Opening up to Diversity talk by @phylogenomics at #UCDPHSA

Opening Up to Diversity !

Jonathan A. Eisen @phylogenomics

!

October 12, 2014 !

UC Davis Pre-Health Student Alliance

Diabetic at Conference

Pubmed Searching

Interesting Relevant Paper

Paywall

Symptom of A New Disease


Closed Accessitis


Closed AccessitisElsevieritis

Disease Known for Many Years


Public Library of Science (PLoS)

• Started in 2000 by • Harold Varmus • Pat Brown • Michael Eisen

• First action was to circulate an open letter on publishing

The Letter

We support the establishment of an online public library that would provide the full contents of the published record of research and scholarly discourse in medicine and the life sciences in a freely accessible, fully searchable, interlinked form. Establishment of this public library would vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences.We recognize that the publishers of our scientific journals have a legitimate right to a fair financial return for their role in scientific communication. We believe, however, that the permanent, archival record of scientific research and ideas should neither be owned nor controlled by publishers, but should belong to the public and should be freely available through an international online public library.To encourage the publishers of our journals to support this endeavor, we pledge that, beginning in September 2001, we will publish in, edit or review for, and personally subscribe to only those scholarly and scientific journals that have agreed to grant unrestricted free distribution rights to any and all original research reports that they have published, through PubMed Central and similar online public resources, within 6 months of their initial publication date.

J- Can you get people to sign this and FAX it to me. 1-786-549-0137. Craig and Claires sigs would be greatly appreciated.I assume I can put your name on it, no?I set up a site http://www.publiclibraryofscience.org to keep lists ofpeople who have signed.-M

PLoS After the Letter (2003)

• > 25,000 people signed the letter • Small increase in open access support

• But not enough • So PLoS announced the launch of their own journals •PLoS Biology •PLoS Medicine

Open Data Experiments

Open Data Experiments

Useful but not convinced

Real Life Intervened

RhoGam

• Supplier • RhoGAM should be administered within 72 hours of

known or suspected exposure to Rh-positive red blood cells.

• Wikipedia • It is given by intramuscular injection as part of

modern routine antenatal care at about 28 weeks of pregnancy, and within 72 hours after childbirth.[5] It is also given after antenatal pathological events that are likely to cause a feto-maternal hemorrhage.[6]

• Question • What happens if you do it even later?

http://en.wikipedia.org/wiki/Antenatal

http://en.wikipedia.org/wiki/Rho(D)_Immune_Globulin

http://en.wikipedia.org/wiki/Rho(D)_Immune_Globulin

Pubmed Search

Relevant Paper

Paywall

You can purchase online access to this article (and all its versions) for a 24-hour period. Articles are US $ 29.95, with some exceptions where prices may vary. Click "Buy Now" to display the price

Relevant Paper 2

Paywall

Access Blocked - What Next?

• Bought lots of articles !

• Tried to contact experts !

• Got friends to get some articles from libraries !

• Got more and more pissed off

Baby Lost

• Benjamin Augustin Eisen stillborn August 29, 2003

Lack of Access

• Scientist without access !

• Would access have helped? !

• Is limiting access useful or needed? !

• Goal of much of scientific and medical research is to spread knowledge

Closed Accessitis Still Prevalent


Cure for Diabetes?

New Diabetes Stem Cell Paper in Cell

Full Text of Paper

Paywall

HHMI Supports Open Access

Social Media Critiques

HHMI Responds

Cure for Cell Accessitis?


Cure for the Disease?

The Microbe Era

MICROBES RUN THE PLANET

The Built Environment

ORIGINAL ARTICLE

Architectural design influences the diversity andstructure of the built environment microbiome

Steven W Kembel1, Evan Jones1, Jeff Kline1,2, Dale Northcutt1,2, Jason Stenson1,2,Ann M Womack1, Brendan JM Bohannan1, G Z Brown1,2 and Jessica L Green1,3

1Biology and the Built Environment Center, Institute of Ecology and Evolution, Department ofBiology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory,Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute,Santa Fe, NM, USA

