New papers on Microbiology of the Built Environment, October 15, 2016

Microbes indoors

ReviewMicroorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station – Maximilian Mora – Frontiers in Microbiology (OA)

Graphical display of the confined habitats addressed in this review
Graphical display of the confined habitats addressed in this review

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. (…) In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards.

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA (paywalled)

Multiple risk factors were identified related to the subsequent patient
Multiple risk factors were identified related to the subsequent patient

To assess whether receipt of antibiotics by prior hospital bed occupants is associated with increased risk for CDI in subsequent patients who occupy the same bed. This is a retrospective cohort study of adult patients hospitalized in any 1 of 4 facilities between 2010 and 2015. Among 100 615 pairs of patients who sequentially occupied a given hospital bed, there were 576 pairs (0.57%) in which subsequent patients developed CDI. Receipt of antibiotics in prior patients was significantly associated with incident CDI in subsequent patients (log-rank P < .01). (…) Receipt of antibiotics by prior bed occupants was associated with increased risk for CDI in subsequent patients. Antibiotics can directly affect risk for CDI in patients who do not themselves receive antibiotics.

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia ($39.95)

Map of the library of Istanbul University, Ground Floor
Map of the library of Istanbul University, Ground Floor

Health problems in people who are in indoor environments with poor ventilation have resulted in an increase in the number of studies regarding air quality. Microorganisms and inferior indoor air-climatic conditions not only affect human health but also cause decay of invaluable materials present in libraries. Therefore, this study aimed to assess the culturable bioaerosol composition and concentration in the library of Istanbul University. The culturable fungal flora, a biodeterioration agent, of the damaged archival materials was also examined. The air was sampled for a year, as were the surfaces of 207 biologically damaged books. (…). The highest amount of fungus was determined in Archive 3, which contained damaged books. The fungal species isolated from the air and books were essentially the same. Therefore, it is important to determine not only the numeric values but also the microbiological composition of fungal colonies because the variety of fungal species is indicative of a deterioration process in effect over a long period. The deterioration of books must be remedied.

ReviewObservation-based metrics for residential dampness and mold with dose–response relationships to health: A review – M. J. Mendell – Indoor Air ($6 to rent, $38 to own)

Associations between health effects and three-level index #23 for moisture damage and visible mold
Associations between health
effects and three-level index #23 for
moisture damage and visible mold

An important proportion of respiratory illness is considered attributable to residential dampness or mold (D/M). Developing health-protective D/M guidelines has been challenging, in part because unhealthy levels of indoor D/M cannot be defined using available microbiological measurements. This review paper explores reported multilevel, observation-based (eg visual or olfactory) D/M metrics for potential in defining unhealthy levels of residential D/M. For many of the 33 multilevel residential D/M metrics identified, health risks generally increased as observed D/M increased. Although some metrics seemed too complex for practical use, simple metrics had among the strongest associations with health outcomes. Available findings suggest the feasibility of setting observation-based D/M thresholds to trigger remedial action, using further improved D/M metrics without microbiological measurements (at least until the actual dampness-related agents that cause illness are better quantified). Additional data would allow setting health-protective D/M thresholds more precisely. Also, metrics could better reflect hidden D/M by more strongly emphasizing mold odor, which has demonstrated strong associations with health effects.

Popular press: Mapping the Subway’s Microbiome – Grégory Fléchet – CNRS News France (OA)

H. Richard, A. Carbone/LCQB
H. Richard, A. Carbone/LCQB

A vast international study is being undertaken to classify, using metagenomics, the bacteria that dwell in the underground transport systems of 50 cities across the globe. (…)  The aim of the operation, repeated several times throughout the day of June 21, 2016, at the entrances of several Paris metro stations, was strictly scientific: to identify the microorganisms that have taken up residence in this suburban environment. This unprecedented study is part of an international consortium framework dubbed MetaSUB (link is external).1 The project, which will be used to create microbial maps of the underground transit networks of the world’s largest cities, already includes 53 international megalopolises including New York, London, São Paulo, Tokyo, Berlin and Shanghai.

Microbes in space

Popular press: What radiation-resistant space fungus can do for drug discovery – Shayla Love – STAT News (OA)

Chernobyl fungi sent to ISS are grown in petri dishes in the lab at NASA’s Jet Propulsion Laboratory.
Chernobyl fungi sent to ISS are grown in petri dishes in the lab at NASA’s Jet Propulsion Laboratory.

