New papers on microbiology of the built environment, March 7, 2016

Microbes in the house

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center – Aaron J. Prussin II – PLOS ONE (OA)

Screen Shot 2016-03-06 at 8.31.36 PMWe have investigated the microbial community of the air in a daycare center, including seasonal dynamics in the bacterial community and the presence of specific viral pathogens. We collected filters from the heating, ventilation, and air conditioning (HVAC) system of a daycare center every two weeks over the course of a year. Amplifying and sequencing the 16S rRNA gene revealed that the air was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes that are commonly associated with the human skin flora. Clear seasonal differences in the microbial community were not evident; however, the community structure differed when the daycare center was closed and unoccupied for a 13-day period. These results suggest that human occupancy, rather than the environment, is the major driver in shaping the microbial community structure in the air of the daycare center.

Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings – Benjamín O. Ortega-Morales – Frontiers in Microbiology (OA)

Screen Shot 2016-03-06 at 8.34.42 PMSoil and rock surfaces support microbial communities involved in mineral weathering processes. Using selective isolation, fungi were obtained from limestone surfaces of Mayan monuments in the semi-arid climate at Yucatan, Mexico.  (…) A substantial proportion of fungi, in particular those isolated from mycelium (59%), were capable of solubilizing calcium by means of organic acid release, notably oxalic acid as evidenced by ion chromatography. Contrary to our hypothesis, nutrient level was not a variable influencing the CaCO3 solubilization ability among isolates. Particularly active fungi (Annulohypoxylon stygium, Penicillium oxalicum, and Rosellinia sp.) were selected as models for bioweathering experiments with limestone-containing mesocosms to identify if other mineral phases, in addition to oxalates, were linked to bioweathering processes. (…) Overall, our results suggest that a diverse fungal community is associated with limestone surfaces insemi-arid climates.

Microbes in medical equipment

The efficacy of disinfectants in the decontamination of dental unit water lines: an in vitro laboratory study – Mrudula Patel – BDJ Open (OA)

Screen Shot 2016-03-06 at 8.36.52 PMThis in vitro laboratory study compared the efficacy of water, sodium percarbonate (SPC) and chlorine dioxide (ClO2) solutions in the disinfection of dental unit water lines (DUWLs). New DUWL tubes were cut, split open, and mono-culture and mixed-culture biofilms of Staphylococcus aureus, Enterococcus faecalis and Streptococcus mutans were grown. Harvested biofilms from the sectioned DUWL tubes were exposed to sterile distilled water, SPC or 5 and 10 p.p.m. ClO2 in both a stationary phase and through a constant flow. (…) At low concentrations, ClO2 with and without flow significantly reduced the mixed-culture biofilm grown in vitro on the sections of the DUWL tubes. Therefore, it has the potential to be used in the patient treatment water, as it is potable at these concentrations, and to decontaminate and limit the biofilm formation in the water lines.

Microbes and food

Microbial Safety of Wood in Contact with Food: A Review – Florence Aviat – Comprehensive Reviews in Food Science and Food Safety (OA)

Cutting boards with fluorescent powder. Left: hardwood. Right: polyethylene.
Cutting boards with fluorescent powder. Left: hardwood. Right: polyethylene.

Food packaging is multifunctional: it protects from harvest to table. Four main groups of materials for direct food contact are mentioned in the literature: wood, glass, plastic, and metal. In this review, the focus is on wooden packaging for direct contact with food. (…) Based on a review of published conclusions from scientific studies over the last 20 y and after a description of the general properties of wooden packaging, we focus on the microbiological status of natural wood. Then, we discuss the parameters influencing the survival of microorganisms on wood. Finally, we report on the transfer of microorganisms from wood to food and the factors influencing this phenomenon. This review demonstrates that the porous nature of wood, especially when compared with smooth surfaces, is not responsible for the limited hygiene of the material used in the food industry and that it may even be an advantage for its microbiological status. In fact, its rough or porous surface often generates unfavorable conditions for microorganisms. In addition, wood has the particular characteristic of producing antimicrobial components able to inhibit or limit the growth of pathogenic microorganisms.

