The microBEnet blog

New papers on Microbiology of the Built Environment, December 3, 2016

Microbes and money

Dirty Money: A Matter of Bacterial Survival, Adherence, and Toxicity – Frank Vriesekoop – Microorganisms (OA)

Zone of inhibition around a UK 5 pence coin
Zone of inhibition around a UK 5 pence coin

In this study we report the underlying reasons to why bacteria are present on banknotes and coins. (…) We treated the various currencies used in this study as microcosms, and the bacterial loading from human hands as the corresponding microbiome. We show that the substrate from which banknotes are produced have a significant influence on both the survival and adherence of bacteria to banknotes. Smooth, polymer surfaces provide a poor means of adherence and survival, while coarser and more fibrous surfaces provide strong bacterial adherence and an environment to survive on. Coins were found to be strongly inhibitory to bacteria with a relatively rapid decline in survival on almost all coin surfaces tested. The inhibitory influence of coins was demonstrated through the use of antimicrobial disks made from coins. Despite the toxic effects of coins on many bacteria, bacteria do have the ability to adapt to the presence of coins in their environment which goes some way to explain the persistent presence of low levels of bacteria on coins in circulation.

Microbes in the kitchen

Video: Good Germs; Bad Germs. Microbes in the kitchen, 14 households, 500 swabs – University of Oxford – YouTube

Obtaining a kitchen sample
Obtaining a kitchen sample

Invisible to the naked eye, yet a constant presence, microbes (‘germs’) live in, on and around us. The researchers in this project collaborate with members of the public to explore and experiment on the microbial life in their kitchens (and in one instance – a cat) and starts to unpick what we really mean by ‘clean’ and ‘dirty’.

Microbes in heritage buildings

Application of biological growth risk models to the management of built heritage – Riccardo Paolini – Techne  (text in Italian with English translation at the end, Open Access)

Palazzo Reale in Milan, Italy
Palazzo Reale in Milan, Italy

The quality of the interior spaces is strongly related to the hygro-thermal conditions which affect the users’ comfort, and may yield to preservation risk for the built heritage. Moreover, careless management of exposition spaces with excessive occupancy may result in moisture loads that promote degradation. In this paper, as a case study, an exposition hall representative of the built heritage is considered. The microbiological growth risk is investigated at two different climate conditions, namely Milan and Barcelona, considering varying ventilation rates and number of visitors. The results outline the need of policies informed by advanced analyses to prevent hygro-thermal risk in the absence of dedicated building services, that cannot always be integrated in built heritage.

Microbes in the hospital

Microbiological surveillance of operation theatres, intensive care units and labor room of a teaching hospital in Telangana, India – S. Kiranmai – International Journal of Research in Medical Sciences

Swab sampling results
Swab sampling results

Hospital-associated infections are the major cause of patient morbidity and mortality. Environmental monitoring by the microbiological testing of surfaces and equipments is useful to detect changing trends of types and counts of microbial flora. The aims of the study were to count CFU (colony forming unit) rate of indoor air, to identify bacterial colonization of surface and equipments isolated from Operation theatres, ICUs and Labor room of a teaching hospital in Telangana, India. (…) The study shows that OTs were having bacterial CFU rate of air varying from 6-72 CFU/m3 and colonized by contaminants like Bacillus sp and pathogens like Klebsiella sp. ICUs were having bacterial CFU rate of air varying from 28-100 CFU/m3 and colonized with contaminant like Bacillus sp., as well as potential pathogens like Klebsiella, Pseudomonas etc. Fungal CFU were also seen both in OTs and ICUs. High level of microbial contamination indicates the needs for periodic surveillance aimed at early detection of bacterial contamination levels and prevention of hospital acquired infections.

Microbes in indoor air

Volatile organic compounds of possible microbial origin and their risks on childhood asthma and allergies within damp homes – Hyunok Choi – Environment International ($39.95)

Environment International cover
Environment International cover

Risk of indoor exposure to volatile organic compounds of purported microbial origin on childhood symptoms of wheezing, rhinitis, and/or eczema, and doctor-diagnosed asthma, rhinitis, and eczema, respectively, remain unclear. To test hypotheses that total sum of 28 microbial volatile organic compounds (Σ26 MVOCs): 1) poses independent risk on doctor-diagnosed asthma, rhinitis, and eczema, respectively, as well as multiple symptom presentation with a minimum of the two of the above conditions (i.e. case); 2) is associated with significant interaction with absolute humidity (AH) on additive scale. (…) Joint occurrence of high Σ28 MVOCs and AH was associated with a significant increase in the case status and asthma risks in an additive scale.

