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

Symptom of A New Disease
Closed Accessitis

Symptom of A New Disease
Elsevieritis
Closed Accessitis

Disease Known for Many Years
Elsevieritis
Closed Accessitis

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 of
people 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
Useful but not convinced

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?

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

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
Elsevieritis
Closed Accessitis

New Diabetes Stem Cell Paper in Cell

Cure for Cell Accessitis?
Elsevieritis
Closed Accessitis

The Microbe Era
MICROBES
RUN THE
PLANET

The Built Environment
The ISME Journal (2012), 1–11
& 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12
www.nature.com/ismej
ORIGINAL ARTICLE
Architectural design influences the diversity and
structure of the built environment microbiome
Bacteria of Public time, the
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 of
Biology, 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
0 Average contribution (%)
Door in
Buildings are complex ecosystems that house trillions of microorganisms interacting with each
other, with humans and with their environment. Understanding the ecological and evolutionary
processes that determine the diversity and composition of the built environment microbiome—the
community of microorganisms that live indoors—is important for understanding the relationship
between building design, biodiversity and human health. In this study, we used high-throughput
sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and
airborne bacterial communities at a health-care facility. We quantified airborne bacterial community
structure and environmental conditions in in
patient out
ventilation and in outdoor air. The phylogenetic Stall Stall diversity handles
rooms exposed to mechanical or window
of airborne bacterial communities was
lower indoors than outdoors, and mechanically Faucet ventilated rooms contained less diverse microbial
communities than did window-ventilated rooms. Bacterial communities in indoor environments
contained many taxa that are absent or rare outdoors, including taxa closely related to potential
human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative
humidity and temperature, were correlated with the diversity and composition of indoor bacterial
communities. The relative abundance of bacteria closely related to human pathogens was higher
indoors 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 that
we can manage indoor environments, altering through building design and operation the community
of 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.2011.211
Subject Category: microbial population and community ecology
Keywords: aeromicrobiology; bacteria; built environment microbiome; community ecology; dispersal;
environmental filtering
Introduction
Humans spend up to 90% of their lives indoors
Toilet seat
Toilet flush handle
Sink floor
microbiome—includes human pathogens and com-mensals
interacting with each other and with their
Microbial Biogeography of Public Restroom Surfaces
Gilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4,
Noah Fierer1,5*
Bacteria of Public Restrooms
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, the
diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited
by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of
the 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: those
found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with
hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor
surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated
bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more
common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female
restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic
observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that
restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear
linkages between communities on or in different body sites and those communities found on restroom surfaces. More
generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found
on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching
of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine
sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the
efficacy of hygiene practices.
Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces. Light blue indicates low
abundance 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 with
hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae, Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were most
abundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in low
abundance 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
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 permits
unrestricted 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 National
Institutes of Health and the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or
preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: noah.fierer@colorado.edu
Introduction
More than ever, individuals across the globe spend a large
portion of their lives indoors, yet relatively little is known about the
microbial diversity of indoor environments. Of the studies that
have examined microorganisms associated with indoor environ-ments,
differences in the relative abundances of specific some surfaces (Figure 1B, Table S2). Most notably, were clearly more abundant on certain surfaces restrooms than male restrooms (Figure 1B). Some family are the most common, and often most abundant, found in the vagina of healthy reproductive age women Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces. Communities were PCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) form clusters distinct from surfaces touched with hands.
doi:10.1371/journal.pone.0028132.g002
most have relied upon cultivation-based techniques to
detect organisms residing on a variety of household surfaces [1–5].
Not surprisingly, these studies have identified surfaces in kitchens
and restrooms as being hot spots of bacterial contamination.
Because several pathogenic bacteria are known to survive on
surfaces for extended periods of time [6–8], these studies are of
obvious importance in preventing the spread of human disease.
However, it is now widely recognized that the majority of
microorganisms cannot be readily cultivated [9] and thus, the
communities and revealed a greater diversity of bacteria on
indoor surfaces than captured using cultivation-based techniques
[10–13]. Most of the organisms identified in these studies are
related to human commensals suggesting that the organisms are
not actively growing on the surfaces but rather were deposited
directly (i.e. touching) or indirectly (e.g. shedding of skin cells) by
humans. Despite these efforts, we still have an incomplete
understanding of bacterial communities associated with indoor
environments because limitations of traditional 16 S rRNA gene
cloning and sequencing techniques have made replicate sampling
and in-depth characterizations of the communities prohibitive.
With the advent of high-throughput sequencing techniques, we
can now investigate indoor microbial communities at an
unprecedented depth and begin to understand the relationship
between humans, microbes and the built environment.
the stall in), they were likely dispersed manually after women used
the toilet. Coupling these observations with those of the
distribution of gut-associated bacteria indicate that routine use of
toilets results in the dispersal of urine- and fecal-associated bacteria
throughout the restroom. While these results are not unexpected,
they do highlight the importance of hand-hygiene when using
public restrooms since these surfaces could also be potential
vehicles for the transmission of human pathogens. Unfortunately,
previous studies have documented that college students (who are
likely the most frequent users of the studied restrooms) are not
always the most diligent of hand-washers [42,43].
Results of SourceTracker analysis support the taxonomic
patterns highlighted above, indicating that human skin was the
primary source of bacteria on all public restroom surfaces
examined, while the human gut was an important source on or
around the toilet, and urine was an important source in women’s
restrooms (Figure 4, Table S4). Contrary to expectations (see
above), soil was not identified by the SourceTracker algorithm as
being a major source of bacteria on any of the surfaces, including
floors (Figure 4). Although the floor samples contained family-level
taxa that are common in soil, the SourceTracker algorithm
probably underestimates the relative importance of sources, like
high diversity of floor communities is likely due to the frequency of
contact with the bottom of shoes, which would track in a diversity
of microorganisms from a variety of sources including soil, which is
known 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,
begun to take
of outside
from plants
hours after
were shut
proportion of
the human
back to pre-vious
which
26 Janu-ary
Journal,
mechanically
had lower
diversity than ones with open win-dows.
availability of fresh air translated
proportions of microbes associ-ated
human body, and consequently,
pathogens. Although this
that having natural airfl ow
Green says answering that
clinical data; she’s hoping
hospital to participate in a study
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
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
100
80
60
40
20
Door out
Soap dispenser
Toi l et f lo o r
SOURCES
Soil
Water
Mouth
Urine
Gut
Skin
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).
on February 9, 2012

Antimicrobials are in Everything

Become a Guardian of Microbial Diversity

Diversity in STEM #DoSomething

Opening up to Diversity talk by @phylogenomics at #UCDPHSA

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Similar to Opening up to Diversity talk by @phylogenomics at #UCDPHSA

Similar to Opening up to Diversity talk by @phylogenomics at #UCDPHSA (20)

More from Jonathan Eisen

More from Jonathan Eisen (20)

Recently uploaded

Recently uploaded (20)

Opening up to Diversity talk by @phylogenomics at #UCDPHSA