Tattoos of Spiderweb

>The spider must be on the other cheek.

My brothers dream come true: baseball meets bioinformatics

James Fraser & Michael Eisen: Baseball Meets Biology

 

Tattoos of Texas Boy

>White trash, bike and a burning street all finished with a wonderful frame. It makes no sense whatsoever.

Letter of support for #UCDavis Chancellor cosigned by ~ 250 faculty #OccupyUCDavis

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.

1. Walter S. Leal, Professor, Entomology
2. Nina Amenta, Professor, Computer Science
3. Francisco J. Samaniego, Distinguished Professor, Statistics
4. Ricardo H. R. Castro, Assistant Professor, Chemical Engineering & Material Science
5. Kevin Johnson, Professor and Dean, Law School (signing in his individual capacity)
6. Eduardo Blumwald, Professor, Plant Sciences
7. Miguel A. Mendez, Professor, Law School
8. Maureen Stanton, Professor, Evolution and Ecology
9. Miguel A. Marino, Distinguished Professor Emeritus, Hydrologic Sciences, Civil & Environmental Engineering, and Biological & Agricultural Engineering
10. Adela De La Torre, Professor, Chicano/a Studies
11. James B. Ames, Professor, Chemistry
12. John E. Bolander, Professor, Civil & Environmental Engineering
13. Charles L. Judson, Emeritus Professor, Entomology
14. Joaquim Silvestre, Professor, Economics
15. Satya Dandekar, Professor and Chair, Medical Microbiology and Immunology
16. James R. Carey, Professor of Entomology and Director, Biodemographic Determinants of Lifespan
17. Emanuel Maverakis, Assistant Professor, Dermatology
18. Abhaya M. Dandekar, Professor, Plant Sciences
19. Renee Tsolis, Associate Professor, Medical Microbiology and Immunology
20. R Holland Cheng, Professor, Molecular & Cellular Biology
21. Robert H. Rice, Professor, Environmental Toxicology
22. Susan Rivera, Professor, Psychology
23. Andre Knoesen, Professor, Electrical and Computer Engineering
24. Lorena Garcia, Assistant Professor, Public Health Science
25. Angela Gelli, Associate Professor, Pharmacology
26. Susan E. Ebeler, Professor, Viticulture & Enology
27. George Bruening, Professor Emeritus, Plant Pathology; Member, National Academy of Sciences
28. Anh-Vu Pham, Professor, Electrical and Computer Engineering
29. Xiaoguang Liu, Assistant Professor, Electrical and Computer EngineeringM. Saif Islam, Professor, Electrical & Computer Engineering
30. S. Geoffrey Schladow, Professor, Civil and Environmental Engineering
31. Venkatesh Akella, Professor, Electrical & Computer Engineering
32. Judith S Stern, Distinguished Professor, Nutrition and Internal Medicine; Member, Institute of Medicine
33. Fu-Tong Liu, Distinguished Professor and Chair, Dermatology
34. Neville Luhmann Jr., Distinguished Professor, Electrical and Computer Engineering
35. William J. Murphy, Professor and Vice Chair of Research, Dermatology and Internal Medicine
36. Susan Kauzlarich, Professor, Chemistry, Recipient of the Presidential Award for Excellence in Science, Mathematics, and Engineering Mentoring
37. Alan Hastings, Distinguished Professor, Environmental Science and Policy; Member, Academy of Arts and Sciences
38. Richard Michelmore, Professor and Director, The Genome Center
39. Sebastian Schreiber, Professor, Evolution and Ecology
40. John S. Werner, Distinguished Professor, Ophthalmology & Vision Science; Neurobiology, Physiology & Behavior
41. Terence M. Murphy, Professor Emeritus, Plant Biology
42. Judy Callis, Professor, Molecular and Cellular Biology
43. Frank McNally, Professor, Molecular and Cellular Biology
44. Susan L. Keen, Senior Lecturer SOE, Evolution and Ecology
45. Kimberley McAllister, Professor, Center for Neuroscience, Neurology, and NPB
46. Joseph F. Antognini, Clinical Professor, Anesthesiology and Pain Medicine
47. Charles A. Fuller, Professor, Neurobiology, Physiology & Behavior
48. W. Martin Usrey, Professor, Center for Neuroscience, Neurobiology, Physiology & Behavior, and Neurology
49. Kyriacos A. Athanasiou, Distinguished Professor & Chair, Biomedical Engineering and Orthopaedic Surgery
50. Sue C. Bodine, Professor, Neurobiology, Physiology and Behavior
51. David M. Rocke, Distinguished Professor, Public Health Sciences and Biomedical Engineering
52. Scott I. Simon Professor and Vice Chair, Biomedical Engineering
53. Leah Krubitzer Professor and MacArthur Fellow, Psychology
