New papers on microbiology of the built environment, January 29, 2016

An oversight of the new papers that I found covering the intersection of humans, buildings, and microbes.

Microbes in buildings

Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital – Tairacan Augusto Pereira da Fonseca – MDPI Int J Environ Res Public Health (OA)

Screen Shot 2016-01-29 at 04.36PM, Jan 29In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera.

Bacteria in a water-damaged building: associations of actinomycetes and non-tuberculous mycobacteria with respiratory health in occupants – J.-H. Park – Indoor Air

Screen Shot 2016-01-29 at 04.43PM, Jan 29We examined microbial correlates of health outcomes in building occupants with a sarcoidosis cluster and excess asthma. We offered employees a questionnaire and pulmonary function testing and collected floor dust and liquid/sludge from drain tubing traps of heat pumps that were analyzed for various microbial agents. (…) Thermophilic actinomycetes and non-tuberculous mycobacteria may have played a role in the occupants’ respiratory outcomes in this water-damaged building.

Microbes in food and drinking water

Ineffective hand washing and the contamination of carrots after using a field latrine – J M Monaghan – Letters in Applied Microbiology

Screen Shot 2016-01-29 at 04.45PM, Jan 29A study was undertaken to simulate the likely effects of a field worker with poor hygienic practices that had returned to work too soon after recovering from an infection by an enteric pathogen. The studies simulated a variety of hand-washing practices from no washing to washing with soap and water followed by an application of alcohol gel after using a field latrine. (…) These results suggest that if no gloves are worn it would be best practice to wash hands with water and soap and apply alcohol gel after using a field latrine. Wearing gloves reduced the risk of contaminating handled produce but workers should still wash their hands after using a field latrine before applying gloves.

Use of matrix-assisted laser desorption/ionization—time of flight (MALDI—TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant – Laura Sala-Comorera – International Journal of Hygiene and Environmental Health

Screen Shot 2016-01-29 at 04.40PM, Jan 29The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. (…) To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI—TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlateâ„¢ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API® gallery-based identification.

Microbes and waste

Metagenomic and quantitative insights into microbial communities and functional genes of nitrogen and iron cycling in twelve wastewater treatment systems – Duntao Shu – Chemical Engineering Journal

Screen Shot 2016-01-29 at 04.54PM, Jan 29To gain a better understanding of bacterial community structures, ecological inter-correlations and functional generalists of nitrogen- and iron-cycling-related bacteria in various wastewater treatment systems (WWTSs), 16 samples collected from 3 industrial, 4 municipal and 5 anaerobic ammonium oxidation (anammox) WWTSs were used to perform metagenomic analysis. A total of 9394 to 17,130 effective reads for 16 samples were obtained from the bacterial 16S rRNA V3—V4 regions using MiSeq sequencing. Taxonomic analysis revealed that Bacteroidetes, Chloroflexi, Proteobacteria, and Planctomycetes were the dominant phyla in these samples. Furthermore, quantitative polymerase chain reaction (qPCR) was conducted and the results revealed that anammox, nrfA, FeOB (iron oxidizing bacteria) and FeRB (iron reducting bacteria) genes had higher abundance when Candidatus Brocadia was the dominant genera in anammox bioreactor.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology – Łukasz JaÅ‚owiecki – PLOS ONE (OA)

Screen Shot 2016-01-29 at 04.51PM, Jan 29The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. (…) Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies.

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors – Igor Shuryak – PLOS ONE (OA)

Screen Shot 2016-01-29 at 04.58PM, Jan 29(…) To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. (…)

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California – Subbarao V. Ravva – PLOS ONE (OA)

Screen Shot 2016-01-29 at 05.02PM, Jan 29F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and necessitates the evaluation of the survival of prototype and environmental isolates of FRNA representing all four genogroups in surface waters from the central coast of California. (…) While most environmental isolates disappeared rapidly at 25°C and in the absence of the host, members of genogroups GIII and GI persisted longer with the host compared to members of GII and GIV. Consequentially, FRNA based source tracking methods can be used to detect phages from recent fecal contamination along with those that persist longer in the environment as a result of cooler temperatures and increased host presence.


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Elisabeth Bik

After receiving my PhD at Utrecht University in The Netherlands, I worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, I joined the Department of Microbiology and Immunology at Stanford, where I have worked on the characterization of the microbiome of human oral, gastric, and intestinal samples, as well as samples from marine mammals. Since November 2016, I am the new Science Editor at uBiome, a microbiome genomics company enabling citizen science. But you might also find me working on the detection of science misconduct, at my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, on Twitter at @MicrobiomDigest.