant-parasitic nematode suggest a role in nutritional symbiosis.Genome Biology & Evolution 7(9):2727-2746. https://academic.oup.com/gbe/article/7/9/2727/592822

2014 Brown AMV, Huynh LY, Bolender CM, Nelson KG, McCutcheon JP. Population genomics of a symbiont in the early stages of a pest invasion. (Invited article for Nature's Microbiome). Molecular Ecology 23:1516-1530. https://onlinelibrary.wiley.com/doi/full/10.1111/mec.12366?casa_token=qgo_GQeeF-UAAAAA%3A0b2z_THIWKw0FgES_sNY7a0rR46J-ci4XpswIArSgmSr1om9KzNE7MXcufbJQsTc2a2Yz6xs7WBLGg

2014 Brown AMV.  Microevolution of insect-bacterial mutualists: a population genomics perspective. In Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Pontarotti, P. (ed.). Springer International, Switzerland p. 247-259. https://link.springer.com/chapter/10.1007/978-3-319-07623-2_12

2010 Brown AMV, Kent ML, Adamson ML. Description of five new Loma (Microsporidia) species in pacific fishes with redesignation of the type species Loma morhua Morrison & Sprague, 1981, based on morphological and molecular species-boundaries tests. Journal of Eukaryotic Microbiology 57(6): 529-553. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1550-7408.2010.00508.x?casa_token=8hxEptCon8gAAAAA%3AZfKSgRJXfVoMmESsVSNhvzDOJTZlUdSj7YgZe7mGPNpbiRlF1kdlYSIXEYLL0880RH2R9VZvOHYopQ

2010 Brown AMV, Kent ML, Adamson ML. Low genetic variation in the salmon and trout parasite Loma salmonae (Microsporidia) supports marine transmission and clarifies species boundaries. Diseases of Aquatic Organisms 91(1): 35-46. https://www.int-res.com/abstracts/dao/v91/n1/p35-46/

2008 Lee R, Williams BAP, Brown AMV, Adamson ML, Keeling PJ, Fast NM. Alpha and beta-tubulin phylogenies support a close relationship between the microsporidia Brachiola algerae and Antonospora locustae.Journal of Eukaryotic Microbiology 55(5): 388-392. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1550-7408.2008.00348.x?casa_token=JCQ9W5BSgQAAAAAA%3AeRgL9Z7ONJzDxZUDB-0fHvXetG0BmxCyqVwUDkFKsLN-9bxe6_sp1uZLrZBCkY1keSpKZ-1zULTzqw

2006 Brown AMV, Adamson ML. Phylogenetic distance of Thelohania butleri Johnston, Vernick and Sprague, 1978 (Microsporidia; Thelohaniidae), a parasite of the smooth pink shrimp Pandalus jordani, from its congeners suggests need for major revision of the genus Thelohania Henneguy, 1892. Journal of Eukaryotic Microbiology 53(6): 445-455. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1550-7408.2006.00128.x?casa_token=ZJnHCbBT8usAAAAA%3AKWxscDguzDiENciEsPdX45PRu2ih-gLNvk5jZtT1dk_34v2tzJdsX_EkyUsSa-rZ1lFvSf64JrdQ_A

2002 Brown AMV, Kent ML.  Molecular diagnostics for Loma salmonae and Nucleospora salmonis (Microsporidia) In Molecular diagnostics of salmonid diseases. Cunningham, C. O. (ed.). Kluwer Academic Publishers, Dordrecht p. 267-283. https://link.springer.com/chapter/10.1007/978-94-017-2315-2_10

2001 Matthews JL, Brown AM, Larison K, Bishop-Stewart JK, Kent ML. Pseudoloma neurophilia n. g., n. sp., a new microsporidium from the central nervous system of the zebrafish (Danio rerio). Journal of Eukaryotic Microbiology 48(2): 227-233. PMID:12095112 https://onlinelibrary.wiley.com/doi/full/10.1111/j.1550-7408.2001.tb00307.x?casa_token=czoXOcuR62oAAAAA%3AQFn6UZOIzVpAu1HoVguKOhMsxem9hRtvVSE7f36Vegd4ziKnaYDRo_aUwCID_AeJJFK07jptlrEBgA

2000 Shaw RW, Kent ML, Brown AMV, Whipps CM, Adamson ML. Experimental and natural host specificity of Loma salmonae (Microsporidia). Diseases of Aquatic Organisms 40(2): 131-136. https://www.int-res.com/abstracts/dao/v40/n2/p131-136/

1997 Shaw RW, Kent ML, Docker MF, Brown AMV, Devlin RH, Adamson ML. A new species of Loma (Microsporea) in shiner perch (Cymatogaster aggregata). Journal of Parasitology 83(2): 296-301. https://www.jstor.org/stable/3284459?casa_token=PNyS0a1RHIwAAAAA%3A2m5Zo5QXEK0fOHjWYgJB61ojNGrFYf_NCJxv7l69O4vsn72oJzWJ9-fVf9oUt_PJPddRDlrPQWU2awTr3yQjFzyp7pw8GVNsX2SeQ-ITEwsbXH9BUQ&seq=1#metadata_info_tab_contents  

Selected Talks

2016       Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Evolutionary genomics of an ancestral Wolbachia from plant-parasitic nematodes. Jun 28-Jul 3, Lamington Park, Queensland, Australia.

2016       Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Evolutionary genomics of rhizosphere endosymbionts: getting to the root of it. Yosemite Symbiosis Workshop, May 6-8. Wawona, Yosemite National Park, CA.

2015      Invited speaker  Brown AMV, Howe DK, Peetz AB, Phillips WS, Zasada IA, Denver DR. Genome skimming: novel insights into plant-parasitic nematode genomics and potential avenues for management. Symposium: Building Applied and Genomic Nematology Partnerships, Society of Nematologists Meetings, Jul 19-24, 2015, East Lansing, MI.

2015       Brown AMV, Dettwyler L, Wernick RI, Denver DR. DeNAngler: a DNA untangling algorithm for mixed strain de novo assembly. Spring Conference of the Center for Genomics and Biocomputing, Oregon State University.

2014      Invited speaker  Brown AMV, Huynh LY, McCutcheon JP. Population genomic and transcriptomic insights into symbiont adaptation during a rapid insect invasion. Horizons in the Field of Symbiosis Member Symposium, Entomological Society of America Meetings, Nov 15-19, 2014, Portland, OR.

2013      Invited speaker  Brown AMV, McCutcheon JP. Microevolution of insect-bacterial mutualists: a population genomics perspective. 17th Evolutionary Biology Meeting at Marseilles, September 17-20, 2013, Marseille, France.

2008      Invited speaker  Brown AMV. Pondering parasitism: meaning out of madness in the microsporidia. Invited talk to faculty at the Hawaiian Institute of Marine Biology (HIMB), University of Hawaii.

2008       Invited speaker  Brown AMV. Meaning out of madness in the microsporidia. Invited talk to the Integrative Graduate Education and Research Traineeship (IGERT) group, University of Hawaii.