54. Yong Duan, Professor. UC Davis Genome Center and Biomedical Engineering
55. Emanuel Epstein, Research Professor, Land, Air and Water Resources; Member, National Academy of Sciences
56. Subhash H. Risbud, Distinguished Professor, Materials Science
57. David P. Fyhrie, Professor, David Linn Endowed Chair, Biomedical Engineering
58. Thomas R. Gordon, Professor and Chair, Plant Pathology
59. Pam Ronald, Professor, Plant Pathology and Genome Center
60. Douglas Cook, Professor, Plant Pathology
61. Charles W. Bamforth, Professor, Food Science and Technology
62. Michael R. Hill, Professor and Vice Chair, Mechanical and Aerospace Engineering
63. Diane M. Beckles, Associate Professor, Plant Sciences
64. Sashi K. Kunnath, Professor and Chair, Civil and Environmental Engineering
65. Mary L. Cadenasso, Associate Professor, Plant Sciences
66. Mary Louise Flint, Extension Entomologist, Entomology
67. John I. Yoder, Professor, Plant Sciences
68. Bryce W. Falk, Professor, Plant Pathology
69. Douglas A. Kelt, Professor, Wildlife, Fish, & Conservation Biology
70. Benjamin J. McCoy, Professor Emeritus, Chemical Engineering
71. Bo Lonnerdal, Distinguished Professor, Nutrition & Internal Medicine
72. J. Bruce German, Professor, Food Science & Technology, Director, Foods for Health Institute
73. Janet F. Roser, Professor, Animal Science
74. Robert K. Washino, Emeritus Professor, Entomology
75. Iannis E. Adamopoulos, Assistant Professor, Internal Medicine
76. Kathryn Dewey, Distinguished Professor, Nutrition
77. Tina Jeoh, Assistant Professor, Biological and Agricultural Engineering
78. Harry H. Cheng, Professor, Mechanical and Aerospace Engineering
79. Michael Denison, Professor, Environmental Toxicology
80. Ye Chen-Izu, Assistant Professor, Pharmacology
81. Trish Berger, Professor, Animal Science
82. Linda J. Harris, Cooperative Extension Specialist, Food Science and Technology
83. Stefan Wuertz, Professor, Civil and Environmental Engineering
84. Rob Y. H. Chai, Professor, Civil and Environmental Engineering
85. Stephen Kowalczykowski, Distinguished Professor, Microbiology, and of Molecular and Cellular Biology; Member, National Academy of Sciences
86. James F. Shackelford, Professor, Chemical Engineering and Materials Science
87. Deb Niemeier, Professor, Civil Engineering
88. Maria Marco, Assistant Professor, Food Science & Technology
89. Brian Mulloney, Distinguished Professor, Neurobiology, Physiology, and Behavior
90. Katherine Ferrara, Professor, Biomedical Engineering
91. William D. Ristenpart, Assistant Professor, Chemical Engineering & Materials Science
92. Jean-Jacques Chattot, Professor, Mechanical and Aerospace Engineering
93. Anita M. Oberbauer, Professor, Animal Science
94. David Gilchrist, Professor Emeritus, Plant Pathology
95. Jay R. Lund, Professor, Civil and Environmental Engineering
96. Carlos E. Puente, Professor, Land Air and Water Resources
97. David Biale, Distinguished Professor, History
98. Lynn Kimsey, Professor, Entomology
99. David Horsley, Associate Professor, Mechanical and Aerospace Engineering
100. Valerie Williamson, Professor, Entomology and Nematology
101. Kyaw Tha Paw U, Professor, Atmospheric Science & Land, Air and Water Resources
102. Matthew J. Wood, Associate Professor, Environmental Toxicology
103. Eduardo A. Silva, Assistant Professor, Biomedical Engineering
104. Ning Pan, Professor, Textiles, Biological & Agricultural Engineering
105. Debra Long, Professor and Chair, Psychology
106. Robert Emmons, Professor, Psychology
107. Brian Trainor, Associate Professor, Psychology
108. Shelley A. Blozis, Associate Professor, Psychology
109. John P. Capitanio, Research Psychologist, Psychology
110. Joy Geng, Assistant Professor, Psychology
111. Valley Stewart, Professor, Microbiology
112. Ann Huff Stevens, Professor, Economics
113. Lisa Oakes, Professor, Psychology
114. Kristin H. Lagattuta, Associate Professor, Psychology
115. Robert Feenstra, Distinguished Professor, Economics
116. Gregory Clark, Professor, Economics
117. George A. Barnett, Professor & Chair, Communication
118. Fadi A. Fathallah, Professor, Biological and Agricultural Engineering
119. Jeff Sherman, Professor, Psychology
120. James E. K. Hildreth, Professor and Dean, College of Biological Sciences (signing in his individual capacity); Member, Institute of Medicine
