Friends who went to Pyle Junior High may appreciate this story more than other people. A few years ago I told my kids a story about throwing up on the Vice Principal of Pyle – Mr Pecos. They got me to tell this story over and over and then one day a new kind creature appeared in their play stories – the evil “Pecoses”. And now Pecoses are everywhere. Here are some pics and a video of some Pecoses
Here is a wrap up, via my twitter posts and responses to them, of the seminar yesterday by Charles M. Vest, ex head of MIT and current head of the National Academy of Engineering. I know it is a bit lazy not to rewrite a summary but I think the tweets do an OK job …
UPDATE – some new links regarding the talk
| phylogenomics Awaiting seminar by CHarles Vest, Pres. of US Natl. Acad. Engineering, past pres. of MIT #UCDavis 11/30/11 4:07 PM |
| phylogenomics Vest seminar “The 21st Century Research University Purpose, Problems and Promise” #UCDavis 11/30/11 4:08 PM |
| phylogenomics Charles Vest http://t.co/NlxrgeeE says Linda Katehi is an admired educational leader throughout the country #UCDavis 11/30/11 4:10 PM |
| phylogenomics Charles Vest: two main challenges for universities now are globalization and access (i.e., access to education) 11/30/11 4:13 PM |
| phylogenomics Charles Vest: currently trend to “brain interaction” across the globe, but need to work on how to connect people & computers better 11/30/11 4:14 PM |
| phylogenomics Vest: FoldIt tool is evidence for “collective intelligence” – the researchers involved weren’t just integrating computers but brains 11/30/11 4:15 PM |
| phylogenomics Vest discussing book A New Culture of Learning by Douglas Thomas and John Seely Brown “www.newcultureoflearning.com/” 11/30/11 4:16 PM |
| phylogenomics Vest says location of universities still matter for many reasons incl. people need to be together and universities are embedded in cultures 11/30/11 4:17 PM |
| phylogenomics Vest: purpose of research universities is “to create opportunity” (1) for graduates, (2) for business/industry (3) nations/regions 11/30/11 4:19 PM |
| phylogenomics Vest: though research universities have many purposes, must be patient b/c hard to predict when benefits will occur 11/30/11 4:20 PM |
| phylogenomics Vest: MIT and Stanford work very well b/c research is side by side w/ applications 11/30/11 4:21 PM |
| phylogenomics Vest: few people understand that research universities are central to innovation (e.g., computing, laser, internet, gennomics) 11/30/11 4:22 PM |
| phylogenomics Note – I might disagree with Vest’s claim that Universities drove genomic innovation 11/30/11 4:23 PM |
| phylogenomics Vest: virtually every job in America depends on one or more university based innovations 11/30/11 4:23 PM |
| phylogenomics Vest six lessons including (1) teaching and research must be intimately intertwined and are inseparable 11/30/11 4:24 PM |
| phylogenomics Vest lesson 2: quality of research university is determined by quality of its faculty 11/30/11 4:25 PM |
| oldivory @phylogenomics I’ve quit telling kids to interview the faculty when applying to colleges. Parents don’t get it either. Ah, well. 11/30/11 4:29 PM |
| phylogenomics @oldivory good idea … 11/30/11 4:30 PM |
| phylogenomics Vest: need in particular young faculty to grow up through rising w/in university 11/30/11 4:26 PM |
| phylogenomics Vest lesson 3: science can flourish only in an open environment #herehere 11/30/11 4:26 PM |
| phylogenomics Vest lesson 4: young faculty must be free to study and teach what they believe is important (e.g., should not be assistants to Sr. faculty) 11/30/11 4:27 PM |
| KSBruno9 @phylogenomics so not the European model. 11/30/11 5:11 PM |
| phylogenomics Vest lesson 5: competition engenders excellence in universities (drives improvement in research, teaching, ideas, facilities, etc) 11/30/11 4:28 PM |
| rmtakata @phylogenomics @carloshotta Mild competition. Wild competition could lead to cheating, forgery, distrust, sabotage… 11/30/11 4:32 PM |
| phylogenomics @rmtakata @carloshotta he did not say it was perfect, just that it can be useful 11/30/11 4:34 PM |