On Aug. 26, the Dragon space capsule dropped into the Pacific Ocean somewhere off the coast of Baja California, Mexico. Onboard were payloads containing fungi that had now grown in two of the most extreme conditions known to man: outer space and the Chernobyl Atomic Energy Station. These fungi are radiation resistant. Thirty years ago, they survived when a routine test led to an explosion that blasted radioactive material throughout northern Ukraine. By sending these fungi to the International Space Station, Kasthuri Venkateswaran, a research scientist at NASA’s Jet Propulsion Lab, and Clay Wang, a professor at the USC School of Pharmacy, have tried to push them to adapt again.

Microbes and food production

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology ($35.95)

Strawberries  Source:

New sanitization methods have been evaluated to improve food safety and food quality and to replace chlorine compounds. However, these new methods can lead to physicochemical and sensory changes in fruits and vegetables. The present study evaluated the effects of acetic acid, peracetic acid, and sodium dodecylbenzenesulfonate isolated or combined with 5 min of ultrasound treatment (40 kHz, 500 W) on strawberry quality over 9 days of storage at 8 °C. The strawberry natural contaminant microbiota (molds and yeasts, mesophilic aerobic and lactic acid bacteria), physicochemical quality (pH, total titratable acidity, total soluble solids, vitamin C, and color), sensory quality (triangle test) and inactivation of Salmonella enterica subsp. enterica intentionally inoculated onto strawberries were analyzed. (…)  Moreover, synergistic effects were observed in contaminant natural microbiota inactivation for all tested compounds during storage, without any major physicochemical or sensory alteration to the strawberries. Therefore, ultrasound treatment can improve the effect of sanitizers that are substitutes of chlorine compounds without altering the quality of strawberries during storage.

Microbes, waste, and pollution

Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities – Asma Asemaninejad – Microbial Ecology ($39.95)

PCA biplot of fungi under increased temperature, elevated atmospheric CO2, and altered water table conditions
PCA biplot of fungi under increased temperature, elevated atmospheric CO2, and altered water table conditions

Peatlands play an important role in global climate change through sequestration of atmospheric CO2. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO2 concentrations). (…)  Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats – Mathilde Jeanbille – Frontiers in Microbiology (OA)

Co-occurrence OTU network based on correlation analysis.
Co-occurrence OTU network based on correlation analysis.

(…) Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). (…) OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. (…)  Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Nitrogen transforming bacteria within a full-scale partially saturated vertical subsurface flow constructed wetland treating urban wastewater – Catiane Pelissari – Science of the Total Environment ($41.95)

Graphical abstract, detail
Graphical abstract, detail

The aim of this study was to characterize the nitrogen transforming bacterial communities within a partially saturated vertical subsurface flow constructed wetland (VF) treating urban wastewater in southern Brazil.(…)  The nitrifying and denitrifying bacterial communities were characterized in wetland cell 3 (764 m2 surface area) over a period of 12 months by using the FISH technique. (…) Based on the identified bacterial dynamics, the partially saturated VF wetland operated under low OLR enabled favorable conditions for simultaneous nitrification and denitrification.

Quality of greywater treated in biochar filter and risk assessment of gastroenteritis due to household exposure during maintenance and irrigation – S.S. Dalahmeh – Journal of Applied Microbiology ($6 to rent, $38 to own)

Concentration of E. coli in the influent (■) and effluent (□) of the studied pilot biochar filter treating household greywater
Concentration of E. coli in the influent (■) and
effluent (□) of the studied pilot biochar filter treating household greywater

This study evaluated treatment of greywater (GW) by a biochar filter in Jordan and assessed the annual risks of infection (Pi-annual), annual risk of disease (Pd-annual) and disease burden (in disability-adjusted life years; DALYs) of gastroenteritis caused by Salmonella spp. and rotavirus due to ingestion of GW during system maintenance and consumption of green onions irrigated with treated and nontreated GW.(…)  The highest risks of gastrointestinal disease were thus associated mainly with direct ingestion of GW when maintaining the system. Garden produce irrigated with GW treated in biochar filter did not display intolerable risks of rotavirus‒based gastroenteritis during summer season in the study area given that the produce is harvested 1 to 2 days, and washed, before consumption.

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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.