121. Sally P. Mendoza, Professor Emeritus of Psychology and Staff Scientist, California National Primate Research Center
122. Peter H. Lindert, Distinguished Research Professor of Economics
123. Scott E. Carrell, Associate Professor, Economics
124. Steven J. Luck, Professor, Psychology, Director, Center for Mind & Brain
125. Robert A. Bell, Professor, Communication
126. Dean Keith Simonton, Distinguished Professor, Psychology
127. Ahmet Palazoglu, Professor & Chair, Chemical Engineering and Materials Science
128. Stephen Lewis, Professor, Electrical and Computer Engineering
129. Delmar Larsen, Assistant Professor, Chemistry
130. Gary N. Cherr, Professor and Interim Director, Bodega Marine Laboratory
131. Mario Biagioli, Distinguished Professor of Science and Technology Studies & Law Director, Center for Science & Innovation Studies
132. Michael D. Toney, Professor, Chemistry
133. Shota Atsumi, Assistant Professor, Chemistry
134. Kirill Kovnir, Assistant Professor, Chemistry
135. Thomas W. Schoener, Distinguished Professor, Evolution and Ecology
136. Simon R. Cherry, Professor, Biomedical Engineering
137. Alyson Mitchell, Professor, Food Science & Technology
138. Kent J. Bradford, Professor, Plant Sciences
139. T. M. DeJong, Professor, Plant Sciences
140. Carlos H. Crisosto, Specialist, Plant Sciences
141. Neil E. Schore, Professor and Vice-chair, Chemistry
142. Louis W. Botsford, Professor, Wildlife, Fish, and Conservation Biology
143. Robert H. Becker, Professor, Physics
144. Marylynn Barkley, Emeritus, Neurobiology, Physiology and Behavior
145. Joseph M. DiTomaso, Cooperative Extension Specialist, Plant Sciences
146. Bruce C. Kirkpatrick, Professor, Plant Pathology
147. Jay A. Rosenheim, Professor, Entomology
148. Hildegarde Heymann, Professor, Viticulture and Enology
149. Douglas Nelson, Professor, Microbiology
150. Richard Grotjahn, Atmospheric Science and Climate Dynamics
151. David Simpson, Professor, English
152. Frederic Chedin, Associate Professor, Molecular and Cellular Biology
153. Alan L. Balch. Distinguished Professor, Chemistry
154. J. Edward Taylor, Professor, Agricultural and Resource Economics
155. Bruce Hartsough, Professor, Biological and Agricultural Engineering
156. Jacquelyn Gervay-Hague, Professor and Chair, Chemistry
157. Nael H. El-Farra, Associate Professor, Chemical Engineering & Materials Science
158. Giovanni Peri, Professor, Economics
159. Carlton Larson, Professor, School of Law
160. Athena Soulika, Assistant Professor, Dermatology
161. Gabriel J. Chin, Professor, Law School
162. Matt Traxler, Professor, Psychology
163. Alan Brownstein, Distinguished Professor, Law School
164. Evelyn Lewis, Professor, Law School
165. Dennis Ventry, Professor, Law School
166. Barbara A. Burrall, Health Sciences Clinical Professor, Dermatology
167. Robert Hillman, Professor, Law School
168. Lovell (Tu) Jarvis, Professor, Agricultural and Resource Economics
169. Donna Shestowsky, Professor, Law School
170. Margaret Johns, Senior Lecturer, Law School
171. Albert Lin, Professor, Law School
172. Rex Perschbacher, Professor, Law School
173. Edward Imwinkelried, Professor, Law School
174. Marilynn Etzler, Professor, Biochemistry
175. Andrea Bjorklund, Professor, Law School
176. Elizabeth Joh, Professor, Law School
177. Tilahun Yilma, Distinguished Professor of Virology; Member, National Academy of Sciences
178. Ashutosh Bhagwat, Professor, Law School
179. Frank Osterloh, Professor, Chemistry
180. Richard M. Frank, Professor, Law School
181. Leslie Kurtz, Professor, Law School
182. Yoko Ono, Assistant Researcher, Dermatology
183. Jinyi Qi,Professor, Biomedical Engineering
184. Courtney G. Joslin, Professor, Law School
185. Isao Fujimoto, Emeritus Senior Lecturer, Community & Regional Development & Asian American Studies
186. R. Paul Singh, Distinguished Professor, Food Engineering
187. Wendy Silk, Professor, Land, Air, and Water Resources
188. Jared T. Shaw, Assistant Professor, Chemistry
189. Joel C. Dobris, Professor of Law, Emeritus
190. Madhavi Sunder, Professor, Law School
191. Donald P. Land, Professor, Chemistry
192. Anupam Chander, Professor, Law School
193. Kit S. Lam, Professor and Chair, Biochemistry and Molecular Medicine
194. Peter B. Moyle, Professor, Wildlife, Fish, and Conservation Biology
195. John M. Labavitch, Professor, Plant Sciences
196. Anthony Wexler, Professor, Mechanical and Aerospace Engineering 