| phylogenomics Vest Lesson 6: fundamental scholarship and research must be equal w/ applied research and innovation 11/30/11 4:29 PM |
| phylogenomics Vest: there is a danger in focus on applied issues that we ignore search for truth – must not be too utilitarian 11/30/11 4:30 PM |
| phylogenomics Vest says “never in his lifetime has it been so hard to hang onto his optimism” b/c Washington is broken 11/30/11 4:32 PM |
| tjsharpton As a young researcher, this concerns me RT @phylogenomics Vest says “never in his lifetime has it been so har… (cont) http://t.co/eZwvMurX 11/30/11 5:23 PM |
| phylogenomics Vest: v. concerned w/ financial pressures on universities especially as it affects access & this started even before recent financial issues 11/30/11 4:33 PM |
| phylogenomics Vest: in the last decade real per student state appropriations have dropped >20% while costs have risen 11/30/11 4:35 PM |
| phylogenomics Vest: response to financial issues will be cut back on low demand classes, fewer low/middle $$ students, decr. in merit based aid & all bad 11/30/11 4:36 PM |
| phylogenomics Vest: the favorite solution to State university financial problems is to seek out of state students; this spirals out of control 11/30/11 4:37 PM |
| phylogenomics Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man” 11/30/11 4:37 PM |
| jim_croft nice… but also woman? RT @phylogenomics: Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man” 11/30/11 4:43 PM |
| phylogenomics @jim_croft I was not endorsing – just reporting 11/30/11 4:44 PM |
| jim_croft @phylogenomics of course – the sentiment is perfect, the wording is excellent, for its time, just a little dated in some circles today. 11/30/11 4:49 PM |
| phylogenomics Vest references Vannevar Bush’s vision “Science The Endless Frontier” for research & for access http://t.co/9n1Q0LAF 11/30/11 4:39 PM |
| phylogenomics Vest references Vannevar Bush Quote on education access http://t.co/LmE1bTF7 11/30/11 4:42 PM |
| phylogenomics Vest: we must be good citizens of the world and contribute to and learn from increasing globalization of education 11/30/11 4:43 PM |
| phylogenomics Vest: all regions of the world are more/more linked/integrated w/ shared environment, challenges, resources, knowledge, humanity 11/30/11 4:45 PM |
| phylogenomics Vest: modern research universities concept was developed from Humboldt University in Germany in 1800s -> JHU in US -> others in US -> global 11/30/11 4:46 PM |
| phylogenomics Vest says he has a hard time contemplating scale of educational expansion in China and India 11/30/11 4:46 PM |
| phylogenomics Vest: the Yin and Yang of Universities are Competition and Collaboration 11/30/11 4:47 PM |
| phylogenomics Vest: people everywhere need opportunity from universities and thus MIT developed “Open Courseware” for anyone to use anywhere/anytime 11/30/11 4:48 PM |
| phylogenomics Vest: Open Courseware movement has spread globally – and it (and related initiatives) are a revolution 11/30/11 4:49 PM |
| mikedelic @phylogenomics I’ve taken free courses from Stanford and MIT that imwoudlnt have been able to back in the day. Love open source education 11/30/11 5:07 PM |
| mikedelic @phylogenomics my favorite was Robert sapolsky’s behavioral biology course from Stanford 11/30/11 5:08 PM |
| phylogenomics Vest: openness is the true spirit of education, democratization and empowerment 11/30/11 4:49 PM |
| phylogenomics Vest refs: “Unlocking the Gates” and “Abelard to Apple” – books about open education 11/30/11 4:50 PM |
| phylogenomics Vest: in 21st century we are observing the early emergence of a “Meta University” via open materials and platforms 11/30/11 4:51 PM |
| phylogenomics Vest: must rekindle spirit of research university as provider of opportunity while also promoting openness 11/30/11 4:52 PM |
| phylogenomics Here is more form Charles Vest on the “meta university” http://t.co/tJ0fNSqo 11/30/11 4:53 PM |
| phylogenomics Vest: analog of Tip ONeil’s “all politics is local” need outreach to get people locally to understand importance of research universities 11/30/11 5:03 PM |
| phylogenomics Questioner asks Vest how to best export notion of democracy/ access 11/30/11 5:09 PM |