Buildings are complex ecosystems that house trillions of microorganisms interacting with eachother, with humans and with their environment. Understanding the ecological and evolutionaryprocesses that determine the diversity and composition of the built environment microbiome—thecommunity of microorganisms that live indoors—is important for understanding the relationshipbetween building design, biodiversity and human health. In this study, we used high-throughputsequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes andairborne bacterial communities at a health-care facility. We quantified airborne bacterial communitystructure and environmental conditions in patient rooms exposed to mechanical or windowventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities waslower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbialcommunities than did window-ventilated rooms. Bacterial communities in indoor environmentscontained many taxa that are absent or rare outdoors, including taxa closely related to potentialhuman pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relativehumidity and temperature, were correlated with the diversity and composition of indoor bacterialcommunities. The relative abundance of bacteria closely related to human pathogens was higherindoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity.The observed relationship between building design and airborne bacterial diversity suggests thatwe can manage indoor environments, altering through building design and operation the communityof microbial species that potentially colonize the human microbiome during our time indoors.The ISME Journal advance online publication, 26 January 2012; doi:10.1038/ismej.2011.211Subject Category: microbial population and community ecologyKeywords: aeromicrobiology; bacteria; built environment microbiome; community ecology; dispersal;environmental filtering

Introduction

Humans spend up to 90% of their lives indoors(Klepeis et al., 2001). Consequently, the way wedesign and operate the indoor environment has aprofound impact on our health (Guenther andVittori, 2008). One step toward better understandingof how building design impacts human healthis to study buildings as ecosystems. Built envi-ronments are complex ecosystems that containnumerous organisms including trillions of micro-organisms (Rintala et al., 2008; Tringe et al., 2008;Amend et al., 2010). The collection of microbiallife that exists indoors—the built environment

microbiome—includes human pathogens and com-mensals interacting with each other and with theirenvironment (Eames et al., 2009). There have beenfew attempts to comprehensively survey the builtenvironment microbiome (Rintala et al., 2008;Tringe et al., 2008; Amend et al., 2010), with moststudies focused on measures of total bioaerosolconcentrations or the abundance of culturable orpathogenic strains (Berglund et al., 1992; Toivolaet al., 2002; Mentese et al., 2009), rather than a morecomprehensive measure of microbial diversity inindoor spaces. For this reason, the factors thatdetermine the diversity and composition of the builtenvironment microbiome are poorly understood.However, the situation is changing. The develop-ment of culture-independent, high-throughputmolecular sequencing approaches has transformedthe study of microbial diversity in a variety ofenvironments, as demonstrated by the recent explo-sion of research on the microbial ecology of aquaticand terrestrial ecosystems (Nemergut et al., 2011)

Received 23 October 2011; revised 13 December 2011; accepted13 December 2011

Correspondence: SW Kembel, Biology and the Built EnvironmentCenter, Institute of Ecology and Evolution, Department of Biology,University of Oregon, Eugene, OR 97405, USA.E-mail: [email protected]

The ISME Journal (2012), 1–11& 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12

www.nature.com/ismej

Microbial Biogeography of Public Restroom SurfacesGilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4,

Noah Fierer1,5*

1 Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America, 2 Department of Computer Science,

University of Colorado, Boulder, Colorado, United States of America, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United

States of America, 4 Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America, 5 Department of Ecology and Evolutionary

Biology, University of Colorado, Boulder, Colorado, United States of America

Abstract

We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, thediversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibitedby bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing ofthe 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla:Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: thosefound on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched withhands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floorsurfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associatedbacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were morecommon in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in femalerestrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomicobservations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate thatrestroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clearlinkages between communities on or in different body sites and those communities found on restroom surfaces. Moregenerally, this work is relevant to the public health field as we show that human-associated microbes are commonly foundon restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touchingof surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determinesources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test theefficacy of hygiene practices.

Citation: Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, et al. (2011) Microbial Biogeography of Public Restroom Surfaces. PLoS ONE 6(11): e28132.doi:10.1371/journal.pone.0028132

Editor: Mark R. Liles, Auburn University, United States of America

Received September 12, 2011; Accepted November 1, 2011; Published November 23, 2011

Copyright: ! 2011 Flores et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was supported with funding from the Alfred P. Sloan Foundation and their Indoor Environment program, and in part by the NationalInstitutes of Health and the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, orpreparation of the manuscript.

Competing Interests: The authors have declared that no competing interests exist.

