NSF Dimensions of Diversity Program Grant

The Animal Host as an Engine of Microbial Diversity


    NSF Dimensions of Diversity

The Investigators

  • PI Angela Douglas,
    Cornell University
  • coPI John Jaenike,
    University of Rochester
  • coPI Greg Loeb,
    Cornell University

Our Questions

  1. The relationship between the taxonomic and functional diversity of microbial communities
    • Can we predict functional traits from taxonomy?
    • How great is the functional redundancy among members of the community?
  2. The significance of mutualistic interactions in promoting taxonomic and functional diversity
    • How animal-microbial interactions create new niches for both partners: to exploit
    • How associations promote evolutionary diversification resources underutilized by other taxa, to escape from predators and pathogens etc.
  • Our System

    The associations of drosophilid flies with gut-borne and inherited microorganisms provide a unique opportunity to investigate how animal-microbial interactions shape the taxonomic and functional diversity of the animal partner and its microbial associates over ecological and evolutionary timescales. We leverage the genomic resources of Drosophila and its microbial partners to integrate the three dimensions of diversity – genetic, taxonomic and functional.

  • A) D. melanogaster ♀/♂
    B) D. simulans ♀/♂
    C) D. sechellia ♀/♂
    D) D. yakuba ♀/♂
    E) D. santomea ♀/♂
    F) D. ananassae ♀/♂
    G) D. pseudoobscura ♀/♂
    H) D. persimilis ♀/♂
    I) D. willistonii ♀/♂

Our Goals

In our system (and any system involving animals), biological diversity has a nested structure and the underlying processes are interactive.

  • AIM 1

    Relationship between taxonomic and functional diversity of the bacterial community

  • AIM 2

    Relationship between functional traits of the host and the taxonomy & function of the bacteria

  • AIM 3

    Taxanomic & functional response of bacteria and host functional response to manipulation of diet, host/gut bacterial association and inherited symbionts

  • AIM 4

    Impact of interactions between bacterial community and host on ecologically-important traits of host

The People

Postdoctoral Researchers

  • Alyssa Bost
  • Vince Martinson
  • Soren Franzenburg

Technical Support

  • Stephen Hesler
  • Gabrielle Brind’Amour
  • Yuan Luo

Undergraduate Researchers

  • Sam Hernandez
  • Alice Albasi
  • Nathan Winans

Publications Supported by this Grant

Adair KL, Wilson M, Bost A and Douglas AE, 2009-2024. Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster. ISME Journal 12: 959-972.
Douglas AE, 2009-2024. What will it take to understand the ecology of symbiotic microorganisms? Environmental Microbiology. Epub 3April.
Inamine H, Ellner SP, Newell PD, Luo Y, Buchon N and Douglas AE, in press. Spatio-temporally heterogeneous population dynamics of gut bacteria inferred from fecal time-series data. mBio 9: e01453-17.
Bost A, Franzenburg S, Adair KL, Martinson VG, Loeb G and Douglas AE, 2017. How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota. Molecular Ecology Epub Nov 7.
Winans NJ, Walter A, Chouaia B, Chaston JC, Douglas AE and Newell PD, 2017. A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria. Molecular Ecology, in press.
Martinson VG, Douglas AE and Jaenike J, 2017. Community structure of gut microbiota within and among sympatric species of wild Drosophila. Ecology Letters 20: 629-39.
Adair KL and Douglas AE, 2016. Making a microbiome: The many determinants of host-associated microbial community composition. Current Opinion in Microbiology 35: 23-29.
Douglas AE and Werren JH, 2016. Holes in the hologenome: why host-microbial symbioses are not holobionts. mBio 7: e02099-15.
Wong A*, Luo Y*, Jing X, Franzenburg S, Bost A and Douglas AE, 2015. The host as driver of the microbiota in the gut and external environment of Drosophila melanogaster. Applied and Environmental Microbiology 81: 6232-6240.
Douglas AE, 2014. The molecular basis of bacterial-insect symbiosis. Journal of Molecular Biology, 23: 3830-7.
Douglas AE, 2013. Microbial brokers of insect-plant interactions revisited. Journal of Chemical Ecology 39, 952-61.