Salmonella in Shell Eggs: Mechanisms, Prevention and Detection – Seockmo K – Omics Journal of Nutrition & Food Sciences (OA)

Screen Shot 2016-03-06 at 8.43.00 PMContaminated shell egg is one of the key Salmonella infection routes for human, causing food-borne illnesses. Multiple salmonellosis infections due to egg contamination still occur in developed countries even though preventive methods, such as vaccination or washing followed by rinsing process, are carried out following certified national standards. Recent outbreaks indicated that current strategies for Salmonella control need to be optimized to further minimize contamination of commercial eggs. Therefore, there is a critical need to develop more sensitive and rapid Salmonella detection methods. In this review, we address (i) egg production; (ii) preventive methods that minimize contamination; (iii) mechanisms of Salmonella contamination; (iv) Salmonella detection methods.

Intensive aquaculture selects for increased virulence and interference competition in bacteria – Lotta-Riina Sundberg – Proceedings of the Royal Society B ($$, no price quoted, but ready to take your credit card number)

Screen Shot 2016-03-06 at 8.46.17 PMAlthough increased disease severity driven by intensive farming practices is problematic in food production, the role of evolutionary change in disease is not well understood in these environments. Experiments on parasite evolution are traditionally conducted using laboratory models, often unrelated to economically important systems. We compared how the virulence, growth and competitive ability of a globally important fish pathogen, Flavobacterium columnare, change under intensive aquaculture. We characterized bacterial isolates from disease outbreaks at fish farms during 2003—2010, and compared F. columnare populations in inlet water and outlet water of a fish farm during the 2010 outbreak. Our data suggest that the farming environment may select for bacterial strains that have high virulence at both long and short time scales, and it seems that these strains have also evolved increased ability for interference competition.

Application of electrolyzed oxidizing water in production of radish sprouts to reduce natural microbiota – Chunling Zhang – Food Control ($35.95)

Screen Shot 2016-03-06 at 8.49.58 PMThe objective of this study was to determine the efficacy of electrolyzed oxidizing (EO) water in reducing natural microbiota on radish seed and sprout during seed soaking and sprouting. EO water with different available chlorine concentrations (…) and different pH (…) were used to soak radish seeds for 12 h and the surviving population of total aerobic bacteria, yeast and mold, and germination rate were determined. (…) The results showed that the population of natural microbiota decreased with increasing ACC of EO water, while no significant difference was observed among EO waters with different pH levels that were applied while soaking the seeds. (…) Therefore, EO water with low ACC and near neutral pH could be used to soak seeds and water sprouts throughout seed germination and sprouting to control the population of natural microbiota on seeds and sprouts.

Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential – Nuwan R. Vithanage – International Dairy Journal ($39.95)

Screen Shot 2016-03-06 at 8.53.15 PMRefrigerated storage of raw milk promotes the growth of psychrotrophic bacteria, some of which produce heat-stable exoenzymes causing dairy product spoilage. The effects of storage conditions and season on the biodiversity of psychrotrophs in raw milk were examined using matrix-assisted laser desorption time of flight mass spectrometry and 16S rRNA analysis. The ability of psychrotrophs to produce protease, lipase and phospholipase C was determined. The predominant genera found were Pseudomonas (19.9%), Bacillus (13.3%), Microbacterium (5.3%), Lactococcus (8.6%), Acinetobacter (4.9%) and Hafnia (2.8%); a considerable number of isolates were hitherto unknown species and genera. (…) Improving the quality of milk products may require differential processing of raw milk depending on the type of microbiota present, storage temperature and seasonality.

Microbiological characteristics of fresh tofu produced in small industrial scale and identification of specific spoiling microorganisms (SSO) – Franca Rossi – LWT – Food Science and Technology ($24.95).
NOTE: Figure 3 in this paper shows 2 lanes (#7 and #8) that look unexpectedly similar. Proceed with caution. 

Note: lanes 7 and 8 look very similar.
Note: lanes 7 and 8 look very similar.