| phylogenomics Vest in response to question expresses dismay at how anyone could support the “Dream Act” http://t.co/FpwekBzu 11/30/11 5:09 PM |
| lukedones @phylogenomics Dismay that anyone would *support* the DREAM Act? Why? 11/30/11 5:12 PM |
| phylogenomics @lukedones do you mean why would anyone be dismayed that some support the act? 11/30/11 5:15 PM |
| lukedones @phylogenomics Yes. Just wondering whether he gave a reason. 11/30/11 5:21 PM |
| phylogenomics @lukedones not that I remember 11/30/11 5:21 PM |
| phylogenomics @lukedones sorry – in looking at the Dream Act I am wondering if he misspoke and meant he supported it … no longer sure what he said 11/30/11 6:24 PM |
| VoteBothell @phylogenomics why no support for Dream Act? 11/30/11 7:01 PM |
| phylogenomics Sorry all; MAJOR error tweeting Charles Vest talk; I wrote he was against Dream Act; I think he/I got that backwards & must be for it 11/30/11 7:19 PM |
| phylogenomics @VoteBothell sorry – I think he must be for it – so either he or I got it backwards 11/30/11 7:20 PM |
| VoteBothell @phylogenomics Great, got it. Enjoy your tweets. I’ve been following you since the pepper spray. My support and thoughts are with UC Davis. 11/30/11 7:22 PM |
| lukedones @phylogenomics Thanks – I expected an academic would be for the Dream Act. 11/30/11 7:26 PM |
| phylogenomics Vest: we need more experimentation with how research is funded to try to find other ways 11/30/11 5:21 PM |
| phylogenomics Vest: should keep systems at basic science agencies but should try new approaches like ARPA-E 11/30/11 5:22 PM |
| phylogenomics Vest views Open Courseware as a new form of publication not really as “classes” per se, b/c not interactive 11/30/11 5:25 PM |
The California Aggie, the UC Davis student newspaper is also doing a great job with covering the Occupy UC Davis saga. Here are some links of interest:
The Davis Enterprise has really come through in the clutch with diverse coverage of the pepper spraying incident as well as diverse, interesting and sometimes unusual letters and comments. Here are some links from them of interest:
News Stories
There was a letter published in the Davis Enterprise (Letter to the Editor – The Davis Enterprise) co-signed by many UC Davis Faculty. I have been sent the letter by Walter Leal, one of the coordinators of the distribution and signing, and he also sent the latest list of faculty signers (which has expanded greatly since the Enterprise letter was published). I am posting the letter and the latest list here. Note – I am also (slowly) adding links to web pages for the faculty so that people can find out more about who they are.
We, the undersigned UC Davis faculty, support the free exchange of ideas on campus and students’ right to peaceful protests. We are appalled by the events of Friday, Nov. 18 in the Quad, but heartened by the Chancellor’s apology and her commitment to listen to and work on the students’ concerns. We strongly believe that Linda Katehi is well-qualified to lead our university through this difficult healing process and oppose the premature calls for her resignation; this is not in the best interest of our university.
Notes (I note – I am copying much of the text from the paper not rewriting it.)
What was sampled?
Ten surfaces (door handles into and out of the restroom, handles into and out of a restroom stall, faucet handles, soap dispenser, toilet seat, toilet flush handle, floor around the toilet and floor around the sink) in six male and six female restrooms evenly distributed across two buildings on the University of Colorado at Boulder campus were sampled on a single day in November 2010.
Surfaces where sampled using sterile, cotton-tipped swabs as described previously [14], [15]. As the 12 restrooms were nearly identical in design, we were able to swab the same area at each location between restrooms. In order to characterize tap water communities as a potential source of bacteria, 1 L of faucet water from six of the restrooms (each building having the same water source for each restroom sampled) was collected and filtered through 0.2 µm bottle top filters (Nalgene, Rochester, NY, USA).
