The microbiology of the built environment talk for #SequencingCity by @phylogenomics

1. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? microBEnet: microbiology of the Built Environment network ! Jonathan A. Eisen University of California, Davis ! May 6, 2014 IBM Sequencing the City Meeting

2. 2010 • The Alfred P. Sloan Foundation announced calls for proposals for a new “Indoor Environment Program” • One project would be to     “… establish an interdisciplinary network of researchers and practitioners that will build the community, operate community web resources, and organize specialized workshops …” Paula Olsiewski

3. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/

4. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?

5. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing

8. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing microBEnet Goals ! • Knowledge dissemination • Networking • Catalyzing collaboration • Gap filling • Producing resources • Teaching openness

9. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing microBEnet Meeting Examples • 2011 Session at Indoor Air • 2011 Citizen Microbiology • 2012 Session at Lake Arrowhead Small Genomes • 2012 Session at Healthy Buildings • 2012 VAMPS/QIIME • 2013 Citizen Microbiology at ASM • 2013 QIIME Workshops • 2013 GSC13 • 2014 Publish or Perish

10. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Education Openness & Sharing microBEnet Future Plans/Ideas ! • Animals in the BE • Microbial Eukaryotes in the BE • Closed ecosystems • Culture collections and reference genomes • Building Science Education • Antimicrobials in the BE • Software Carpentry • Bioinformatics workshops • Ideas wanted

11. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Education Openness & Sharing microBEnet Future Plans/Ideas ! • Animals in the BE • Microbial Eukaryotes in the BE • Closed ecosystems • Culture collections and reference genomes • Building Science Education • Antimicrobials in the BE • Software Carpentry • Bioinformatics workshops • Ideas wanted

13. http:// www.google. com/ http:// www.google.c om/imgres? Digital and Social Science New Paper Blog Post Twitter Facebook Page LinkedIn GroupPubmed Commons Mendeley

14. http:// www.google. com/ http:// www.google.c om/imgres? Digital and Social Science New Paper Twitter Facebook Page LinkedIn GroupMendeley

15. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Rachel Adams

19. http:// www.google. com/ http:// www.google.c om/imgres? Digital and Social Science Meeting Storify Twitter Facebook Page LinkedIn GroupBlog

20. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Allison Fish

21. http:// www.google. com/ http:// www.google.c om/imgres? Monthly Newsletter • Summary of blog posts • “Resource of the Month” • “People Behind the Science” video series… “Project of the Month” • Recent and upcoming meetings Mary Jo Seminoff

22. http:// www.google. com/ http:// www.google.c om/imgres? People Behind the Science Holly Bik Amy Pruden

23. http:// www.google. com/ http:// www.google.c om/imgres? News Tracking Brooke Borel

24. http:// www.google. com/ http:// www.google.c om/imgres? Blog Post About News Holly Ganz

26. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://en.wikipedia.org/wiki/File:TsunamiHazardSign.svg

27. http:// www.google. com/ http:// www.google.c om/imgres? Digital and Social Science New Paper Blog Post Twitter Facebook Page LinkedIn GroupPubmed Commons Mendeley

28. http:// www.google. com/ http:// www.google.c om/imgres? Social Reference Collections • 149 members • 950 papers • Curated Tags

29. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Author Contacts Google Scholar Pages Tagging Blog Journal Club New People’s Starting Point RSS Feeds

