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

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microBEnet:

microbiology of the Built Environment network

!
Jonathan A. Eisen

University of California, Davis

!
May 6, 2014

IBM Sequencing the City Meeting

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

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http://www.microbe.net/

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• Knowledge dissemination
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• Animals in the BE
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• Closed ecosystems
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genomes
• Building Science Education
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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; ;

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Reading Specific Journals

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Newman M E J PNAS 2004;101:5200-5205
Gaps in the Field
Full Text DB
Co-authorship Networks

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Software Carpentry
Jenna Lang
Tracy Teal

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Data Carpentry

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QIIME Workshops

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Collaborative Micro Edu/research
Jo Handelsman Tiffany Tsang

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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

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Swab to Genome Workflow
Dunitz et al. in prep
Madison Dunitz

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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

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Citizen Microbiology
Laura Sauder

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The Rise of Citizen Science
Caren Cooper
Darlene Cavalier

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Citizen Microbiology Meetings
Darlene Cavalier

Phone Microbiome
Georgia Barguil
Georgia Barguil
Jack Gilbert

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Wild Life of Your Home
Slide from Holly Menninger, CoPI on the project
Holly Meninger
Rob Dunn

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Many Other Citizen Microbiology Efforts
Jessica Richman

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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

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Data Papers

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Slideshare

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Altmetrics
Heather Piwowar

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Tracking microBEnet metrics

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How To Use Social Media
Holly Bik
Miriam Goldstein

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Meetings
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Citizen
Science
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Education
Openness
&
Sharing
What Next?
Sustainability
More BE/BS
Press Forward
Wikipedia Integration
RewardsMatchmaking
Network Analysis
Protocols
Training on use
Reporter Guides

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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