Viable airborne microbial counts from air-cooling units with and without complaints of urine and body odors – Ka Man Lai – Aerobiologia ($39.95)

Cannot read the paper, so here is the Aerobiologia cover
Cannot read the paper, so here is the Aerobiologia cover

Viable airborne microbial counts are commonly used in indoor air quality (IAQ) assessment, but studies linking the microbial counts to a specific type of indoor microbial contamination are limited. We hypothesize that the airborne microbial counts can differentiate air-cooling units with and without complaints of urine and body odors. The keratinolytic property of some isolated bacteria prompts to the hypothesis that keratinase is present in the units to break down keratins, structural proteins that form human skin scales, as sources of amino acids and ammonium to produce the odors. Seven bacterial species and four fungal species were identified in the units and room air. (…)  Viable airborne microbial counts can help IAQ inspectors to identify potential odor-causing air-cooling units. Keratins may be broken down in the units and associated with the odor complaints.

Laboratory experiments on indoor bioaerosol deposition onto various surface materials – Vuokko Lappalainen –  IAQVEC 2016 papers (Open Access)

The test chamber, coordinate system and surface sample points.
The test chamber, coordinate system and surface sample points.

Increasingly, people spend their time indoors and at the same time cases of unacceptable indoor air quality are on the rise. (…) In BITEFA project, bioaerosol deposition on various surface materials and flow fields were studied with Penicillium brevicompactum spores in a duct form test chamber. The air velocities of the system were similar to those in ventilated apartment buildings. Three commonly used materials were placed on horizontal and vertical surfaces at various flow field locations in the test chamber. Deposition was measured with cultural based and digital microscopic methods. As expected, clear differences were observed on deposition rates which was highest for horizontal upward facing surfaces and lowest for ceiling with low air velocity. Results indicate that viable bioaerosol deposition rate is highly dependent on particle size, air velocity and air flow direction towards the surface. Smaller non-viable particles are available deposit on all surfaces, vertical and horizontal. Because of smaller size of particles, the gravitation is not the major deposition mechanism. Small particles deposit by interception and diffusion. This study gives more information on practice of surface bioaerosol sampling in indoor environment investigations.

Assistant Professor in Microbial Systems Biology at U. Tennessee, Knoxville

**Please circulate to interested colleagues. Review of applications begins today!

The Department of Microbiology and the National Institute for Mathematical and Biological Synthesis (NIMBioS) at the University of Tennessee, Knoxville invite applications for a tenure-track faculty position at the rank of Assistant Professor in the area of Microbial Systems Biology, with a primary appointment in Microbiology. We seek applicants whose research will center on modeling the metabolism, regulation, evolution, and other emergent properties of microbial systems on the intracellular, community, or ecosystem level. Such research should integrate multiple types of experimental data, possibly including biomolecular “omics” data, into a mathematical framework for microbial systems. It is anticipated that candidates will have experience and interests in the synthesis of experimental and observational data through quantitative modeling and theory: a competitive start-up for creating a mathematics or theory based research group to collaborate with empiricists will be available. The successful candidate will address questions that complement existing strengths in the Microbiology department, and the cross-disciplinary approaches supported by NIMBioS. There also exist opportunities to interact with groups and facilities in the nearby Oak Ridge National Laboratory.

A PhD in a computational, statistical or mathematical sciences or a biological field as well as relevant postdoctoral research experience are required. The successful candidate is expected to establish an innovative, externally-funded research program and contribute to the departmental teaching mission at the undergraduate and graduate levels. The position will start as early as August 1, 2017, and the salary will be competitive.

Applications should include a brief cover letter, CV with list of publications, a 2-3 page outline of research interests, and a separate 1-2 page description of teaching interests. Please provide the contact information for three individuals who are familiar with the applicant and would be willing to provide letters of recommendation. Please email the application as a single pdf file to Letters should be addressed to Dr. Steven Wilhelm, Professor of Microbiology, and informal inquiries may be sent to him at Review of applications will begin Dec 1, 2016 and will continue until the position is filled.