How did they get DNA?
Genomic DNA was extracted from the swabs and filters using the MO BIO PowerSoil DNA isolation kit following the manufacturer’s protocol with the modifications of Fierer et al. [14].
How did they get sequence data?
A portion of the 16 S rRNA gene spanning the V1–V2 regions was amplified using the primer set (27 F/338R), PCR mixture conditions and thermal cycling conditions described in Fierer et al. [15]. PCR amplicons of triplicate reactions for each sample were pooled at approximately equal amounts and pyrosequenced at 454 Life Sciences (Branford, CT, USA) on their GS Junior system. A total of 337,333 high-quality partial 16 S rRNA gene sequences were obtained from 101 of the 120 surface samples collected, averaging approximately 3,340 sequences per sample (ranging from 513–6,771) (Table S1) in 4 GS Junior runs, with the best run containing 116,004 high-quality reads. An additional 16,416 sequences (ranging from 2161–5084 per sample) were generated for five of the six water samples collected for source tracking analysis. Each sample was amplified with a unique barcode to enable multiplexing in the GS Junior runs. The barcoded sequencing reads can be separated by data analysis software providing high confidence in assigning sequencing read to each sample. Sequence data generated as part of this study is available upon request by contacting the corresponding author.
How did they analyze the data?
All sequences generated for this study and previously published data sets used for source tracking (see below) were processed and sorted using the default parameters in QIIME [16]. Briefly, high-quality sequences (>200 bp in length, quality score >25, exact match to barcode and primer, and containing no ambiguous characters) were trimmed to 300 bp and clustered into operational taxonomic units (OTUs) at 97% sequence identity using UCLUST [17]. Representative sequences for each OTU were then aligned using PyNAST [18] against the Greengenes core set [19] and assigned taxonomy with the RDP-classifier [20]. Aligned sequences were used to generate a phylogenetic tree with FastTree [21] for both alpha- (phylogenetic diversity, PD)[22] and beta-diversity (unweighted UniFrac) [23] metrics. The unweighted UniFrac metric, which only accounts for the presence/absence of taxa and not abundance, was used to determine the phylogenetic similarity of the bacterial communities associated with the various restroom surfaces. The UniFrac distance matrix was imported into PRIMER v6 where principal coordinate analysis (PCoA) and analysis of similarity (ANOSIM) were conducted to statistically test the relationship between the various communities [24]. In order to eliminate potential biases introduced by sampling depth, all samples (including those used in source tracking) were rarified to 500 sequences per sample for taxonomic, alpha-diversity (PD), beta-diversity (UniFrac) and source tracking comparisons.
Sourcetracking
To determine the potential sources of bacteria on restroom surfaces and how the importance of different sources varied across the sampled locations, we used the newly developed SourceTracker software package [25]. The SourceTracker model assumes that each surface community is merely a mixture of communities deposited from other known or unknown source environments and, using a Bayesian approach, the model provides an estimate of the proportion of the surface community originating from each of the different sources. When a community contains a mixture of taxa that do not match any of the source environments, that portion of the community is assigned to an “unknown” source. Potential sources we examined included human skin (n = 194), mouth (n = 46), gut (feces) (n = 45) [26] and urine (n = 50), as well as soil (n = 88) [27] and faucet water (n = 5, see above). For skin communities, sequences collected from eight body habitats (palm, index finger, forearm, forehead, nose, hair, labia minora, glans penis) from seven to nine healthy adults on four occasions were used to determine the average community composition of human skin [26]. The mouth (tongue and cheek swabs), gut and urine communities were determined from the same individuals although the urine-associated communities were not published in the initial report of these data [26]. While urine is generally considered to be sterile, it does pick up bacteria associated with the urethra and genitals [28], [29]. The average soil community was determined from a broad diversity of soil types collected across North and South America [27].
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Notes on Sourcetracking
Abstract to paper:
Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.
Some lines from paper
We developed SourceTracker, a Bayesian approach to identifying sources and proportions of contamination in marker-gene and functional metagenomics studies. Our approach models contamination as a mixture of entire source communities into a sink community, where the mixing proportions are unknown.
