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microBEnet: Perspectives on trying to nurture a growing MoBE field

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microBEnet: Perspectives on trying to nurture a growing MoBE field

  1. 1. microBEnet: 
 Perspectives on trying to nurture a growing MoBE field October 11, 2017 Talk for #MoBE17 Jonathan A. Eisen UC Davis @phylogenomics
  2. 2. Outline • Background on microBEnet • Lessons learned • Future plans
  3. 3. Outline • Background on microBEnet • Lessons learned • Future plans
  4. 4. microBEnet • Funded in 2011 in response to call from Sloan Foundation “Establish an interdisciplinary network of researchers and practitioners that will build the community, operate community web resources, and organize specialized workshops” • Mission Supporting, promoting, accelerating, and improving work at the interface of microbiology and the built environment.
  5. 5. microBEnet Stakeholders Other MoBE 
 Practitioners Sloan MoBE
  6. 6. microBEnet example activities Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing
  7. 7. See microBE.net for more detail
  8. 8. Sloan MoBE Publications • 315 papers • 1633 authors • Curated by David Coil, Julia Maritz et al • Analysis by Daniel Hicks and Carl Stahmer
  9. 9. Sloan MoBE Publications by Year
  10. 10. Sloan MoBE Publications by Journal
  11. 11. Sloan MoBE Citations per Article Total: 16,316 I10 index: 136 H index: 49
  12. 12. Sloan MoBE Citations x Pub Date
  13. 13. Sloan MoBE Papers w/ >100 Cits title cite_count journal pub_year QIIME allows analysis of high-throughput community sequencing data 6216 Nature Methods 2010 Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi 1248 Proceedings of the National Academy of Sciences of the United States of America 2012 An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea 973 ISME Journal 2012 Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences 803 Nature Biotechnology 2013 Ironing out the wrinkles in the rare biosphere through improved OTU clustering 642 Environmental Microbiology 2010 Quantifying microbial communities with 454 pyrosequencing: Does read abundance count? 255 Molecular Ecology 2010 Opportunistic pathogens enriched in showerhead biofilms 219 Proceedings of the National Academy of Sciences of the United States of America 2009 Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems 189 PLoS ONE 2011 Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics 163 Proceedings of the National Academy of Sciences of the United States of America 2010 Sequencing our way towards understanding global eukaryotic biodiversity 157 Trends in Ecology and Evolution 2012 A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data 148 Bioinformatics 2015 Longitudinal analysis of microbial interaction between humans and the indoor environment 135 Science 2014 Human occupancy as a source of indoor airborne bacteria 129 PLoS ONE 2012 Phylogeny, identification and nomenclature of the genus Aspergillus 128 Studies in Mycology 2014 Efficient de novo assembly of single-cell bacterial genomes from short- read data sets 125 Nature Biotechnology 2011 Architectural design influences the diversity and structure of the built environment microbiome 125 ISME Journal 2012 Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data 118 Methods in Ecology and Evolution 2013 The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome 109 GigaScience 2012 House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus 108 Proceedings of the National Academy of Sciences of the United States of America 2014 Biodiversity and biogeography of the atmosphere 107 Philosophical Transactions of the Royal Society B: Biological Sciences 2010 Life-threatening infectious diseases of childhood: Single-gene inborn errors of immunity? 103 Annals of the New York Academy of Sciences 2010 Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging 102 Proceedings of the National Academy of Sciences of the United States of America 2011