For more information, visit

All qualified applicants will receive equal consideration for employment and admissions without regard to race, color, national origin, religion, sex, pregnancy, marital status, sexual orientation, gender identity, age, physical or mental disability, or covered veteran status. Eligibility and other terms and conditions of employment benefits at The University of Tennessee are governed by laws and regulations of the State of Tennessee, and this non-discrimination statement is intended to be consistent with those laws and regulations. In accordance with the requirements of Title VI of the Civil Rights Act of 1964, Title IX of the Education Amendments of 1972, Section 504 of the Rehabilitation Act of 1973, and the Americans with Disabilities Act of 1990, The University of Tennessee affirmatively states that it does not discriminate on the basis of race, sex, or disability in its education programs and activities, and this policy extends to employment by the University. Inquiries and charges of violation of Title VI (race, color, and national origin), Title IX (sex), Section 504 (disability), ADA (disability), Age Discrimination in Employment Act (age), sexual orientation, or veteran status should be directed to the Office of Equity and Diversity (OED), 1840 Melrose Avenue, Knoxville, TN 37996-3560, telephone (865) 974-2498. Requests for accommodation of a disability should be directed to the ADA Coordinator at the Office of Equity and Diversity.

Evaluating the impacts of synthetic and natural indoor surface finishes on the microbiome

The Sloan Foundation gave me one more thing to be grateful for this Thanksgiving: a grant to evaluate the impacts of different surface finishes on the indoor microbiome. My previous work identified a relationship between antimicrobial chemicals and antibiotic resistance genes in dust.  This new project will build upon these results using an experimental system to evaluate if exposure to antimicrobial surfaces increases antibiotic resistance in indoor microbes.

Schematic of the experimental design. A mixed bacterial culture enriched from indoor dust will be used to inoculate small coupons prepared with different surface finishes. The effect of the surface finish on the viability and antibiotic resistance of the initial bacterial community will be assessed by counting colonies on agar plates and agar plates supplemented with antibiotic, respectively.
Schematic of the experimental design. A mixed bacterial culture enriched from indoor dust will be used to inoculate small coupons prepared with different surface finishes. The effect of the surface finish on the viability and antibiotic resistance of the initial bacterial community will be assessed by counting colonies on agar plates and agar plates supplemented with antibiotic, respectively.

This project will address the question: does the presence of synthetic or natural antimicrobials in surface finishes select for viable antibiotic-resistant microbes in the built environment? To answer this question, we will use bacterial cultures enriched from indoor dust and expose them to various surface finishes, including synthetic antimicrobial paint and natural clay paint with no added antimicrobial agent.

Paints often contain antimicrobial chemicals to extend their shelf life and prevent degradation, preserving the appearance of the paint once it has been applied. Many different antimicrobials, including the much-maligned triclosan, as well as newer ingredients like nano materials, or alkyl dimethyl benzyl quaternary ammonium chloride (aka “quat”). The long-term impacts of using such chemicals in the built environment on the development and spread of antibiotic resistance in the indoor microbiome is currently unknown.

The results of this work will help us understand how antibiotic resistance develops and spreads in the built environment. Ultimately, this work will enable consumers and manufacturers to make informed decisions about which materials to use in the built environment to promote desired microbial outcomes.

If you’re interested in this project or want to work on something similar, please get in touch with the Hartmann lab!

New papers on Microbiology of the Built Environment, November 19, 2016

Microbes in the city

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City – Holly M. Bik – mSphere (OA). News coverage at EurekAlert, ScienceDaily, and NYMagazine.

Relative abundances of bacterial/archaeal groups in 16S rRNA data set.
Relative abundances of bacterial/archaeal groups in 16S rRNA data set.

(…) Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. (…)  Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes.

ReviewAirborne particulate matter pollution in urban China: A chemical mixture perspective from sources to impacts – Ling Jin – National Science Review (OA)

 Scope of the review covering key scientific issues surrounding PM mixtures
Scope of the review covering key scientific issues surrounding PM mixtures

Rapid urban and industrial development has resulted in severe air pollution problems in developing countries such as China, especially in highly industrialized and populous urban clusters. Dissecting the complex mixtures of airborne particulate matter (PM) has been a key scientific focus in the last two decades, leading to significant advances in understanding physicochemical compositions for comprehensive source apportionment. (…) The microbiome, an integral dimension of the PM mixture, is an unexplored frontier in terms of identities and functions in atmospheric processes and human health. In this review, we identify the major gaps in addressing these issues, and recommend a holistic framework for evaluating the sources, processes, and impacts of atmospheric PM pollution. (…)

Review: Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments – Andrés Núñez – International Microbiology (OA)

 Volumetric Hirst-type spore trap for fungi and pollen collection employed in aerobiological studies
Volumetric Hirst-type spore trap for fungi and pollen collection
employed in aerobiological studies

The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance.(…) Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. (…) Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments.