SourceTracker’s distinguishing features are its direct estimation of source proportions and its Bayesian modeling of uncertainty about known and unknown source environments.
SourceTracker outperformed these methods (NAIVE BAYES AND RANDOM FORESTS) because it allows uncertainty in the source and sink distributions, and because it explicitly models a sink sample as a mixture of sources.
SourceTracker also assumes that an environment cannot be both a source and a sink, and we recommend research into bidirectional models.
Based on our results, simple analytical steps can be suggested for tracking sources and assessing contamination in newly acquired datasets. Although source-tracking estimates are limited by the comprehensiveness of the source environments used for training, large-scale projects such as the Earth Microbiome Project will dramatically expand the availability of such resources. SourceTracker is applicable not only to source tracking and forensic analysis in a wide variety of microbial community surveys (where did this biofilm come from?), but also to shotgun metagenomics and other population-genetics data. We made our implementation of SourceTracker available as an R package (http://sourcetracker.sf.net/), and we advocate automated tests of deposited data to screen samples that may be contaminated before deposition.
Who was there?
A total of 19 phyla were observed across all restroom surfaces with most sequences (≈92%) classified to one of four phyla: Actinobacteria,Bacteroidetes, Firmicutes or Proteobacteria (Figure 1A, Table S2). Previous cultivation-dependent and –independent studies have also frequently identified these as the dominant phyla in a variety of indoor environments [10]–[13]. Within these dominant phyla, taxa typically associated with human skin (e.g. Propionibacteriaceae,Corynebacteriaceae, Staphylococcaceae and Streptococcaceae) [30]were abundant on all surfaces (Figure 1A). The prevalence of skin bacteria on restroom surfaces is not surprising as most of the surfaces sampled come into direct contact with human skin, and previous studies have shown that skin associated bacteria are generally resilient and can survive on surfaces for extended periods of time [31], [32]. Many other human-associated taxa, including several lineages associated with the gut, mouth and urine, were observed on all surfaces (Figure 1A). Overall, these results demonstrate that, like other indoor environments that have been examined, the microbial communities associated with public restroom surfaces are predominantly composed of human-associated bacteria.
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Figure 1. Taxonomic composition of bacterial communities associated with public restroom surfaces.
(A) Average composition of bacterial communities associated with restroom surfaces and potential source environments. (B) Taxonomic differences were observed between some surfaces in male and female restrooms. Only the 19 most abundant taxa are shown. For a more detailed taxonomic breakdown by gender including some of the variation see Supplemental Table S2.
doi:10.1371/journal.pone.0028132.g001
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Comparative analysis
Comparisons of the bacterial communities on different restroom surfaces revealed that the communities clustered into three general categories: those communities found on toilet surfaces (the seat and flush handle), those communities on the restroom floor, and those communities found on surfaces routinely touched with hands (door in/out, stall in/out, faucet handles and soap dispenser) (Figure 2, Table 1). By examining the relative abundances of bacterial taxa across all of the restroom samples, we can identify taxa driving the overall community differences between these three general categories. Skin-associated bacteria dominate on those surfaces (the circles in Figure 2) that are routinely and exclusively (we hope) touched by hands and unlikely to come into direct contact with other body parts or fluids (Figure 3A). In contrast, toilet flush handles and seats (the asterisk-shaped symbols in Figure 2) were relatively enriched in Firmicutes (e.g.Clostridiales, Ruminococcaceae, Lachnospiraceae, etc.) andBacteroidetes (e.g. Prevotellaceae and Bacteroidaceae) (Figure 3B). These taxa are generally associated with the human gut [26],[33]–[35] suggesting fecal contamination of these surfaces. Fecal contamination could occur either via direct contact (with feces or unclean hands) or indirectly as a toilet is flushed and water splashes or is aerosolized [36]–[38]. From a public health perspective, the high number of gut-associated taxa throughout the restrooms is concerning because enteropathogenic bacteria could be dispersed in the same way as human commensals. Floor surfaces harbored many low abundance taxa (Table S2) and were the most diverse bacterial communities, with an average of 229 OTUs per sample versus most of the other sampled locations having less than 150 OTUs per sample on average (Table S1). The 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, more abundant on floor surfaces (Figure 3C, Table S2). Interestingly, some of the toilet flush handles harbored bacterial communities similar to those found on the floor (Figure 2, Figure 3C), suggesting that some users of these toilets may operate the handle with a foot (a practice well known to germaphobes and those who have had the misfortune of using restrooms that are less than sanitary).