Conference Presentations

August 2017: Karen Adair is an invited speaker at the Annual Meeting of the Ecological Society of America 2017, in the symposium “The Extended Phenotype of Microbial Communities: When and How Do Microbes Affect Plants, Animals, and Their Interactions?”
June 2017: Karen Adair participated in the Pan-microbial Trait Ecology Investigative Workshop at Knoxville TN, sponsored by the National Institute for Mathematical and Biological Synthesis (NIMBioS) and organized by Elena Litchman, Christine Hawkes, and Chris Klausmeier
September 2016: Oral presentation to the International Congress of Entomology (Orlando, FL) by Vince Martinson
September 2016: Poster presentation to the American Society of Microbiology Conference on Beneficial Microbes (Seattle, WA) by Karen Adair.
November 2015: Invited Oral Presentation to the Annual Meeting of the Entomological Society of America, Symposium on Synergy in Arthropod Genomics (Minneapolis, MN). Using genomics to define the taxonomic and functional diversity of gut microbiota in drosophilid flies. Alyssa Bost, Vince Martinson, John Jaenike, Greg Loeb and Angela Douglas.
July 2015: Poster Presentation at the Gordon Research Conference on Ecological and Evolutionary Genomics (Bideford, ME). Individual variation in the gut microbiome of wild mushroom-feeding Drosophila. Vince Martinson and John Jaenike
June 2015: Poster Presentation at the Gordon Research Conference on Animal-Microbe Symbioses (Waterville, NH). Big Questions about small things: functional interactions between drosophilid flies and their gut microbiota from a molecular perspective. Alyssa Bost, Soeren Franzenburg, Nathan Winans, and Angela Douglas
March 2015: Invited Speaker at Entomological Society of America Eastern Branch Annual Meeting (Rehoboth, DE). Short- and long-term approaches to managing the invasive species Drosophila suzukii in the northeast. Greg Loeb and Anna Wallingford.
December 2014: Invited Speaker at Annual Meeting of the Entomological Society of America (Portland, OR). SWD overwintering biology and use of wild host plants in the northeast US. Greg Loeb
September 2014: Poster Presentation at Beneficial Microbes Meeting of the American Society for Microbiology (Washington DC). Fruit flies: ecological engineers of the abundance and composition of the bacterial communities. Alyssa Bost, Yuan Luo, Adam Wong, Peter Newell, Xiangfeng Jing, Angela Douglas.
June 2014: Contributed talk to Evolution Conference (Raleigh, NC). Individual variation in the gut microbiome of wild mushroom-feeding Drosophila. Vince Martinson


To elucidate the patterns of host and microbial diversity and the underlying processes, we are combining genomic, metagenomics and transcriptomic datasets with laboratory and field experiments. Our analyses involve associations between multiple drosophilid species and their microbiota.
The datasets are currently available to project participants here, and will be made publicly available through this website and public data repositories (NCBI etc) on publication or completion of the project.


Outreach Events

1. Shifting the Paradigm: Microbes as Animal Helpmates

Exhibition at Mann Library, Cornell University (4 November 2023 – 30 January 2024)

Biologists from around the world use photography and other media to examine and celebrate the intricate relationship between macro-organisms and their microbial partners. Our exhibition is designed to promote interaction and mutual understanding between the sciences and humanities. The opening event on 4th November 2014 included a lecture by the President’s Council for Cornell Women A.D. White Professor at Large, Professor Margaret McFall Ngai, (shown above) followed by a reception.

Together with the photographic contributions from twelve internationally-renowned research groups, the exhibition includes poetry of Dr Tiffany Taylor created especially for this event, explanatory posters of the physics underlying the advanced microscopical methods, and time-lapse video movies that complement the static photographs and micrographs.

This exhibition is now on permanent display at the University of Cornell.

