New papers on Microbiology of the Built Environment, August 14, 2016

Microbes on shoes

Review: Shoe soles as a potential vector for pathogen transmission: A systematic review – Tasnuva Rashid – Journal of Applied Microbiology (OA)

Shoe soles are possible vectors for infectious diseases. Although studies have been performed to assess the prevalence of infectious pathogens on shoe soles and decontamination techniques, no systematic review has ever occurred. The aim of this study was to perform a systematic review of the literature to determine the prevalence of infectious agents on shoe bottoms and possible decontamination strategies. (…) In conclusion, a high prevalence of microbiologic pathogens was identified from shoe soles studied in the healthcare, community, and animal worker setting. An effective decontamination strategy for shoe soles was not identified. Studies are needed to assess the potential for contaminated shoes to contribute to the transmission of infectious pathogens.

Microbes indoors 

Environmental and mucosal microbiota and their role in childhood asthma – Lena T. Birzele – Allergy ($6 to rent, $38 to own)

High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways. DNA from mattress dust and nasal samples of 86 school-age children was analyzed by 454-pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units bacterial diversity and composition was related to farm exposure and asthma status. (…) The stronger inverse association of asthma and bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.

Detection of volatile metabolites of moulds isolated from a contaminated library (in Venice, Italy)- Anna Micheluz – Journal of Microbiological Methods ($39.95)

The principal fungal species isolated from a contaminated library environment were tested for their microbial volatile organic compound (MVOC) production ability. (…) A total of 55 different MVOCs were detected and isopropyl alcohol, 3-methyl-1-butanol and 2-butanone were the principal compounds in common between the selected fungal species. (…) The results demonstrated the potential use of this method for the detection of fungal contamination phenomena inside Cultural Heritage’s preservation environments.

Quantitative filter forensics for indoor particle sampling – D. Haaland – Indoor Air ($6 to rent, $38 to own)

(…) In this study, we summarize past filter forensics research to explore what it reveals about the sampling technique and the indoor environment. There are 60 investigations in the literature that have used this sampling technique for a variety of biotic and abiotic contaminants. Many studies identified differences between contaminant concentrations in different buildings using this technique. Based on this literature review, we identified a lack of quantification as a gap in the past literature. Accordingly, we propose an approach to quantitatively link contaminants extracted from HVAC filter dust to time-averaged integrated air concentrations. (…)

Effects of biocide treatments on the biofilm community in Domitilla’s catacombs in Rome – Clara Urzì – Science of the Total Environment ($41.95)

Different types of biofilms are widespread on lithic faces of the Catacombs of Domitilla (Rome, Italy) due to the favorable microclimatic conditions (temperature, high RH% and low irradiance). The biofilm, once established, becomes particularly dangerous due to the coverage of valuable surfaces causing spoilage, softening of materials and mineral precipitation. It is common practice to treat these surfaces with biocides in order to eradicate the microorganisms present. (…) This study exemplifies the real risks of applying biocide treatments on complex microbial communities and pinpoints the necessity of subjecting treatments to monitoring and reassessment. Moreover, the work showed the potential of bacteria isolated after the treatment for use, under controlled conditions, in combatting unwanted microbial growth in that they possess a positive tropism toward stressed microorganisms and high hydrolytic enzymatic activity against cell components (e.g. cellulose, chitin and pectin). A tentative protocol is proposed.

Microbes and pets

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat – Embriette R. Hyde – mSystems (OA)

Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. (…)

Microbes and hospitals

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes – Paula King – PLOS ONE (OA)

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. (…). We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Microbes and waste

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris – Sonja Oberbeckmann – PLOS ONE (OA)

(…) This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. (…) These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET substrate. (…)


Microbes in drinking water

Ceramic water filters help prevent illness worldwide – Francis Odyniec – Finger Lakes Times

Fecal contamination of drinking water in Kericho District, Western Kenya: role of source and household water handling and hygiene practices – Johana Kiplagat Too – Journal of Water and Health

Refined assessment of associations between drinking water residence time and emergency department visits for gastrointestinal illness in Metro Atlanta, Georgia – Karen Levy – Journal of Water and Health

Neighborhood diversity of potentially pathogenic bacteria in drinking water from the city of Maroua, Cameroon – Jessica Healy-Profitós – Journal of Water and Health

Disinfection of Escherichia coli and Pseudomonas aeruginosa by copper in water – Andrew M. Armstrong – Journal of Water and Health

Microbes and wastewater

Survival of Helicobacter pylori in the wastewater treatment process and the receiving river in Michigan, USA – Xiaohui Bai – Journal of Water and Health



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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.