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Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces.
Communities were clustered using PCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) surfaces form clusters distinct from surfaces touched with hands.
doi:10.1371/journal.pone.0028132.g002
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Table 1. Results of pairwise comparisons for unweighted UniFrac distances of bacterial communities associated with various surfaces of public restrooms on the University of Colorado campus using the ANOSIM test in Primer v6.
doi:10.1371/journal.pone.0028132.t001
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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
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Comparisons 2 (Gender)
While the overall community level comparisons between the communities found on the surfaces in male and female restrooms were not statistically significant (Table S3), there were gender-related differences in the relative abundances of specific taxa on some surfaces (Figure 1B, Table S2). Most notably, Lactobacillaceae were clearly more abundant on certain surfaces within female restrooms than male restrooms (Figure 1B). Some species of this family are the most common, and often most abundant, bacteria found in the vagina of healthy reproductive age women [40], [41] and are relatively less abundant in male urine [28], [29]. Our analysis of female urine samples collected as part of a previous study [26] (Figure 1A), found that Lactobacillaceae were dominant in urine, therefore implying that surfaces in the restrooms where Lactobacillaceae were observed were contaminated with urine. Other studies have demonstrated a similar phenomenon, with vagina-associated bacteria having also been observed in airplane restrooms [11] and a child day care facility [10]. As we found that Lactobacillaceae were most abundant on toilet surfaces and those touched by hands after using the toilet (with the exception of 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].
Source Tracking
Human sources:
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).
Soil not an apparent source:
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 soils, that contain highly diverse bacterial communities with no dominant OTUs and minimal overlap between those OTUs in the sources and those found in the surface samples. As soils typically have large numbers of OTUs that are rare (i.e. represented by very few sequences) and the OTU overlap between different soil samples is very low [27], it is difficult to identify specific OTUs indicative of a soil source.
Other potential sources:
The other potential sources we examined, mouth and faucet water, made only minor bacterial contributions to restroom surface communities either because these potential source environments rarely come into contact with restroom surfaces (the mouth – we hope) or they harbor relatively low concentrations of bacteria (faucet water) (Figure 4). While we were able to identify the primary sources for most of the surfaces sampled, many other sources, such as ventilation systems or mops used by the custodial staff, could also be contributing to the restroom surface bacterial communities. More generally, the SourceTracker results demonstrate how direct comparison of bacterial communities from samples of various environment types to those gathered from other settings can be used to determine the relative contribution of that source across samples. Although many of the source-tracking results evident from the restroom surfaces sampled here are somewhat obvious, this may not always be the case in other environments or locations. We could use the same techniques to identify unexpected sources of bacteria from particular environments as was observed recently for outdoor air [44].
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Figure 4. Results of SourceTracker analysis showing the average contributions of different sources to the surface-associated bacterial 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
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While we have known for some time that human-associated bacteria can be readily cultivated from both domestic and public restroom surfaces, little was known about the overall composition of microbial communities associated with public restrooms or the degree to which microbes can be distributed throughout this environment by human activity. The results presented here demonstrate that human-associated bacteria dominate most public restroom surfaces and that distinct patterns of dispersal and community sources can be recognized for microbes associated with these surfaces. Although the methods used here did not provide the degree of phylogenetic resolution to directly identify likely pathogens, the prevalence of gut and skin-associated bacteria throughout the restrooms we surveyed is concerning since enteropathogens or pathogens commonly found on skin (e.g. Staphylococcus aureus) could readily be transmitted between individuals by the touching of restroom surfaces.
Jonathan Eisen's Lab 