  14. 14. Jacobs Jr. DeSalle Dentinger Amend Brown Thiagarajan Rismani−Yazdi Cavallin Tringe Houbraken Adams Edlund Ramette Reich Olariaga Marr Unterseher Taylor Ganz Vineis Huse Fliegerova Huttenhower Goll Stanish Bates Robertson Samerpitak Northcutt Stenson Paczian Bernstein Nayak Brugler Andrews−Pfannkoch Gerlach Larsen Wilke Lukacs Kirkup Crespo−Medina Miletto Gobet Arens Handley Sharon Silva Pereira Menninger Antonelli Freese Waterhouse Raveh−Sadka Zaneveld Prussin Lymperopoulou McDonald Ladau Vikram Bhangar Novotny Chang Gräfenhan Liimatainen Niskanen Briand Hughes Spies Wada−Katsumata Pacifici Uejio Wilkening Biermann Bik Nguyen Ahrendt Lauber Kovács O'Dwyer Nilsson Simon Böer Hoisington Gibbons Meijer StielowPino−Bodas Knights Jimenez Visagie Badger Pollard Eisen González Goodrich Aime Xu Yang Yilmaz Venter Zivkovic Mills Blaser Kelly Lebrilla Griffith Samson Bruns Ownby Stout Busby Johnston Yilmaz Barberán Bobe Assabgui Rieken Probst Sain Stephens Bibby Kuczynski Pirrung Walters Bahram Valm Clements Clemente Hartmann Smilowitz Kleindienst Laber Sangwan Neches Frese Flores Sarmiento−Ramírez Robert Leavitt Morowitz Robbins−Pianka Stevens Eren Hospodsky Vaas Womack Pasut Gu Licina Yee−Greenbaum Severance Dannemiller Stielow Jeffries Hubka Carver Wendel Landon Brami Lang Zamora Maharachchikumbura Duong Meadow Tang Dolatabadi Ross Bokulich Owens Trimble Ursell Smith Lumbsch Hastie Zaman Rideout Hewitt Duda Davis Baker Lax Jungbluth Friedman Klein Sedio Shogan Henley Wang Moktali Jospin Pace Peterson Coimbra Masters Green Johnson Leff Totten Frank Taylor Rhoads Weiss Lewis Tanney Vázquez−Baeza Gryzenhout Knight Knight Knight Knight Wang Ambrosio Schoch Hall O'Connor Ling He Qian Luongo Moriyama Levin Knight Egidi Silva Altrichter Barreto Ramos Hugenholtz Hampton−Marcell Knight Braithwaite Wang Chase Bateman Herkert Diéguez−Uribeondo Zalar Gozdz Grim Guo Oliveira Scott Alcaïs Kotter Gibson Shipunova Klaassen Al−Hatmi Brasch Munshi−South Boekhout Tanaka Garner Lomascolo Hasegawa Ziemann Weir Baron Duncan Hasan de Beer Hong Stout Brenner Mitchell Wu Mason Schwartz Kelley Fouquier Hull Brown Ishida Vu Dedesko Morgan Baker Brooks Jan..i.. Gandara Kolewe Schwake Favel Olsiewski Weber Foox Cao Durrett Huttenhower Saghbini Chen Reeves Tighe Afshinnekoo Edwards Church Firek Pevzner Li Betancourt Román Gilbert Moore Donohue Pollard Gonzalez Lee Lin Jensen Mills McMahon Ji Dangl Flanagan Ahrendt Liu Li Wild Pruden Zhu Tessler Ko Masarweh Shani Cavalier Brown Kirmiz Medina Chen Song Larson Gerwick Moreno Lee Buffington Hsu Hickey Bolyen Mhuireach Shiffer Schriml Dada Madden Sun Moussa Martin Chen Seifert Levin Hernandez Flemming Kolokotronis Garcia−Houchins Hofstetter Petkovits Mark Welch Garcia−Hermoso Stombaugh Pivniouk Nalyanya Grzymski Van Diepeningen Quaedvlieg Estep Mongodin Täubel Dantas SchrimlYooseph Divakar Mark Welch Woyke Zoratti Harb Postolache Lasken Shendell Desantis Ercolini Stenroos Kentsis Chitsaz Kõljalg Planet Maxon Brestelli Keady Peccia Tesler Redecker Moncalvo Lauro Lemon Dijksterhuis Telleria Salit Boetius Awerbuch Hambleton Gunde−Cimerman Begerow Pinney Untereiner Dominguez−Bello Rivers Bizet Stajich Buyck Kissinger Schmitt Thaler Alverdy Warneke Brunk Stoeckert Jr. Kinney Vágvölgyi Baumgartner Bohannan Dueñas Camper Pryor de Gouw Oldenbourg Papp Kirk Roelofs Groenewald Boekhout Levesque Cardinali Siddall Fuhrman Stoeckle Hedlund Gent Dewhirst Friesen Spangler Schal Keegan Borisy Banfield Lowry Pevzner Perrone Nazaroff de Hoog Lindow Nealson Sogin Paulsen Frisvad Goddard Grube Vercelli Yaguchi Falkinham Pei Crous McCormick Crespo Wingfield D'Souza Amato An Hyde Lombardo Morrison Abel German Ostrowski Seifert Harrison Dupont Varga Roos Pace Larsen Kelley Casanova Ren Mason Hughes Ziegler Voigt Silverman Larsson Rosenfeld Jacobs Colwell Williamson Gilbert James Thomas Meyer Zhang Hsu Hansen Hernandez Dunn Fischer Moore Fox Meyer Jain Edwards Fox Henderson Arai Goldstein Siegel Yamamoto García Weiß Gonzalez Zhou Johnson Miller Miller Miller Martin Harris Brown Narechania Coil Louis−Seize Holinger Bandeira Irinyi Glass Bischof Lewis Ledford Yurkov Underwood RajaHirooka Mueller Lombard Northen Lynch Luangsa−ard Abarenkov Eberhardt Tedersoo Knight Garrido Fierer Dorrestein Bartels Groenewald Kembel Sachs Kocsubé Lemay Wiedemann Damm Fadrosh Emerson Darling Maestre Kline Caporaso McLean Desai Huffman Brodie Sloan MoBE Co-Author Networks
  15. 15. Live …
  16. 16. Outline • Background on microBEnet • Lessons learned • Future plans