197. Robyn M. Rodriguez, Associate Professor, Asian American Studies
198. Robert H Smiley, Dean and Professor Emeritus, Graduate School of Management
199. Daniel L. Simmons, Professor, Law School
200. Annaliese K. Franz, Assistant Professor, Chemistry
201. Eric E. Conn, Professor Emeritus, Plant Biochemistry; Member, National Academy of Sciences
202. Carlito Lebrilla, Distinguished Professor, Chemistry
203. Clayton Tanaka, Professor, Law School
204. Lisa Pruitt, Professor, Law School
205. Sherman Stein, Professor Emeritus, Mathematics
206. Charles F. Shoemaker, Professor, Food Science & Technology
207. M. Levent Kavvas, Civil and Environmental Engineering
208. Patricia A. Conrad, Professor of Parasitology, School of Veterinary Medicine
209. Yannis F Dafalias, Professor, Civil Engineering
210. Hsing-Jien Kung, Distinguished Professor, Biochemistry & Molecular Medicine
211. Jean VanderGheynst, Professor, Biological and Agricultural Engineering
212. Themis J. Michailides, Plant Pathologist in AES, Department of Plant Pathology
213. Mary Christopher, Professor, Veterinary Medicine
214. Harold G. Levine, Professor and Dean, School of Education (signing in his individual capacity)
215. Dennis Pendleton, Dean UC Davis Extension (signing in his individual capacity)
216. Rena Zieve, Professor, Physics
217. Georgia Drakakaki, Assistant Professor, Plant Sciences
218. Michael W. Maher, Professor, Graduate School of Management
219. Michael J. Singer, Professor Emeritus, Land, Air and Water Resources
220. Jeffrey Mount, Professor, Geology
221. Nicholas Curro, Associate Professor, Physics
222. David Woodruff, Professor, Graduate School of Management
223. Howard J. Spero, Chair, Geology
224. Louise Kellogg, Professor, Geology
225. Chih-Ling Tsai, Professor, Graduate School of Management
226. Peter Schiffman, Emeritus Professor, Geology
227. Howard W. Day, Professor, Geology
228. Kenneth L. Verosub, Distinguished Professor, Geology
229. Shannon W. Anderson, Professor, Graduate School of Management
230. Warren Pickett, Distinguished Professor of Physics
231. Athanasios Geromichalos, Assistant Professor, Economics
232. Ryosuke Motani, Professor, Geology
233. Christine Bruhn, Extension Specialist, Food Science and Technology
234. Hemant K. Bhargava, Associate Dean, Graduate School of Management
235. Shirley Chiang, Professor, Physics
236. Eldridge Moores, Professor Emeritus, Geology
237. Qing-Zhu Yin, Associate Professor, Geology
238. Abigail Thompson, Professor, Mathematics
239. John M. Boone, Professor and Vice Chair (Research) of Radiology; Professor, Biomedical Engineering
240. Ken Joy, Professor, Computer Science
241. Michelle Yetman, Associate Professor, Graduate School of Management
242. Shannon McCormack, Acting Professor, Law School
243. John W. Poulos, Professor of Law Emeritus, Law School
244. Hearne Pardee, Chair, Art Studio
245. Bruce D. Hammock, Distinguished Professor, Entomology; Member, National Academy of Sciences
246. Margaret Ferguson, Professor, English
247. Gina Werfel, Professor, Art
248. Michael D. Lairmore, Dean, School of Veterinary Medicine (signing in his individual capacity)
249. Damian C. Genetos, Assistant Research Professor, Anatomy, Physiology, and Cell Biology
250. Greg Kuperberg, Professor, Mathematics
251. Andrew Waldron, Professor, Mathematics
252. Alex Mogilner, Professor, Neurobiology, Physiology and Behavior and Mathematics
253. Anne Schilling, Professor, Mathematics
254. Joseph A. Biello, Associate Professor, Mathematics
255. Constantin Genigeorgis, Professor Emeritus, School of Veterinary Medicine
256. Annabeth Rosen, Professor Art & Art History
257. Becca Thomases, Assistant Professor, Mathematics
258. Dennis L Matthews, Director of the Center for Biophotonics and Professor, School of Medicine
259. Margherita Heyer-Caput, Professor, French & Italian (signing in her individual capacity)
260. Stephen M. Lane, Adjunct Professor Neurological Surgery
261. Michael Kapovich, Professor, Mathematics
262. John R. Roth, Distinguished Professor, Microbiology; Member, National Academy of Sciences
263. Anthony Tyson, Distinguished Professor, Department of Physics; Member, National Academy of Sciences
264. Konstantinos Zarbalis, Assistant Professor, Davis Medical Center Department of Pathology
265. Fumio Matsumura, Distinguished Professor, Environmental Toxicology