* E-mail: [email protected]

Introduction

More than ever, individuals across the globe spend a largeportion of their lives indoors, yet relatively little is known about themicrobial diversity of indoor environments. Of the studies thathave examined microorganisms associated with indoor environ-ments, most have relied upon cultivation-based techniques todetect organisms residing on a variety of household surfaces [1–5].Not surprisingly, these studies have identified surfaces in kitchensand restrooms as being hot spots of bacterial contamination.Because several pathogenic bacteria are known to survive onsurfaces for extended periods of time [6–8], these studies are ofobvious importance in preventing the spread of human disease.However, it is now widely recognized that the majority ofmicroorganisms cannot be readily cultivated [9] and thus, theoverall diversity of microorganisms associated with indoorenvironments remains largely unknown. Recent use of cultiva-tion-independent techniques based on cloning and sequencing ofthe 16 S rRNA gene have helped to better describe these

communities and revealed a greater diversity of bacteria onindoor surfaces than captured using cultivation-based techniques[10–13]. Most of the organisms identified in these studies arerelated to human commensals suggesting that the organisms arenot actively growing on the surfaces but rather were depositeddirectly (i.e. touching) or indirectly (e.g. shedding of skin cells) byhumans. Despite these efforts, we still have an incompleteunderstanding of bacterial communities associated with indoorenvironments because limitations of traditional 16 S rRNA genecloning and sequencing techniques have made replicate samplingand in-depth characterizations of the communities prohibitive.With the advent of high-throughput sequencing techniques, wecan now investigate indoor microbial communities at anunprecedented depth and begin to understand the relationshipbetween humans, microbes and the built environment.

In order to begin to comprehensively describe the microbialdiversity of indoor environments, we characterized the bacterialcommunities found on ten surfaces in twelve public restrooms(six male and six female) in Colorado, USA using barcoded

PLoS ONE | www.plosone.org 1 November 2011 | Volume 6 | Issue 11 | e28132

the stall in), they were likely dispersed manually after women usedthe toilet. Coupling these observations with those of thedistribution of gut-associated bacteria indicate that routine use oftoilets results in the dispersal of urine- and fecal-associated bacteriathroughout the restroom. While these results are not unexpected,they do highlight the importance of hand-hygiene when usingpublic restrooms since these surfaces could also be potentialvehicles for the transmission of human pathogens. Unfortunately,previous studies have documented that college students (who arelikely the most frequent users of the studied restrooms) are notalways the most diligent of hand-washers [42,43].

Results of SourceTracker analysis support the taxonomicpatterns highlighted above, indicating that human skin was theprimary source of bacteria on all public restroom surfacesexamined, while the human gut was an important source on oraround the toilet, and urine was an important source in women’srestrooms (Figure 4, Table S4). Contrary to expectations (seeabove), soil was not identified by the SourceTracker algorithm asbeing a major source of bacteria on any of the surfaces, includingfloors (Figure 4). Although the floor samples contained family-leveltaxa that are common in soil, the SourceTracker algorithmprobably underestimates the relative importance of sources, like

Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces. Light blue indicates lowabundance while dark blue indicates high abundance of taxa. (A) Although skin-associated taxa (Propionibacteriaceae, Corynebacteriaceae,Staphylococcaceae and Streptococcaceae) were abundant on all surfaces, they were relatively more abundant on surfaces routinely touched withhands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae, Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were mostabundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in lowabundance on all restroom surfaces, they were relatively more abundant on the floor of the restrooms we surveyed. Figure not drawn to scale.doi:10.1371/journal.pone.0028132.g003

Figure 4. Results of SourceTracker analysis showing the average contributions of different sources to the surface-associatedbacterial communities in twelve public restrooms. The ‘‘unknown’’ source is not shown but would bring the total of each sample up to 100%.doi:10.1371/journal.pone.0028132.g004

Bacteria of Public Restrooms


high diversity of floor communities is likely due to the frequency ofcontact with the bottom of shoes, which would track in a diversityof microorganisms from a variety of sources including soil, which isknown to be a highly-diverse microbial habitat [27,39]. Indeed,bacteria commonly associated with soil (e.g. Rhodobacteraceae,Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average,more abundant on floor surfaces (Figure 3C, Table S2).Interestingly, some of the toilet flush handles harbored bacterialcommunities similar to those found on the floor (Figure 2,Figure 3C), suggesting that some users of these toilets may operatethe handle with a foot (a practice well known to germaphobes andthose who have had the misfortune of using restrooms that are lessthan sanitary).

