New papers on microbiology of the built environment, July 9, 2016

Microbes and the built environment sensu stricto

This short review in Trends in Microbiology is open access, very relevant for this blog, and received quite some press.

Review: Buildings, Beneficial Microbes, and Health – Jordan Peccia, Sarah E. Kwan – Trends in Microbiology (OA)

Screen Shot 2016-07-09 at 9.07.11 AMBacteria and fungi in buildings exert an influence on the human microbiome through aerosol deposition, surface contact, and human and animal interactions. As the identities and functions of beneficial human microbes emerge, the consequences of building design, operation, and function must be understood to maintain the health of occupants in buildings.

Invite good bacteria into home: scientists – MSN
Why architects should let the microbes in – Science Daily
Letting the right microbes into your house is healthy – Katherine Lindemann – ResearchGate Blog
Should architecture take our microbial health into account? Let the right bugs in – Coby McDonald – Popular Science
New study finds that designers are neglecting beneficial microbes – Tom Bawden –

Microbes in veterinary clinics

Antimicrobial-resistant Escherichia coli in hospitalised companion animals and their hospital environment – I. Tuerena – Journal of Small Animal Practice (OA)

Screen Shot 2016-07-09 at 9.34.22 AM(Also included sampling from floors, keyboards and examination tables) Antimicrobial resistance is a growing concern with implications for animal health. This study investigated the prevalence of antimicrobial resistance among commensal and environmental Escherichia coli isolated from animals sampled in referral hospitals in the UK.(…) Escherichia coli resistant to key antimicrobials were isolated from hospitalised animals and the practice environment. We identified the emergence of the inhibitor resistant and extended spectrum beta-lactamase blaTEM-158 in companion animals. Further investigation to determine risk factors for colonisation with antimicrobial-resistant bacteria is needed to provide evidence for antimicrobial stewardship and infection control programmes.

Microbes and food production

Microbiological and Functional Quality of Ready-to-Eat Arugula as Treated by Combinations of UV-C and Nonconventional Modified Atmospheres – Cielo Char – Journal of Food Processing and Preservation ($6 to rent, $38 to own)

Screen Shot 2016-07-09 at 9.18.57 AMThe industry of ready-to-eat vegetables is interested in developing environmentally friendly sanitization techniques such as the ultraviolet light (UV-C). (…) The UV-C factor significantly affected enterobacteria counts and the total antioxidant activity showed an increase on the second day, mostly for the 15 kJ/m−2 dose combined either with He or Ar (1.28 and 1.31 mg trolox equivalent/g (fw), respectively). UV-C was the determining factor on the effectivity of the combined treatments, delaying the microbial growth and preserving the functional quality of ready-to-eat-arugula.

Factors associated with Shiga toxin-producing Escherichia coli shedding in dairy and beef cattle – Cristina Venegas-Vargas – Applied and Environmental Microbiology ($25 for 1 day)

Screen Shot 2016-07-09 at 9.23.11 AMShiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic uremic syndrome. Cattle are the primary reservoir for STEC, and food or water contaminated with cattle feces is the most common source of infections in humans. Consequently, we conducted a cross-sectional study of 1,096 cattle in six dairy herds (n=718 animals) and five beef herds (n=378 animals) in the summers of 2011 and 2012 to identify epidemiological factors associated with shedding. (…)These data suggest that the stress or the negative energy balance associated with lactation may result in increased STEC shedding frequencies in Michigan during the warm summer months. Future prevention strategies aimed at reducing stress during lactation or isolating high-risk animals could be implemented to reduce herd-level shedding levels and avoid transmission of STEC to susceptible animals and people.

Press: Researchers, farmers collaborate to prevent E. coli – Science Daily

Screen Shot 2016-07-09 at 9.24.54 AMA collaborative Michigan State University study involving microbiologists, epidemiologists, animal scientists, veterinarians, graduate students, undergraduates and farmers could lead to better prevention practices to limit dangerous E. coli bacteria transmissions. (…)  “Reducing STEC colonization and shedding in cattle can decrease the likelihood of these bacterial pathogens from entering the food supply and causing foodborne infections in people,” said Shannon Manning, MSU molecular biologist and principal investigator of the study.

Microbes, humans, and water

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments (OA)

Paris Sewers Museum, Wikipedia
Paris Sewers Museum, Wikipedia

How do you feel when you hear the words “wastewater,” “sludge,” “sewer,” and “sewage”? These words may make you feel uncomfortable. However, as Victor Hugo wrote in “Les Misérables,” these words are inevitably related to human society. (…) In “Les Misérables,” Jean Valjean carries wounded Marius on his shoulder through a long and difficult route in the Paris sewer system in order to save his life, and this leads to an outcome that makes Cosette and, perhaps, Jean Valjean himself happy. Unraveling the complete picture of the ecology and physiology of and interactions between microbes in the water infrastructure is also challenging. The happy ending of this story has not yet been reached.

Microbiological investigations on the water of a thermal bath at Budapest – Sára Szuróczk – Acta Microbiologica et Immunologica Hungarica ($25)

Gellért Baths, Wikipedia
Gellért Baths, Wikipedia

Thermal baths are unique aquatic environments combining a wide variety of natural and anthropogenic ecological factors, which also appear in their microbiological state. There is limited information on the microbiology of thermal baths in their complexity, tracking community shifts from the thermal wells to the pools. In the present study, the natural microbial community of well and pool waters in Gellért bath was studied in detail by cultivation-based techniques. (…) . The most dominant member in the well water was a new taxon, its similarity to Hartmannibacter diazotrophicus as closest relative was 93.93%.

Microbes, soils, and human activity

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere ($41.95)

Screen Shot 2016-07-09 at 9.26.53 AMLead (Pb) contamination at shooting ranges is a public health concern because Pb is a toxic metal. An experiment was conducted to determine the effect of two best management practices; bullet removal and vegetation, on bioavailability and leachability of Pb in three shooting range (SR) soils. St. Augustine grass was grown in sieved (2 mm) and un-sieved SR soils for 8 weeks after which leachates, soil and plant samples were analyzed. (…)  Grasses had a higher plant biomass in unsieved soils suggesting tolerance to the presence of bullets in the unsieved soils. Results suggest that bullet removal probably increased microbial activity and Pb bioavailability in the soil. The leaching and bioavailability of Pb in shooting range soils depends on biological activities and chemical processes in the soil.

Limited recovery of soil microbial activity after transient exposure to gasoline vapors – Jakub J. ModrzyÅ„ski – Environmental Pollution ($35.95)

Screen Shot 2016-07-09 at 9.29.44 AMDuring gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. (…) Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation.

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal – Andrew M. Cortese – Restoration Ecology ($6 to rent, $38 to own)

Screen Shot 2016-07-09 at 9.32.25 AMRevegetation following dam removal projects may depend on recovery of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal communities, which perform valuable ecosystem functions. This study assessed the availability and function of AM and EM fungi for plants colonizing dewatered reservoirs following a dam removal project on the Elwha River, Olympic Peninsula, Washington, United States. (…) Thus, revegetating plants have access to AM and EM fungi following dam removal, and EM formation may be especially important for plant P uptake in reservoir soils. However, availability of mycorrhizal fungi declines with distance from established plant communities. Furthermore, EM fungal communities in recently dewatered reservoirs may not be as effective at forming beneficial mycorrhizae as those from mature plant communities. Whole soil inoculum from mature plant communities may be important for the success of revegetating plants and recovery of mycorrhizal fungal communities.


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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.