Angela and Thomas Bosch at the opening event for the exhibition at the University of Kiel

The exhibition are also on permanent display at the Christian Albrechts University in Kiel, Germany, with the opening event on 2nd May 2017. This initiative has been made possible by the DFG-funded Collaborative Research Center “Origin and Function of Metaorganisms”, and we thank Professor Thomas Bosch and colleagues at the DFG-CRC for their support.

We have also exhibited the material at the Gordon Research Conference on Animal-Microbe Symbioses held at Mount Snow, Vermont on 11-15 June 2017.

2. Drosophilid identification workshops

Workshop Resources

In September 2016, coPIs John Jaenike and Greg Loeb provided a hands-on drosophilid identification workshop for researchers and practitioners, as in previous years (see below). Much of the emphasis in this year’s workshop was on the invasive D. suzukii, a serious pest of the soft fruit industry, to ensure accurate identification of this and native species. A new drosophilid pest species, Zaprionus indianus, is currently invading the Northeast, and future identification workshops will include this species.

In September 2015, coPI John Jaenike presented a workshop on identification of local species of Drosophila with the support of coPI Greg Loeb and Steve Hessler. A total of 13 participants from Cornell University, University of Rochester, and SUNY-Oswego attended. Participants were provided with photographs prepared especially for this workshop and insect samples collected by Dr Jaenike. The Drosophila photographs were taken from a forthcoming Guide to the Drosophilidae of the Upper Midwest and Northeast that is being written by Dr. Jaenike and Dr. Thomas Werner. Preparation of the guide has been supported in part by the Dimensions of Diversity grant. The participants were provided hands-on advice and support in identification. Several participants brought their own flies to be identified. For example, Kyle Martin, a graduate student with Dr Raguso at Cornell, brought two unidentified Drosophila that appear to form leks in Calycanthus flowers. These two flies were identified as a male D. affinis and a male D. putrida. Steve Hessler also brought in a fly that he had tentatively identified these as D. deflecta, but Dr. Jaenike determined that its pattern of wing pigmentation indicated that it was the closely related D. quinaria.



In spring 2014 (pictured), coPIs Greg Loeb and John Jaenike, together with Steve Hesler, conducted a hands on workshop on identification of Drosophila suzukii and other local Drosophila species for Cornell Cooperative Extension field staff involved in pest monitoring in fruit crops. Greg has also conducted three one-day workshops on the biology and management of D. suzukii held in NY State in fall of 2014 and winter of 2015. Workshops were attended by approximately 100 fruit growers and other industry representatives.

3. A Guide to the Drosophilids of the Midwest and Northeast

co-PI John Jaenike has co-authored with Thomas Werner a taxonomic guide to Drosophila species and other drosophilids in our region. This essential guide is available as a pdf here. We thank the Rochester University Library for their support of this initiative, which will facilitate future research on the diversity of drosophilids.

The book was launched at the University of Rochester on 12 June 2023 with a lecture given by John - and a party to celebrate

4. Workshops on the genome-scale diversity of bacteria associated with drosophilid flies and other insects

The 2014/15 group of students at the March workshop, where the students learned computational methods for the annotation of bacterial genomes.

The 2015/16 group of students at the January workshop, where the students learned how to prepare bacterial DNA for genome sequencing

Researchers supported by this grant contribute to genomics workshops designed to make the tremendous advances in the new field of genomics more widely available to higher education institutions. This initiative is funded by NSF (grant NSF IOS-1354743) .

In 2014-15 and 2015-16, we 0rganized workshops to enrich genomics courses being taught at Corning Community College, NY and Mansfield University of Pennsylvania, in collaboration with Dr. Brenda Gustin (CCC) and Dr Jeanne Kagle (UM). Each of five students from each institution sequenced the genome of a bacterium. They spent a first week-long visit to the laboratory of PI-Douglas to prepare the DNA from “their” bacterium for Illumina sequencing and to learn about the underlying principles; and a second visit to learn how to assemble and annotate the reads for “their” bacterium. At the end of each academic year, we had The Grand Finale Symposium, where the students reported on their findings, heardabout genomic research at Cornell University and learned how to upload the genome of “their” bacterium to NCBI.