microbenet: perspectives on trying to nurture a growing mobe field

microBEnet: Perspectives on trying to

nurture a growing MoBE field October 11, 2017Talk for #MoBE17

Jonathan A. EisenUC Davis

@phylogenomics

Outline

• Background on microBEnet

• Lessons learned

• Future plans

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.

microBEnetStakeholders

Other MoBE Practitioners

Sloan MoBE

microBEnet example activities

Meetings &

Workshops

Citizen Science

Digital &

Social Media

Information (Overload)

Education

Openness &

Sharing

See microBE.net for more detail

Sloan MoBE Publications• 315 papers

• 1633 authors

• Curated by David Coil, Julia Maritz et al

• Analysis by Daniel Hicks and Carl Stahmer

Sloan MoBE Publications by Year

Sloan MoBE Publications by Journal

Sloan MoBE Citations per Article

Total: 16,316 I10 index: 136 H index: 49

Sloan MoBE Citations x Pub Date

Sloan MoBE Papers w/ >100 Citstitle cite_count journal pub_year

QIIME allows analysis of high-throughput community sequencing data 6216 Nature Methods 2010Nuclear 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

2012An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

973 ISME Journal 2012Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences 803 Nature Biotechnology 2013Ironing out the wrinkles in the rare biosphere through improved OTU clustering

642 Environmental Microbiology 2010Quantifying 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 2011Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics


2010Sequencing our way towards understanding global eukaryotic biodiversity

157 Trends in Ecology and Evolution 2012A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data

148 Bioinformatics 2015Longitudinal 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 2014Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

125 Nature Biotechnology 2011Architectural design influences the diversity and structure of the built environment microbiome

125 ISME Journal 2012Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data 118 Methods in Ecology and Evolution 2013The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome

109 GigaScience 2012House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus


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 2010Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging


2011

Jacobs Jr.

DeSalle

Dentinger

Amend

Brown

Thiagarajan

Rismani−Yazdi

Cavallin

Tringe

Houbraken

AdamsEdlund

Ramette

Reich

Olariaga

Marr

Unterseher

Taylor

Ganz

Vineis

Huse

Fliegerova

Huttenhower

Goll

Stanish

Bates

Robertson

Samerpitak

NorthcuttStenson

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

NovotnyChang

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

PirrungWalters

Bahram

Valm

Clements

Clemente

Hartmann

Smilowitz

Kleindienst

Laber

Sangwan

Neches

FreseFlores

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

ZamoraMaharachchikumbura

Duong

Meadow

Tang

Dolatabadi

Ross

Bokulich

Owens

Trimble

Ursell

Smith

Lumbsch

Hastie

Zaman

RideoutHewitt

Duda

Davis

Baker

Lax

Jungbluth

Friedman

Klein

Sedio

Shogan

Henley

Wang

Moktali

Jospin

Pace

Peterson

Coimbra

Masters

GreenJohnson

Leff

Totten

Frank

Taylor

Rhoads

Weiss

Lewis

Tanney

Vázquez−Baeza

Gryzenhout

Knight

KnightKnight

KnightWang

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 BeerHong

Stout

Brenner

Mitchell

Wu

Mason

SchwartzKelley

Fouquier

Hull

Brown

Ishida

Vu

Dedesko

Morgan

BakerBrooks

Jan..i..

Gandara

Kolewe

Schwake

Favel

OlsiewskiWeber

Foox

Cao Durrett

Huttenhower

Saghbini

Chen

Reeves

Tighe

Afshinnekoo

Edwards

Church

Firek

Pevzner

Li

Betancourt Román

Gilbert

Moore

DonohuePollard

Gonzalez

Lee

Lin

Jensen

Mills

McMahon

Ji

Dangl

Flanagan

Ahrendt

Liu

LiWild

Pruden

Zhu

Tessler

Ko

Masarweh

Shani

Cavalier Brown

Kirmiz

Medina

Chen

Song

LarsonGerwick

Moreno

Lee

Buffington

HsuHickey

Bolyen

Mhuireach

Shiffer

Schriml

Dada

Madden

Sun

Moussa

Martin

ChenSeifert

Levin

Hernandez

Flemming

Kolokotronis

Garcia−Houchins

HofstetterPetkovits

Mark Welch

Garcia−Hermoso

Stombaugh

Pivniouk

Nalyanya

Grzymski

Van Diepeningen

Quaedvlieg

Estep

MongodinTäubel

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

CamperPryor

de Gouw

Oldenbourg

Papp

Kirk

Roelofs

Groenewald

BoekhoutLevesque

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

GarcíaWeiß

Gonzalez

Zhou

JohnsonMiller

Miller

Miller

Martin

Harris

Brown

Narechania

Coil

Louis−Seize

Holinger

Bandeira

Irinyi

Glass

Bischof

Lewis

Ledford

Yurkov

Underwood

RajaHirooka

Mueller

Lombard

Northen

LynchLuangsa−ard

Abarenkov

Eberhardt

Tedersoo

Knight

Garrido

FiererDorrestein

Bartels

Groenewald

Kembel

Sachs

Kocsubé

Lemay

Wiedemann

Damm

Fadrosh

EmersonDarling

Maestre

Kline

CaporasoMcLean

Desai

Huffman

Brodie

Sloan MoBE Co-Author Networks

Live …

Outline


• Lessons learned

• Future plans

Lesson 1: People are everything Senior Personnel• David Coil• Holly Ganz• Jenna Lang• Guillaume Jospin• Holly Bik • Simon Dvorak• MJ Seminoff• Dongying WuPhD Students• Russell Neches• Katie Dahlhausen• Wendy Brown• Sonia Ghose• Ashley VaterCollaborators• Deb Niemeier• Daniel Hicks • Carl Stahmer• Alana Firl• Liz Lester• Tom SharptonUndergrads• 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

Lesson 2: Importance of History

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)

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)

Lesson 5: Identify & Fill Gaps• Citizen Science

• Live or Dead Microbes

• AIBE

• Reference Genomes

• Space Vehicles

• Standards and Methods

• What Else?

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

Outline


• Lessons learned

• Future plans

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

Acknowledgements 1Senior Personnel• David Coil • Holly Ganz• Jenna Lang• Guillaume Jospin• Holly Bik • Simon Dvorak• MJ Seminoff• Dongying WuPhD Students• Russell Neches• Katie Dahlhausen• Wendy Brown• Sonia Ghose• Ashley VaterCollaborators• Deb Niemeier• Daniel Hicks • Carl Stahmer• Alana Firl• Liz Lester• Tom SharptonUndergrads• 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

Acknowledgements 2

Paula Olsiweski