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University (no access for me)

Sissoo tree, Moon Valley Nurseries, Arizona
Sissoo tree, Moon Valley Nurseries, Arizona

(…)  phyllosphere dynamics are not well understood in urban environments, and this environment has never been studied in the City of Phoenix, which maintains roughly 92,000 city trees. The phyllosphere will grow if the City of Phoenix is able to achieve its goal of 25% canopy coverage by 2030, but this begs the question: How and where should the urban canopy expand? I addressed this question from a phyllosphere perspective by sampling city trees of two species, Ulmus parvifolia (Chinese Elm) and Dalbergia sissoo (Indian Rosewood) in parks and on roadsides. (…) Roadside trees had fewer bacteria (10 OTUs) that were significantly more abundant when compared to park trees, but several have been linked to the remediation of petroleum combustion by-products. These findings, that were not available prior to this study, may inform the City of Phoenix as it is designing its future urban forests.

Microbes in the hospital

Molecular epidemiology of Staphylococcus epidermidis in neonatal intensive care units –  Hiie Soeorg – APMIS ($6 to rent, $38 to own).

Baby at a Neonatal Intensive Care Unit. Source: Wikipedia
Baby at a Neonatal Intensive Care Unit. Source: Wikipedia

Late-onset sepsis (LOS) in preterm neonates is increasingly reported to be associated with gut-colonizing Staphylococcus epidermidis. We aimed to describe the molecular epidemiology of S. epidermidis colonizing the gut of neonates hospitalized in two neonatal intensive care units. S. epidermidis from rectal swabs were typed by multilocus variable-number tandem-repeat analysis (MLVA), randomly chosen isolates of predominant MLVA types additionally by multilocus sequence typing. (…)  Overall, the prevalence of mecA, icaA, IS256, and ACME was 91.4%, 28.1%, 64%, and 77%, respectively. Of the mecA-positive isolates (n = 127), 43.9% carried SCCmec type IV. Of eight episodes of LOS, four were caused by ST2 and two by ST5. Preventing gut colonization with nosocomial epidemic S. epidermidis in hospitalized neonates could contribute to the prevention of LOS.

Microbes in drinking water

Exposure to Contaminated Drinking Water and Health Disparities in North Carolina – Frank Stillo – American Journal of Public Health ($22).

Water well drilling rig, West Virginia, USA. Source: Wikipedia.
Water well drilling rig, West Virginia, USA. Source: Wikipedia.

Objectives: To examine drinking water quality in majority Black periurban neighborhoods in Wake County, North Carolina, that are excluded from nearby municipal water service and to estimate the health benefits of extending water service. We tested 3 samples collected July through December 2014 in 57 private wells for microbial contaminants. (…) An estimated 22% of 114 annual emergency department visits for acute gastrointestinal illness could be prevented by extending community water service. Predominantly Black periurban neighborhoods excluded from municipal water service have poorer quality drinking water than do adjacent neighborhoods with municipal services. These disparities increase the risk of emergency department visits for acute gastrointestinal illness.

Microbes and recreational water

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology (OA)

Locations of the study sites. (A) East Fork Lake, (B) Delaware Lake, and (C) Madison Lake in Ohio.
Locations of the study sites. (A) East Fork Lake, (B) Delaware Lake, and (C) Madison Lake in Ohio.

The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. (…) unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.

Microbes, pesticides, and pollution

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology ($25 for 1 day access). News coverage by UPI and ASM.

Buccal swab sampling. Source:
Buccal swab sampling. Source:

In a longitudinal agricultural community cohort sampling of 65 farmworker and 52 non-farmworker adults, we investigated agricultural pesticide exposure associated changes in the oral buccal microbiota. We found a seasonally persistent association between the detected blood concentration of the insecticide Azinphos-methyl and the taxonomic composition of the buccal swab oral microbiome. (…)  The spring/summer ‘exposed’ microbiome cluster with significantly less bacterial diversity was enriched for farmworkers and contained 27 of the 30 individuals who also had Azinphos-methyl agricultural pesticide exposure detected in the blood.

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater – Dongping Wang – Microbiology Open (OA)

Location of TA-16 and other Laboratory technical areas at Los Alamos National Laboratory
Location of TA-16 and other Laboratory technical areas at Los Alamos National Laboratory

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive released to the environment as a result of weapons manufacturing and testing worldwide. At Los Alamos National Laboratory, the Technical Area (TA) 16 260 Outfall discharged high-explosives-bearing water from a high-explosives-machining facility to Cañon de Valle during 1951 through 1996. These discharges served as a primary source of high-explosives and inorganic-element contamination in the area. (…)  In this study, we examined the microbial diversity in a monitoring well completed in perched-intermediate groundwater contaminated by RDX, and examined the response of the microbial population to biostimulation under varying geochemical conditions. (…) The results suggest that strict anaerobic conditions are needed to stimulate RDX degradation under the TA-16 site-specific conditions.