RIDE IN PEACE

 

Our good Friend Cintrone came through to add a piece to his collection to celebrate the life of a fallen friend and business partner.

Journal club today on bacteria in toilets - posting some notes here

I am heading a journal club discussion today of the following paper: PLoS ONE: Microbial Biogeography of Public Restroom Surfaces

I am going to use this page/post to put up some notes for the discussion.  Fortunately I have a good guide in this - Rob Dunn wrote a nice commentary/review for Scientific American blogs: Public bathrooms house thousands of kinds of bacteria

Stay tuned/come back to this page as I will be posting some more notes. Any suggestions for other things to look at/discuss would be welcome.

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. 

How did they collect samples?

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].

---------------------------------------------------------------
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.

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

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).

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

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

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

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].

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

Conclusion

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.

Supporting Information Top

Table S1.

Public restroom surfaces sampled and comparison of alpha-diversity metrics for each restroom surface. Note that all alpha-diversity values were determined from 500 randomly selected sequences from each sample.

(DOC)

Table S2.

Average taxonomic composition of bacterial communities associated with female (F) and male (M) public restroom surfaces. Numbers in parentheses indicate the standard error of the mean (SEM). Taxonomy was determined using the RDP-classifier for 500 randomly selected sequences from each sample.

(DOC)

Table S3.

Results of ANOSIM test comparing the bacterial communities associated with male and female restroom surfaces.

(DOC)

Table S4.

Results of SourceTracker analysis showing percentage of microbial community contributions of different source environments to restroom surfaces. Values are the average of ten resamplings with the standard error of the mean reported in parentheses.

(DOC)