While the overall community level comparisons between thecommunities found on the surfaces in male and female restroomswere not statistically significant (Table S3), there were gender-

related differences in the relative abundances of specific taxa onsome surfaces (Figure 1B, Table S2). Most notably, Lactobacillaceaewere clearly more abundant on certain surfaces within femalerestrooms than male restrooms (Figure 1B). Some species of thisfamily are the most common, and often most abundant, bacteriafound in the vagina of healthy reproductive age women [40,41]and are relatively less abundant in male urine [28,29]. Ouranalysis of female urine samples collected as part of a previousstudy [26] (Figure 1A), found that Lactobacillaceae were dominant inurine, therefore implying that surfaces in the restrooms whereLactobacillaceae were observed were contaminated with urine. Otherstudies have demonstrated a similar phenomenon, with vagina-associated bacteria having also been observed in airplanerestrooms [11] and a child day care facility [10]. As we foundthat Lactobacillaceae were most abundant on toilet surfaces andthose touched by hands after using the toilet (with the exception of

Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces. Communities were clustered usingPCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) surfacesform clusters distinct from surfaces touched with hands.doi:10.1371/journal.pone.0028132.g002

Table 1. Results of pairwise comparisons for unweighted UniFrac distances of bacterial communities associated with varioussurfaces of public restrooms on the University of Colorado campus using the ANOSIM test in Primer v6.

Door in Door out Stall in Stall outFaucethandle

Soapdispenser

Toilet flushhandle Toilet seat Toilet floor

Door in

Door out 20.139

Stall in 0.149 20.053

Stall out 20.074 20.083 20.037

Faucet handle 20.062 20.011 20.092 20.040

Soap dispenser 20.020 0.014 20.060 20.001 0.070

Toilet flush handle 0.376* 0.405* 0.221 0.350* 0.172* 0.470*

Toilet seat 0.742* 0.672* 0.457* 0.586* 0.401* 0.653* 0.187*

Toilet floor 0.995* 0.988* 0.993* 0.961* 0.758* 0.998* 0.577* 0.950*

Sink floor 1.000* 0.995* 1.000* 0.974* 0.770* 1.000* 0.655* 0.982* 20.033

The R-statistic is shown for each comparison with asterisks denoting comparisons that were statistically significant at P#0.01.doi:10.1371/journal.pone.0028132.t001

Bacteria of Public Restrooms


10 FEBRUARY 2012 VOL 335 SCIENCE www.sciencemag.org 650

NEWSFOCUS

CR

ED

ITS

(T

OP

TO

BO

TT

OM

): (P

HO

TO

) C

OU

RT

ES

Y G

ILB

ER

TO

FLO

RE

S; (C

HA

RT

) G

. E

. F

LO

RE

S E

T A

L.,

PLO

S O

NE

6, 1

1 (2

01

1);

PH

OT

O B

Y S

ISIR

A G

OR

TH

ALA

In just that short time, the microbes had begun to take on a “signature” of outside air (more types from plants and soil), and 2 hours after the windows were shut again, the proportion of microbes from the human body increased back to pre-vious levels.

The s tudy, which appeared online 26 Janu-ary in The ISME Journal, found that mechanically ventilated rooms had lower microbial diversity than ones with open win-dows. The availability of fresh air translated into lower proportions of microbes associ-ated with the human body, and consequently, fewer potential pathogens. Although this result suggests that having natural airfl ow may be healthier, Green says answering that question requires clinical data; she’s hoping to convince a hospital to participate in a study to see if the incidence of hospital-acquired infections is associated with a room’s micro-bial community.

For his part, Peccia, who is also a Sloan grantee, is merging microbiology and the

physics of aerosols to look more closely at how the movement of air affects microbes. Peccia says his group is building on work by air-quality engineers and scientists, but “we want to add biology to the equation.”

Bacteria in air behave like other particles; their size dictates how they disperse or settle. Humans in a room not only shed microbes from their skin and mouths, but they also drum up microbial material from the fl oor as

they move around. But to quantify those con-tributions, Peccia’s team has had to develop new methods to collect airborne bacteria and extract their DNA, as the microbes are much less abundant in air than on surfaces.