In this study, the microbiological characteristics of ready-to-eat fresh tofu produced by a small company in Northern Italy were investigated to unveil the abundance and composition of the microbiota and the identity and provenance of the specific spoiling microorganisms (SSO). Culture-dependent (RAPD-PCR and 16S rRNA gene sequencing) and culture-independent (PCR-DGGE) analyses were carried out on soybean lots and derived fresh tofu samples collected in different months and on two samples subjected to thermal abuse to simulate the interruption of the cold chain. Lactic acid bacteria species predominated in correctly preserved fresh tofu and bacterial species able to grow after thermal abuse mostly derived from the raw materials and belonged to heat labile species, thus suggesting that a more efficient heat treatment can increase the shelf-life of the product.

Microbes and recreation

Microfungi Potentially Pathogenic for Humans Reported in Surface Waters Utilized for Recreation – Anna Biedunkiewicz – CLEAN — Soil, Air, Water ($38)

Screen Shot 2016-03-06 at 9.16.14 PMFungal infections are commonly reported among outdoor bathers. Recreational water reservoirs are an important element of the mycosis epidemiological chain in the biosphere because they can be a source of fungi from municipal wastes, of asymptomatic carriers or bathers carrying mycoses. Yeast-like fungi and moulds were isolated from samples of four surface water baths and five swimming pools in 2011—2012. Membrane filters and standard laboratory-based protocols were used to identify the isolated fungi. (…) In swimming pool waters, the key factors that determined higher numbers of fungi were increased temperature, followed by low concentrations of chlorine ions. Together with the bacteriological and physicochemical analysis, constant mycological monitoring of recreational water (lake pools and swimming pools) should be a standard inspection element to reduce sanitary and epidemiologic risks to people using these water reservoirs for recreational purposes.

Microbes, pollution, and waste

Review: Bacterial communities in full-scale wastewater treatment systems – Agnieszka Cydzik-Kwiatkowska – World Journal of Microbiology and Biotechnology (OA)

Screen Shot 2016-03-06 at 9.17.51 PMBacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds – Mohd Faidz Mohamad Shahimin – Science of The Total Environment ($41.95)

Screen Shot 2016-03-06 at 9.20.57 PMOil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (…) or four (…) n-alkanes under methanogenic conditions for ~ 600 d. (…) 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. (…) These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation.

8 thoughts on “New papers on microbiology of the built environment, March 7, 2016

  1. Re: Microbes in the house

    Here’s another reference on a similar vein: “Architectural Design Drives the Biogeography of Indoor Bacterial Communities” by Steven W. Kembel, James F. Meadow, Timothy K. O’Connor, Gwynne Mhuireach, Dale Northcutt, Jeff Kline, Maxwell Moriyama, G. Z. Brown, Brendan J. M. Bohannan, Jessica L. Green
    PLOS ONE, January 29, 2014 DOI: 10.1371/journal.pone.0087093


    And a study in Chicago:

    Hope this helps – welcome your thoughts.

    1. Thanks for the links, Andrew! Very relevant for this blog.

      Actually, the Kembel paper was already discussed here by Amanda Makowiecki in January 2015. See here:

      The Hospital Microbiome Project has been featured here before as well.

      But thank you so much – these are two very relevant studies for the audience here, so it’s very much appreciated and good to see a reminder!

    1. Yes, it is depressing. Especially if the data is questionable as in the one example I pointed out. When I am at work, I don’t even see the costs. Being on the Stanford Internet, most (publication) doors are open for me. But when I post from home, it hits me how expensive some of these are. Yeah for Open Access!

        1. No, this was the first time that I posted the actual costs. Some offer to “rent” the pdf. But hard to understand how it costs so much to generate a PDF, when author already submits everything in electronic format and when peer reviewers (and many editors) do almost all the work for free.

  2. Thanks for your frequent contributions to this web site and especially for those that connect indoor environment and indoor microbiome, part of primary purpose for which the microBEnet project has been funded..

    1. Hal – as I have said before, we have chosen to expand microBEnet to not just include the indoor microbiome. I guess you do not like that but it is part of our plan to try and bring in people from other communities and also find a way to sustain funding for the site after Sloan Funding runs out. Again, I guess you don’t like this because you keep posting about this but I think our approach to reach out beyond just indoor microbiome topics has been very successful.

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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 human microbiome in thousands of oral, gastric, and intestinal samples. I currently study the microbiome of marine mammals. When I am not in the lab, I can be found working on my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, or on Twitter at @MicrobiomDigest.