Screening and In Situ Monitoring of Potential Petroleum Hydrocarbon Degraders in Contaminated Surface Water – Bulent Icgen – Clean Soil Air Water ($6 to rent, $38 to own).

Bioremediation. Source:
Bioremediation. Source:

Incomplete combustion of fossil fuels and other anthropogenic activities result in contamination of surface water by petroleum hydrocarbons. These pollutants can have severe effects on aquatic life and human health. In petroleum bioremediation, oil degrading microorganisms are utilized to remove petroleum hydrocarbons from polluted water. However, monitoring and identifying microorganisms capable of degrading petroleum hydrocarbons is very challenging. In the current study, bacteria isolated from a river alongside a petroleum refinery were assessed for their petroleum hydrocarbon degradation abilities. (…) The results revealed that species of Acinetobacter successfully populate the polluted surface water and have high potential for petroleum bioremediation.

Microbes in space

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space – Luis Zea – PLOS ONE (OA). News coverage at

Astronaut Mike Hopkins operating one of the GAPs containing the AES-1 experiment onboard ISS (Photo credit: NASA).
Astronaut Mike Hopkins operating one of the GAPs containing the AES-1 experiment onboard ISS (Photo credit: NASA, source: PLOS ONE).

Bacteria behave differently in space, as indicated by reports of reduced lag phase, higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics. These phenomena are theorized, at least in part, to result from reduced mass transport in the local extracellular environment, where movement of molecules consumed and excreted by the cell is limited to diffusion in the absence of gravity-dependent convection. However, to date neither empirical nor computational approaches have been able to provide sufficient evidence to confirm this explanation. Molecular genetic analysis findings, conducted as part of a recent spaceflight investigation, support the proposed model. This investigation indicated an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity—all of which can be associated with reduced extracellular mass transport.


NASEM Microbiomes of the Built Environment Study – Webcast 12/1 of Meeting #4

Got this by email:

Good afternoon –

The fourth meeting of the National Academies of Sciences, Engineering, and Medicine’s committee on Microbiomes of the Built Environment: From Research to Application will be a mostly closed meeting so that the committee can work on finalizing their recommendations and conclusions for the final report, but will contain a brief open session to hear from five experts who will address remaining pertinent topics. The open session will be held from 9am – 12:30pm EST on December 1, and will be webcast internationally. We have attached the open session’s agenda to this email for your use.

We invite you to register to watch the webcast by visiting If you have any questions, please email and a member of the study’s staff will get back to you as soon as possible.

Thank you for your continued engagement on this topic!

With best regards,

MOBE Meeting 4 Public Agenda.pdf

Rapid biophotonic detection of Legionella?

Quick post here (h/t to Paula Olsiewski for the link) about a cool-sounding new device for the rapid detection of Legionella.   I can’t say that I’m on board with the fanciful claims made in the press release (e.g. “The risk of catching fatal Legionnaires’ disease from air conditioning units has been dramatically reduced“) but the technology does look really interesting.  It’s a light-based detection system that claims to be able to detect the presence of Legionella in under an hour.  Obviously this is a big improvement over selective culturing, but whether it will actually be competitive with PCR-based assays or even rapid genome sequencing remains to be seen.  The project website is here.

New papers on Microbiology of the Built Environment, November 12, 2016

It’s been a couple of weeks since my last posts due to some work-related trips and changing jobs. Since last week, I am the new Science Editor at uBiome. So here is a longish post to catch up with papers and news articles on microbes of the Built Environment.

Microbes and buildings

Popular press‘Living buildings’ could use bacteria for heat, electricity and repairs – Helen Massy-Beresford – Horizon Magazine

Bricks containing microbial fuel cells, as on display at the Venice Biennale, could one day heat our homes. Image courtesy of LIAR.
Bricks containing microbial fuel cells, as on display at the Venice Biennale, could one day heat our homes. Image courtesy of LIAR.

Inserting bacteria into bricks and concrete could help generate heat, circulate air and repair cracks, according to researchers who are designing innovative construction materials to transform bricks and mortar into living buildings with a reduced environmental footprint. Rachel Armstrong, professor of experimental architecture at Newcastle University, UK, says that she believes cities of the future will be powered by the natural biological processes of bacteria and will behave more like living organisms. (…) Prof. Armstrong is coordinating the EU-funded LIAR project, which aims to harness the potential of the metabolic burning of living organisms for heating systems, replacing the burning of fossil fuels and dramatically cutting the carbon footprint of the buildings we live and work in.