In one recent study, they used air fi lters to sample airborne particles and microbes in a classroom during 4 days during which students were present and 4 days during which the room was vacant. They measured the abundance and type of fungal and bac-terial genomes present and estimated the microbes’ concentrations in the entire room. By accounting for bacteria entering and leav-

ing the room through ventilation, they calculated that people shed or resuspended about 35 million bacterial cells per person per hour. That number is much higher than the several-hundred-thousand maximum previously estimated to be present in indoor air, Peccia reported last fall at the American Association for Aerosol Research Conference in Orlando, Florida.

His group’s data also suggest that rooms have “memories” of past human inhabitants. By kick-ing into the air settled microbes from the fl oor, occupants expose themselves not just to the microbes of a person coughing next to them, but also possibly to those from a person who coughed in the room a few hours or even days ago.

Peccia hopes to come up with ways to describe the distribution of bacteria indoors that can be used in conjunction with exist-ing knowledge about particulate matter and chemicals in designing healthier buildings. “My hope is that we can bring this enough to the forefront that people who do aerosol sci-ence will fi nd it as important to know biology as to know physics and chemistry,” he says.

Still, even though he’s a willing partici-

pant in indoor microbial ecology research, Peccia thinks that the field has yet to gel. And the Sloan Foundation’s Olsiewski shares some of his con-cern. “Everybody’s gen-erating vast amounts of

data,” she says, but looking across data sets can be diffi cult because groups choose dif-ferent analytical tools. With Sloan support, though, a data archive and integrated analyt-ical tools are in the works.

To foster collaborations between micro-biologists, architects, and building scientists, the foundation also sponsored a symposium on the microbiome of the built environment at the 2011 Indoor Air conference in Austin, Texas, and launched a Web site, MicroBE.net, that’s a clearinghouse of information on the fi eld. Although Olsiewski won’t say how long the foundation will fund its indoor microbial ecology program, she says Sloan is committed to supporting all of the current projects for the next few years. The program’s ultimate goal, she says, is to create a new fi eld of scientifi c inquiry that eventually will be funded by tradi-tional government funding agencies focused on basic biology and environmental policy.

Matthew Kane, a microbial ecologist and program director at the U.S. National Sci-ence Foundation (NSF), says that although there was interest in these questions prior to the Sloan program, the Sloan Foundation has taken a directed approach to funding the research, and “I have no doubt that their investment is going to reap great returns.” So far, though, NSF has funded only one study on indoor microbes: a study of Pseudomonas bacteria in human households.

As studies like Green’s building ecology analysis progress, they should shed light on how indoor environments differ from those traditionally studied by microbial ecologists. “It’s important to have a quantitative under-standing of how building design impacts microbial communities indoors, and how these communities impact human health,” Green says. But it remains to be seen whether we’ll someday design and maintain our build-ings with microbes in mind.

–COURTNEY HUMPHRIES

Courtney Humphries is a freelance writer in Boston and author of Superdove.

100

80

60

40

20

0

Ave

rag

e c

on

trib

uti

on

(%

)

Door in

Door out

Stall i

n

Stall o

ut

Faucet h

andles

Soap disp

enser

Toile

t seat

Toile

t flu

sh h

andle

Toile

t flo

or

Sink f

loor

SOURCES

Soil

Water

Mouth

Urine

Gut

Skin

Outside infl uence. Students prepare to sample air outside a class-room in China as part of an indoor ecology study.

Bathroom biogeography. By swabbing different surfaces in public restrooms, researchers determined that microbes vary in where they come from depend-ing on the surface (chart).

Published by AAAS

on

Febr

uary

9, 2

012

ww

w.s

cien

cem

ag.o

rgD

ownl

oade

d fro

m

The Human Microbiome

Antimicrobials are in Everything

Become a Guardian of Microbial Diversity

Diversity in STEM

Diabetic at Conference

Diversity in STEM

Diversity in STEM #DoSomething

Opening up to Diversity talk by @phylogenomics at #UCDPHSA

Science

Transcript of Opening up to Diversity talk by @phylogenomics at #UCDPHSA