30. http:// www.google. com/ http:// www.google.c om/imgres? Journals Publishing MoBe work 35th International Conference on Environmental Systems (ICES); 8th European Symposium on Space Environmental Control Systems (ESSECS), Rome, Italy, July 11, 2005.; 39th COSPAR Scientific Assembly. Held 14-22 July 2012, in Mysore, India. Abstract PE.1-2-12, p.2076; ADVANCES IN APPLIED MICROBIOLOGY; AIHAJ : a journal for the science of occupational and environmental health and safety; AIR QUALITY MONOGRAPHS (AMSTERDAM), VOL. 2. HEALTH IMPLICATIONS OF FUNGI IN INDOOR ENVIRONMENTS; INTERNATIONAL WORKSHOP, BAARN, NETHERLANDS, NOVEMBER 9-13, 1992; AJN The American …; APMIS : Acta Pathologica, Microbiologica, et Immunologica Scandinavica; ASHRAE Transactions; ASM News-American …; ASTM Special Technical Publication; Abstracts of Papers of the American Chemical Society; Abstracts of the General Meeting of the American Society for Microbiology; Acta Allergologica; Acta Astronautica; Acta Dermato Venereol; Acta astronautica; Acta tropica; Advanced Materials Research; Advances in Applied Microbiology; Advances in Space Research; Advances in applied microbiology; Advances in preventive medicine; Aerobiologia; Aerosol Science and Technology; Aerosol and Air Quality Research; Aerospace medicine; African Journal of Biotechnology; African Journal of Microbiology Research; African health sciences; Aiha Journal; Air & Water Borne Diseases; Air Quality Monographs (Amsterdam); Allergie und Asthma; Allergologie; Allergy; Allergy (Copenhagen); American Environmental Laboratory; American Industrial Hygiene Association Journal; American Industrial Hygiene Conference on Industrial Hygiene in the World of Tomorrow, Orlando, FL (USA), 13-18 May 1990; American Journal of Epidemiology; American Journal of Infection Control; American Journal of Respiratory and Critical Care Medicine; American Scientist; American Water Works Association; American journal of epidemiology; American journal of industrial medicine; American journal of infection control; American journal of respiratory and critical care medicine; Anales de Biologia; Ann Agric Environ Med; Annali dell'Istituto superiore di sanità; Annals of Agricultural and Environmental Medicine : AAEM; Annals of Allergy; Annals of Allergy, Asthma, & Immunolology; Annals of Occupational Hygiene; Annals of agricultural and environmental medicine : AAEM; Appl Microbiol Biotechnol.; Appl. Environ. Microbiol.; Applied Biochemistry …; Applied Mechanics and Materials; Applied Occupational and Environmental Hygiene; Applied and Environmental Microbiology; Applied and environmental microbiology; Applied and …; Applied microbiology and biotechnology; Applied occupational and environmental hygiene; Arch. Intern. Med; Archives of Environmental & Occupational Health; Archives of Environmental Health; Archives of Environmental Health.; Archives of Internal Medicine; Archives of environmental & occupational health; Archives of environmental health; Archives of oral biology; Asian Pacific Journal of Tropical Disease; Astrobiology; Atmospheric Environment; Atmospheric Environment Part B Urban Atmosphere; Atmospheric Research; BMC bioinformatics; BMC biology; BMC infectious diseases; BMC microbiology; Biocontrol Science; Biocontrol science; Bioengineered; Biofilms; Biofouling; Bioinformatics; Bioinformatics (Oxford, England); Biological Reviews; Biologija; Biologist; Biosafety; Bioscience, biotechnology, and biochemistry; Biosecurity and bioterrorism : biodefense strategy, practice, and science; Biosensors & bioelectronics; Brazilian Journal of Microbiology; British Microbiology Research Journal; Bromatologia i Chemia Toksykologiczna; Building and Environment; Bulletin de la Societe Francaise de Mycologie Medicale; CANADIAN JOURNAL OF MICROBIOLOGY; CLEAN - Soil, Air, Water; California and western medicine; Canadian Journal of Civil Engineering; Canadian Journal of Microbiology; Canadian Medical Association journal; Canadian journal of microbiology; Canadian respiratory journal : journal of the Canadian Thoracic Society; Chemical Engineering Journal; Chemosphere; Chest; Clean - Soil, Air, Water; Clean – Soil, Air, Water; Clin. Microbiol. Rev.; Clinical & Experimental Allergy; Clinical Infectious Diseases; Clinical Microbiology Newsletter; Clinical Microbiology Reviews; Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology; Clinical and translational science; Community health studies; Continental J. Medical Research; Critical reviews in microbiology; Critical reviews in toxicology; Current Microbiology; Current Opinion in Biotechnology; Current allergy and asthma reports; Current microbiology; Current opinion in biotechnology; Czech Mycology; Diagnostic microbiology and infectious disease; Ecological Indicators; Ecological applications : a publication of the Ecological Society of America; Electronic Journal of Biotechnology; Emerging Infectious Disease; Encyclopedia of environmental microbiology; Encyclopedia of microbiology; Energy and Buildings; Environment India; Environment International; Environment international; Environmental Engineering and Management Journal; Environmental Forensics; Environmental Health Perspectives; Environmental Health.; Environmental Health.Perspectives; Environmental