Paper from ACADIA conferenceBiocement from genetically modified bacteria could react to changes in environment – Brian Wang – Next Big Future

An artist's impression of bacteria forming building foundations
An artist’s impression of bacteria forming building foundations

A team of scientists from Newcastle and Northumbria universities, led by architecture academic Dr Martyn Dade-Robertson, are investigating how they can create a new kind of material – biocement – where engineered cells react to changes in the environment and strengthen the soil around them. Their research is outlined in a paper which will be presented at the ACADIA conference, in Michigan, USA, this week. The team have identified dozens of genes in E. Coli bacteria which are regulated by pressures of 10atm (10 times that of sea level). Using this, they are modifying the bacteria to create a ‘gene circuit’ which would enable the bacteria to respond to their environment by producing ‘biocements’.

Microbes in the hospital

Microbiological sentinel events at neurological hospital: a retrospective cohort study – Annalia Asti – Journal of Medical Microbiology ($35)

The purpose of this study is to describe the epidemiological surveillance of microbiological sentinel events (SE) carried out between 2012-2014 at the Neurological Hospital Carlo Besta, Milano, Italy. The Setting is inpatient care with Multi- Drug-Resistance infections. (…) Preventive actions and their effectiveness on Acinetobacter baumanii, the primary cause in our division of MDR infections in 2012, has ensured a reduction of the incidence of the same; preventive actions and their effectiveness allowed us to intercept microbiological SE and trigger appropriate precautionary behaviour and isolation.

Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital – Applied Microbiology and Biotechnology ($39.95)

Terminal disinfection and daily cleaning have been performed in hospitals in Taiwan for many years to reduce the risks of healthcare-associated infections. However, the effectiveness of these cleaning approaches and dynamic changes of surface microbiota upon cleaning remain unclear. Here, we report the surface changes of bacterial communities with terminal disinfection and daily cleaning in a medical intensive care unit (MICU) and only terminal disinfection in a respiratory care center (RCC) using 16s ribosomal RNA (rRNA) metagenomics. (…) We concluded that cleaning changes might contribute to the difference in diversity between two wards.

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis – An Hotterbeekx – Scientific Reports (OA)

Cladogram showing the association of distinct ETT microbial components (OTUs) with the 3 groups of ETTs defined by culture
Cladogram showing the association of distinct ETT microbial components (OTUs) with the 3 groups of ETTs defined by culture

Ventilator-associated pneumonia (VAP) is one of the commonest hospital-acquired infections associated with high mortality. VAP pathogenesis is closely linked to organisms colonizing the endotracheal tube (ETT) such as Staphylococcus epidermidis and Pseudomonas aeruginosa, the former a common commensal with pathogenic potential and the latter a known VAP pathogen. However, recent gut microbiome studies show that pathogens rarely function alone. Hence, we determined the ETT microbial consortium co-colonizing with S. epidermidis or P. aeruginosa to understand its importance in the development of VAP and for patient prognosis. Using bacterial 16S rRNA and fungal ITS-II sequencing on ETT biomass showing presence of P. aeruginosa and/or S. epidermidis on culture, we found that presence of P. aeruginosa correlated inversely with patient survival and with bacterial species diversity.

An immobilized liquid interface prevents device associated bacterial infection in vivo – Jiaxuan Chen – Biomaterials ($35.95). Also see: Bacteria can’t get a grip on self-healing, slippery surface. Inspired by nature, a high-tech, low-adhesive coating for medical devices could help prevent infection – EurekAlert

Virtually all biomaterials are susceptible to biofilm formation and, as a consequence, device-associated infection. The concept of an immobilized liquid surface, termed slippery liquid-infused porous surfaces (SLIPS), represents a new framework for creating a stable, dynamic, omniphobic surface that displays ultralow adhesion and limits bacterial biofilm formation. A widely used biomaterial in clinical care, expanded polytetrafluoroethylene (ePTFE), infused with various perfluorocarbon liquids generated SLIPS surfaces that exhibited a 99% reduction in S. aureus adhesion with preservation of macrophage viability, phagocytosis, and bactericidal function.

From IDSA: Nurses’ Scrubs Carry Bad Bacteria. Healthcare workers, patients, and environment form ‘transmission triangle’ – Liz Highleyman – MedPage Today
Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and drinking water

Drinking water: One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria – Antonia Bruno – Microbiology Open (OA)

Experimental workflow to test and validate the efficacy of TFF
Experimental workflow to test and validate the efficacy of TFF

We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high-throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples.

Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System – E. I. Prest – PLOS ONE (OA)

Heatmap of pair-wise Pearson’s correlation coefficients
Heatmap of pair-wise Pearson’s correlation coefficients

Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC).

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of Microbiology Research (OA)

The current study assessed the drinkability of water in 25 schools in Cruz das Almas BA Brazil. Total coliforms, Escherichia coli, Enterococcus, mesophylls and psichrotrophic bacteria were evaluated, coupled with color, turbidity, free residual chlorine, dissolved oxygen and biochemical oxygen demands. Water samples were collected at four sites: the first tap within the supply network or within the alternative supply (first site), main reservoir (second site), kitchen water (third site) and drinking water troughs (fourth site). (…) Results show that health risks in schools in Cruz das Almas may be solved by adequate water treatment, periodical cleaning of reservoirs and proper maintenance of taps and filters.

Microbes and pollution

Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages – Amanda R. McCormick – Ecosphere (OA)

nMDS ordination comparing bacterial assemblages collected in 10 study streams.
nMDS ordination comparing bacterial assemblages collected in 10 study streams.

The ecological dynamics of microplastic (<5 mm) are well documented in marine ecosystems, but the sources, abundance, and ecological role of microplastic in rivers are unknown and likely to be substantial. Microplastic fibers (e.g., synthetic fabrics) and pellets (e.g., abrasives in personal care products) are abundant in wastewater treatment plant (WWTP) effluent, and can serve as a point source of microplastic in rivers. The buoyancy, hydrophobic surface, and long transport distance of microplastic make it a novel substrate for the selection and dispersal of unique microbial assemblages. We measured microplastic concentration and bacterial assemblage composition on microplastic and natural surfaces upstream and downstream of WWTP effluent sites at nine rivers in Illinois, United States.

Microbes and cultural heritage

Weathering of a Roman Mosaic—A Biological and Quantitative Study on In Vitro Colonization of Calcareous Tesserae by Phototrophic Microorganisms – Addolorata Marasco – PLOS ONE (OA)

Calothrix membranacea on tessera
Calothrix membranacea on tessera

The potential impact of cyanobacteria and microalgae on the weathering of calcareous tesserae from a Roman mosaic of the II Century CE has been followed through in vitro experiments. Laboratory tests were carried out by inoculating mosaic tiles with single strains of Cyanobacteria or Chlorophyta to evaluate the roles of pioneer phototrophic microrganism on the resulting architecture of biofilms. The interaction between tesserae and strains was assessed at the whole substratum and micrometer scales, by image analysis and Confocal Laser Scanning (CLS) microscopy, respectively.

The “Koala Poop Microbiome” Class at UC Davis

You know sometimes you use a working title for something for long enough that it becomes the title? Like “Snakes on a Plane”.  That’s what happened in this case,  we also meant to come up with a name for this class… never did and so the official name at the registrar is “Koala Poop”.  Awesome.

So last Spring quarter Ashley Vater and I teamed up to teach a “Swabs to Genomes” class here at UC Davis.  Our summary of the class, with course materials, can be found here at microBEnet.   The big problems with that class were the cost and difficulty of genome sequencing in only 10 weeks.  So this time, Ashley, Katie Dahlhausen and I decided to try a version that focused more on the microbiology, without genome sequencing.  We also took ideas from a similar class taught by Cameron Thrash at LSU.

The background for this project is Katie’s PhD work which focuses on the koala gut microbiome.  Her crowdfunded research project is looking how koalas (which require bacteria to break down tannins in their limited diet) respond to antibiotic treatment (for rampant Chlamydia infections).  In this class, the students are attempting to isolate ~100 bacterial strains from koala feces under several combinations of conditions; anaerobic/aerobic, RT/37C, tannin positive/negative, BHI versus LB versus CBA media.  They will isolate the bugs, extract DNA, perform 16S Sanger PCR, identify the bugs (including making phylogenetic trees), and then screen these isolates for resistance to 10 common antibiotics (including the two actually used with koalas).

As with the last class, we are requiring the students to blog here on microBEnet as part of the class, although this time we’re adding a “peer review” component to the process which will delay the posts a bit.   Those blogs will be found on a dedicated page here, and at the end of the quarter I’ll post a summary of the class, along with the results and all the class materials.

Stay tuned!