  17. 17. Lesson 1: People are everything Senior Personnel • David Coil • Holly Ganz • Jenna Lang • Guillaume Jospin • Holly Bik • Simon Dvorak • MJ Seminoff • Dongying Wu PhD Students • Russell Neches • Katie Dahlhausen • Wendy Brown • Sonia Ghose • Ashley Vater Collaborators • Deb Niemeier • Daniel Hicks • Carl Stahmer • Alana Firl • Liz Lester • Tom Sharpton Undergrads • Petra Dahms External Collaborators and Advisors • Hal Levin • Shelly Miller • Darlene Cavalier • Science Cheerleaders • Jack Gilbert & lab • Josh Neufeld & lab • Mark Severance • Chris Mason & MetaSub team • Amy Pruden & lab • Rob Knight & lab • Brian Klein & lab • Rob Dunn & Lab • Aaron Darling • Rachel Adams • Lynn Schriml • Anne Madden • Gwynne Mhuireach • Jessica Green & Kevin Van Den Wymelenberg & BioBE team • Rich Corsi • Parag Vaishampayan • Rachel Adams • 100s of guest bloggers Undergrads Continued • Dana De Vries • Greg Kincheloe • Karley Lujan • Briana Pompa-Hogan • Madison Dunitz • Jennifer Flanagan • Hannah Holland-Moritz • Alex Alexiev • Ruth Lee • Makayla Betts • Tynisha Koenigsaecker • Amanda Diep • Jonathan Lo • Jessica Doctor • Zachary Bendiks • Dakota Bevans • Akshay Sethi • Lakshmi Bharadwaj • Sabreen Aulakh • Wan Nurul Naszeerah • Shawn Hoon San • Camilla Dayrit • Muntaha Samad
  18. 18. Lesson 2: Importance of History
  19. 19. Lesson 2: Importance of History
  20. 20. Lesson 3: Diversity Matters • Microbial diversity (taxa, genomic, functional) still poorly characterized in most BEs • Diversity of BEs (type, location, materials, etc) still poorly sampled • Diversity of approaches • Human diversity (occupants, researchers, participants) should be broad (gender, age, career stage, race and ethnicity, country, field, institution)
  21. 21. Lesson 4: Communication Matters • Social media can be a powerful tool • Platforms for community building are still limited • Work with the press but don’t oversell • Language and culture important to deal with when crossing so many disciplines • Open scholarship benefits and risks important to discuss from the beginning • Don’t be isolated (conceptually, collaboratively, internationally)
  22. 22. Lesson 5: Identify & Fill Gaps • Citizen Science • Live or Dead Microbes • AIBE • Reference Genomes • Space Vehicles • Standards and Methods • What Else?
  23. 23. Lesson 6: Education & Engagement Critical • Public engagement via citizen science • Research based courses and education activities • Edutainment is OK and even good • Courses and course materials needed • SciComm classes • Integration of Wikipedia editing into education activities
  24. 24. Outline • Background on microBEnet • Lessons learned • Future plans
  25. 25. microBEnet future … • General principles • Maintain the core. • Broad targeting of activities. • Streamline and sustain. • Integration and synergy. • Activities • Network hub • Edutrain • Reference data • Expansion of themes
  26. 26. Acknowledgements 1 Senior Personnel • David Coil • Holly Ganz • Jenna Lang • Guillaume Jospin • Holly Bik • Simon Dvorak • MJ Seminoff • Dongying Wu PhD Students • Russell Neches • Katie Dahlhausen • Wendy Brown • Sonia Ghose • Ashley Vater Collaborators • Deb Niemeier • Daniel Hicks • Carl Stahmer • Alana Firl • Liz Lester • Tom Sharpton Undergrads • Petra Dahms External Collaborators and Advisors • Hal Levin • Shelly Miller • Darlene Cavalier & SciCheer • Jack Gilbert & lab • Josh Neufeld & lab • Mark Severance • Chris Mason & MetaSub team • Amy Pruden & lab • Rob Knight & lab • Brian Klein & lab • Rob Dunn & Lab • Aaron Darling • Rachel Adams • Lynn Schriml • Anne Madden • Despoina Lymperopoulou • Gwynne Mhuireach • Jessica Green & Kevin Van Den Wymelenberg & BioBE team • Rich Corsi • Parag Vaishampayan • Rachel Adams • 100s of guest bloggers Undergrads Continued • Dana De Vries • Greg Kincheloe • Karley Lujan • Briana Pompa-Hogan • Madison Dunitz • Jennifer Flanagan • Hannah Holland-Moritz • Alex Alexiev • Ruth Lee • Makayla Betts • Tynisha Koenigsaecker • Amanda Diep • Jonathan Lo • Jessica Doctor • Zachary Bendiks • Dakota Bevans • Akshay Sethi • Lakshmi Bharadwaj • Sabreen Aulakh • Wan Nurul Naszeerah • Shawn Hoon San • Camilla Dayrit • Muntaha Samad
  27. 27. Acknowledgements 2 Paula Olsiweski

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