Microbiology; Environmental Monitoring and Assessment; Environmental Research; Environmental Science & Technology; Environmental engineering science; Environmental health : a global access science source; Environmental health perspectives; Environmental microbiology; Environmental monitoring and assessment; Environmental research; Environmental science & technology; Environmental science and pollution research international; Environmental toxicology; Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceské lékarské spolecnosti J.E. Purkyne; Ethiopian Journal of Health Sciences; European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery; FEMS Microbiology Ecology; FEMS microbiology ecology; FEMS microbiology letters; FEMS microbiology …; Fems (Fed Eur.Microbiol.Soc) Microbiol.Lett.; Food and Environmental Virology; Frontiers in Microbiology; Frontiers in bioscience (Scholar edition); Fungal Biology; Fungal Genetics and Biology; Fungal biology; Future microbiology; Gefahrstoffe Reinhaltung Der Luft; Genome Biology; Genome research; Gigiena i Sanitariya; Grana; Gravitational and Space Biology; HANDBOOK OF ENVIRONMENTAL CHEMISTRY; HVAC&R Research; Habitation (Elmsford, …; Healthy Buildings 2012; Helsingin Kaupungin Ymparistokeskuksen Julkaisuja; Hokkaido Igaku Zasshi The Hokkaido Journal Of Medical Science; Human molecular genetics; Humans in Outer Space—Interdisciplinary Odysseys; IAF, International Astronautical Congress, 43 rd, …; Igiene Moderna; Immunology; Indian journal of medical microbiology; Indoor Air; Indoor air; Indoor and Built Environment; Industrial Health; Inhalation toxicology; Innovative Food Science & Emerging Technologies; International Biodeterioration & Biodegradation; International Biodeterioration and Biodegradation; International Journal of Astrobiology; International Journal of Current Microbiology and Applied Sciences; International Journal of Food Science & Technology; International Journal of Hygiene and Environmental Health; International Journal of Microbiology Research; International Journal of Scientific and Research Publications; International Journal of Speleology; International Journal of Systematic Bacteriology; International Journal of Systematic and Evolutionary Microbiology; International archives of allergy and immunology; International journal of antimicrobial agents; International journal of environmental health research; International journal of environmental research and public health; International journal of food microbiology; International journal of hygiene and environmental health; International journal of molecular sciences; International journal of occupational safety and ergonomics : JOSE; International …; J R Soc Interface; JAMA : the journal of the American Medical Association; JAPCA; JAPI; JPL Publication 12-12; Journal of Aerosol Science; Journal of Allergy and Clinical Immunology; Journal of Animal Science; Journal of Applied Environmental and Biological Sciences; Journal of Applied Microbiology; Journal of Bacteriology; Journal of Building Physics; Journal of China University of Mining & Technology (English Edition); Journal of Clinical Microbiology; Journal of Cultural Heritage; Journal of Environment and Earth Science; Journal of Environment and Health; Journal of Environmental Engineering and Science; Journal of Environmental Health; Journal of Environmental Monitoring; Journal of Experimental and Integrative Medicine; Journal of Food Safety; Journal of Genetics; Journal of Hospital Infection; Journal of Hospital …; Journal of Infection; Journal of Intelligent Manufacturing; Journal of Medical Entomology; Journal of Medical research and Practice; Journal of Microbiological Methods; Journal of Microelectromechanical Systems; Journal of Occupational and Environmental Hygiene; Journal of Public Health Management and Practice; Journal of Scientific and Industrial Research; Journal of animal science; Journal of applied microbiology; Journal of bacteriology; Journal of basic microbiology; Journal of clinical microbiology; Journal of clinical pathology; Journal of environmental monitoring : JEM; Journal of environmental sciences (China); Journal of exposure science & environmental epidemiology; Journal of foot and ankle research; Journal of forensic sciences; Journal of hazardous materials; Journal of hospital infection; Journal of investigational allergology & clinical immunology; Journal of investigational allergology & clinical immunology : official organ of the International Association of Asthmology (INTERASMA) and Sociedad Latinoamericana de Alergia e Inmunologia; Journal of microbiological methods; Journal of microbiology (Seoul, Korea); Journal of occupational and environmental hygiene; Journal of occupational health; Journal of the Air & Waste Management Association; Journal of the Air & Waste Management Association (1995); Journal of the Formosan Medical Association = Taiwan yi zhi; Journal of the Indian Academy of Wood Science; Journal of the Mississippi Academy of Sciences; Journal of the National Institute of Public Health; Journal of the Royal Society Interface; Journal of the Royal Society Interface the Royal Society; Journal of the Royal Society, Interface / the Royal Society; Journal of theoretical biology; Letters in applied