Assistant Professor Microbial Ecology at University of Oregon

Assistant Professor Microbial Ecology

Institute of Ecology and Evolution and Department of Biology University of Oregon

The University of Oregon Institute of Ecology and Evolution ( and the Department of Biology invite applications for a tenure-track position (Assistant Professor) in microbial ecology. We are particularly interested in candidates whose research addresses fundamental concepts in microbial ecology at the population, community or ecosystem level. Successful candidates may use a variety of modern approaches (computational, molecular and/or laboratory culture) to study the ecology of microorganisms (bacteria, archaea, fungi, protists, or viruses) in laboratory systems, natural ecosystems (marine, aquatic or terrestrial) or within hosts (plant, animal or human). An outstanding research program and a commitment to excellence in teaching at the undergraduate and graduate levels is expected. Ph.D. required. Candidates who promote and enhance diversity are strongly desired. Interested persons should apply online to the University of Oregon IE2 SEARCH at Applicants should submit a cover letter, a curriculum vitae, statement of research accomplishments and future research plans, a description of teaching experience and philosophy, and three letters of

recommendation. Submission of up to 3 selected reprints is encouraged. For full posting and application directions, see To be assured of consideration, application materials should be uploaded by November 23, 2016, but the search will remain open until the position is filled.

The UO is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

MicrobialEcologistAd_v2 at 10-18-16.pdf

Assessing biochemical activity and metagenomic codes to a “T”

We’re recruiting a student/postdoc for this project! If it sounds interesting, please contact the Huttenhower Lab!

We were happy to hear that we’ve been funded by the Sloan Foundation to continue our study of microbes on the Boston subway. Our original study involved 1) identifying which microbes were resident in this built environment, 2) understanding their functional potential, and 3) quantifying gene families of interest, including antibiotic resistance and virulence factors. In brief, we found that it’s not so bad – even (and perhaps especially) on a crowded subway, you’re surrounded mainly by harmless microbes largely from human skin.

However, this still leaves many open questions in terms of public health. Although we now know what microbes are present, the built-environment is chemically unique, and we have yet to characterize which microbes are biochemically active, persistent, or dead. Metagenomic surveys reveal which metabolic pathways are present, but this may include DNA from inactive cells. It also does not identify which pathways are transcriptionally active, driving the cells that do persist in the built environment. Finally, since we collected all train samples at one time point and all touchscreen samples at another time point, we have limited knowledge on how stable different locations’ microbial activities are over time.

Project OverviewTo determine which microbes are active, we will use a combination of ‘omics approaches on newly collected samples that include metagenomics, metatranscriptomics, and metabolomics. From this, we can identify live bacteria (DNA) based on those that are transcriptionally active (RNA). We can further determine which metabolites are being produced by 1) associating taxonomic profiles with metabolites, 2) identifying genes within taxa that correspond to these metabolic pathways, and 3) confirming pathway activation through transcriptomic data. Cases in which interacting genes, transcripts, and metabolites covary (or are co-absent) provide “guilt-by-association” evidence of new functional annotations, novel biochemical pathways, or metabolite contributions from non-microbial sources.

To construct microbial signatures for different built environments, we will use the hitting set algorithm generated by Eric Franzosa, a research associate in the lab. This was developed to identify human hosts by their persistent microbial strain combinations, and in this study, we will test how these “codes” may identify individual built-environments as well. In brief, we will determine sets of features (taxa, genes, functions) that are unique to train lines and stations. We can then evaluate how stable these microbial codes are between our previous and new collections. Together, these features may provide a strategy for characterizing recently-visited environments using microbes newly acquired by an individual.

Generally, it is believed that microbes in the built environment originate from their human inhabitants and surrounding environments. This was the case in our last study, e.g. contrasting the presence of environmental taxa on indoor versus outdoor touchscreens, the prevalence of skin microbes on trains, and the presence of vaginal microbes on seats but not seatbacks. In terms of macroecology, urbanization frequently reduces biodiversity,1 though there are select animals such as pigeons and sparrows that thrive in (or more typically near) the built environment.2 Analogously, there may also be specific microbes that thrive and contribute to the built environment, which will be increasingly important to understand as more people move to cities. Overall, this study will help identify these microbes and the mechanisms they use to survive, as well as determine how stably they inhabit built environments across time.


1. Sol, D., Lapiedra, O., Gonzalez-Lagos, C. (2013). Behavioural adjustments for a life in the city. Animal Behaviour, 85, 1101-1112.
2. Kark, S., Iwaniuk, A., Schalimtzek, A. and Banker, E. (2007), Living in the city: can anyone become an ‘urban exploiter’?. Journal of Biogeography, 34: 638–651. doi:10.1111/j.1365-2699.2006.01638.x