microbiology; Life Science Journal; Materials Chemistry and …; Measurement; Medical mycology : official publication of the International Society for Human and Animal Mycology; Medycyna pracy; Micologia Italiana; Microbial Ecology; Microbial ecology; Microbiological research; Microbiology and Immunology; Microbiology and Molecular Biology Reviews; Microbiology and immunology; Microbiome; Mikologiya I Fitopatologiya; Mikrobiyoloji bulteni; Molecular and Cellular Probes; Molecular ecology; Mycologia; Mycologia Helvetica; Mycological Research; Mycological research; Mycopathologia; Mycoses; Mycotaxon; N Eng J Med; NASA; NASAAmes Summer High School Apprenticeship …; NASA Technical Reports Server; NATO ASI Series Series 2 Environment; Nature; Nature Methods; Nature methods; Nature reviews. Microbiology; New England Journal of Medicine; New England and Regional Allergy Proceedings; Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology; Occupational and Environmental Medicine; Occupational medicine (Philadelphia, Pa.); Origins of Life and …; PDA journal of pharmaceutical science and technology / PDA; PLoS Comput Biol; PLoS Med; PLoS Medicine; PLoS ONE; PLoS Pathogens; PLoS medicine; PLoS pathogens; Pathogens; Pediatric Allergy and Immunology; Pediatrics; PeerJ; Philosophical Transactions of the Royal Society of London - Series B: Biological Sciences; Photochemistry and photobiology; Planetary and Space Science; Plant Disease; PloS one; Plos Computational Biology; Polish Journal of Environmental Studies; Preventive Veterinary Medicine; Proceedings of the ASHRAE conference IAQ '87: practical control of indoor air problems; May; Arlington, VA. Atlanta, GA: American Society of Heating, Refrigerating, and Air-Conditioning Engineers, Inc; Proceedings of the Indoor Air 2002 Conference; Proceedings of the National Academy of Sciences; Proceedings of the National Academy of Sciences of the United States of America; Proceedings of the Royal Society of London. Series B. Biological Sciences; Proceedings. Biological sciences / The Royal Society; Public.Health.Reports; Recent research developments in infection & immunity. Vol. 1. Part I; Research in microbiology; Research in veterinary science; Research in …; Respiratory medicine; Reviews in Medical Microbiology; Revista iberoamericana de micología; Risk Analysis; Roczniki Panstwowego Zakadu Higieny; Roczniki Panstwowego Zakladu Higieny; Roczniki Państwowego Zakładu Higieny; SAE Special Publications; SAE Technical Paper; SAE Technical …; SAE transactions; STUDIES IN SURFACE SCIENCE AND CATALYSIS; Saudi Journal of Biological Sciences; Scandinavian Journal of Work, Environment and Health.; Science; Science (New York, N.Y.); Science of The Total Environment; Science of the Total Environment; Science of the Total …; Scientific Reports; Sick Building Syndrome: In Public Buildings and …; Simpozium IX Mezhdunarodnogo Kongressa po …; Standards in Genomic Sciences; Stress Challenges and Immunity in Space; Systematic and applied microbiology; Taiwan Journal of Public Health; Taiwanese Journal of Agricultural Chemistry and Food Science; Talanta; The 6th International Conference on Indoor Air Quality, Ventilation &Energy Conservation in Buildings (IAQVEC 2007), Sendai, Japan, 28-31 October, 2007; The Analyst; The Annals of Occupational Hygiene; The Annals of occupational hygiene; The European respiratory journal : official journal of the European Society for Clinical Respiratory Physiology; The European respiratory journal official journal of the European Society for Clinical Respiratory Physiology; The FEBS journal; The ISME journal; The International Journal of Tuberculosis and Lung Disease; The Journal Of Allergy; The Journal of allergy and clinical immunology; The Journal of asthma : official journal of the Association for the Care of Asthma; The Journal of experimental medicine; The Journal of hospital infection; The Journal of infectious diseases; The Science of the total environment; The Veterinary Journal; The human equation: health and comfort proceedings IAQ; The new microbiologica official journal of the Italian Society for Medical Odontoiatric and Clinical Microbiology SIMMOC; Thorax; Tidsskrift for den Norske laegeforening tidsskrift for praktisk medicin ny raekke; Toxicology Letters (Shannon); Toxicology and Industrial Health; Trends in Microbiology; Trends in biotechnology; Trends in ecology & evolution; Trends in microbiology; U S Navy medicine; Veterinarnomeditsinski nauki; Virology journal; WJCID World Journal of Clinical Infectious Diseases; Waste management & research; Water Air and Soil Pollution; Water Research; Water science and technology; Water, Air, & Soil Pollution; World Journal of Microbiology and Biotechnology; World Mycotoxin Journ; XIX NORDIC CONGRESS ON ALLERGOLOGY; Zbornik Matice Srpske za Prirodne Nauke; Zentralbl.Bakteriol.Mikrobiol.Hyg.Abt.; Zentralblatt fuer Bakteriologie Parasitenkunde Infektionskrankheiten und Hygiene Erste Abteilung Originale Reihe B Hygiene Krankenhaushygiene Betriebshygiene Praeventive Medizin; Zentralblatt fur Hygiene und Umweltmedizin; Zentralblatt fur Hygiene und Umweltmedizin International journal of hygiene and environmental medicine; eLife; mBio; …; … Meeting of the American Society of …; …Science and Technology; ;

33. http:// www.google. com/ http:// www.google.c om/imgres? Reading Specific Journals

38. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Newman M E J PNAS 2004;101:5200-5205 Gaps in the Field Full Text DB Co-authorship Networks

40. http:// www.google. com/ http:// www.google.c om/imgres? Software Carpentry Jenna Lang Tracy Teal

41. http:// www.google. com/ http:// www.google.c om/imgres? Data Carpentry

42. http:// www.google. com/ http:// www.google.c om/imgres? QIIME Workshops

43. http:// www.google. com/ http:// www.google.c om/imgres? Collaborative Micro Edu/research Jo Handelsman Tiffany Tsang

44. http:// www.google. com/ http:// www.google.c om/imgres? BE Reference Genomes • 7 students • Cultured organisms isolated from a variety of built environments • Identify, sequence, assemble, annotate, publish a genome each • 5 papers published so far in Genome Announcements • All Data released • Student blog • Brachybacterium muris (Jonathon Lo): • Microbacterium sp (Zach Bendiks): • Curtobacterium flaccumfaciens (Jennifer Flanagan) • Dietzia sp (Amanda Diep): • Kocuria rosea (Jessica Doctor): • Leucobacter sp (Dakota Bevans, Hannah Holland-Moritz): Hannah Holland-Moritz

45. http:// www.google. com/ http:// www.google.c om/imgres? Swab to Genome Workflow Dunitz et al. in prep Madison Dunitz

46. http:// www.google. com/ http:// www.google.c om/imgres? Aquarium Biogeography • Biogeography and succession • Extensive chemical “metadata” collected • 16S surveys and metagenomics • Using MBE tools • Coordinated by Jenna Lang, David Coil, Matt Haggerty • Advice from Josh Neufeld & Laura Sauder • Papers in progress Undergraduates: •Sabreen Aulakh •Alex Alexiev •Akshay Sethi •Andrew Shaver •Jennifer Flanagan •Lakshmi Bharadwaj High School: •Kevin Yang •In collaboration with Kenneth Kubo at American River College ! Sabreen Aulakh

47. http:// www.google. com/ http:// www.google.c om/imgres? Citizen Microbiology Laura Sauder

49. http:// www.google. com/ http:// www.google.c om/imgres? The Rise of Citizen Science Caren Cooper Darlene Cavalier

50. http:// www.google. com/ http:// www.google.c om/imgres? Citizen Microbiology Meetings Darlene Cavalier

51. Phone Microbiome Georgia Barguil Georgia Barguil Jack Gilbert

52. http:// www.google. com/ http:// www.google.c om/imgres? Wild Life of Your Home Slide from Holly Menninger, CoPI on the project Holly Meninger Rob Dunn

53. http:// www.google. com/ http:// www.google.c om/imgres? Many Other Citizen Microbiology Efforts Jessica Richman

57. MICROBES

59. http:// www.google. com/ http:// www.google.c om/imgres? Teaching and Spreading Openness • Open Access publishing • Repositories and preprints • Open Data release • Data and Metadata publishing • Open Source Software • CC licenses on digital products • Recording and posting talks, slides • Post publication peer review

60. http:// www.google. com/ http:// www.google.c om/imgres? Data Papers

61. http:// www.google. com/ http:// www.google.c om/imgres? Slideshare

62. http:// www.google. com/ http:// www.google.c om/imgres? Altmetrics Heather Piwowar

63. http:// www.google. com/ http:// www.google.c om/imgres? Tracking microBEnet metrics

64. http:// www.google. com/ http:// www.google.c om/imgres? How To Use Social Media Holly Bik Miriam Goldstein

66. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? Meetings & Workshops Citizen Science Digital & Social Media Information (Overload) Education Openness & Sharing What Next? Sustainability More BE/BS Press Forward Wikipedia Integration RewardsMatchmaking Network Analysis Protocols Training on use Reporter Guides

67. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/

68. Evolution & Ecology of Microbiomes Disturbance & RestorationPopulation Biology Biogeography Phylogenetic Ecology Community Assembly

The microbiology of the built environment talk for #SequencingCity by @phylogenomics

The microbiology of the built environment talk for #SequencingCity by @phylogenomics

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The microbiology of the built environment talk for #SequencingCity by @phylogenomics