New papers on microbiology of the built environment, April 29, 2016

New papers on microbes and the built environment.

Microbes and fermenting households

Samples collected through the Second Annual San Diego Fermentation Festival: From Sample to Multi-Omics Conclusions in under 48 Hours – Robert A. Quinn – mSystems (OA)

Screen Shot 2016-04-28 at 05.19PM, Apr 28(…) Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (, and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. (…)

Microbes in cooling systems

Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air

Screen Shot 2016-04-28 at 05.51PM, Apr 28Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a four-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hyper-variable regions of the 16S/18S Ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonasbacteria becoming the most prevalent taxa towards the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.

Microbes in pipes (Note: 2 papers from 2015)

Distribution System Water Quality Affects Responses of Opportunistic Pathogen Gene Markers in Household Water Heaters – Hong Wang – Environmental Science & Technology

Screen Shot 2016-04-28 at 05.39PM, Apr 28Illustrative distribution system operation and management practices shaped the occurrence and persistence of Legionella spp., nontuberculous mycobacteria (NTM), Pseudomonas aeruginosa, and two amoebae host (Acanthamoeba spp., Vermamoeba vermiformis) gene markers in the effluent of standardized simulated household water heaters (SWHs). The interplay between disinfectant type (chlorine or chloramine), water age (2.3—5.7 days) and materials (polyvinyl chloride (PVC), cement or iron) in upstream simulated distribution systems (SDSs) profoundly influenced levels of pathogen gene markers in corresponding SWH bulk waters. (…) This study highlights the importance and challenges of distribution system management/operation to help control opportunistic pathogens.

Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System – C. Kimloi Gomez-Smith – Environmental Science & Technology

Screen Shot 2016-04-28 at 05.46PM, Apr 28The quantity and composition of bacterial biofilms growing on 10 water mains from a full-scale chloraminated water distribution system were analyzed using real-time PCR targeting the 16S rRNA gene and next-generation, high-throughput Illumina sequencing. (…). Despite spatial variation of community composition and bacterial abundance in water main biofilms, the communities on the interior main surfaces were surprisingly similar, containing a core group of operational taxonomic units (OTUs) assigned to only 17 different genera. Bacteria from the genus Mycobacterium dominated all communities at the main wall-bulk water interface (25—78% of the community), regardless of main age, estimated water age, main material, and the presence of corrosion products. (…) Sulfate-reducing bacteria from the genus Desulfovibrio, which have been implicated in microbially influenced corrosion, dominated all communities located underneath corrosion tubercules (arithmetic mean = 67.5% of the community). This research provides novel insights into the quantity and composition of biofilms in full-scale drinking water distribution systems, which is critical for assessing the risks to public health and to the water supply infrastructure.

Microbes in space

Four-year bacterial monitoring in the International Space Station–Japanese Experiment Module “Kibo” with culture-independent approach – Tomoaki Ichijo – MPJ Microgravity

Screen Shot 2016-04-28 at 05.23PM, Apr 28(…) We performed microbial monitoring in the Japanese Experiment Module “Kibo”, a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. (…) Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo.

Microbes at sea

Doctoral thesis: Characterization and comparison of microbial communities from different tourist ports in Mediterranean Sea and evaluation of applicability of bioremediation treatments – Enrica Bullita – Università di Cagliari (OA)

Screen Shot 2016-04-28 at 05.28PM, Apr 28The general objective of this work was to evaluate and compare the applicability of different bioremediation approaches of seawaters and sediments in Mediterranean tourist ports. Particularly, it was directed to contribute to the answer to two following main questions: -Do different tourist ports share the same bacterial communities? -Do bioremediation strategies have similar applicability in different tourist port areas? The specific aims of the present study were: 1. Definition and comparison of the pollution status of seawater. 2. Comparison of the bacterial communities in seawater. 3. Characterization of the dominant cultivable hydrocarbon-degrading bacteria from seawater and sediments. 4. Comparison of the effects of biostimulation treatment on bacterial communities in seawater at laboratory scale. 5. Comparison of the effect of bioaugmentation treatments on PAH degradation in sediments at laboratory scale.

Microbes in food

The microbiological quality of pasteurized milk sold by automatic vending machines – Apostolos S. Angelidis – Letters in Applied Microbiology ($6 to rent, $38 to own)

Screen Shot 2016-04-28 at 05.35PM, Apr 28The microbiological quality of pasteurized milk samples (n = 39) collected during 13 weekly intervals from three automatic vending machines (AVM) in Greece was investigated. Microbiological counts [total aerobic (TAC), total psychrotrophic (TPC), Enterobacteriaceae (EC) and psychrotrophic aerobic bacterial spore counts (PABSC)] were obtained at the time of sampling and at the end of shelf-life (three days) after storage of the samples at 4 or 8°C. (…)  From a microbiological standpoint the data indicate that the AVM milk samples meet the quality standards of pasteurized milk. However, the pre-packaged, retail milk samples yielded better results in terms of TAC, TPC and EC, compared to the AVM samples at the end of shelf-life.

Microbes of the past

Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology ($6 to rent, $38 to own)

Screen Shot 2016-04-28 at 05.53PM, Apr 28A not very comprehensive list of 15 links, with the microbial communities of shipwrecks, fossilized feces, paint on Tutankhamun’s tomb, and Otzi’s metagenome. No abstract. Several links lead to Wikipedia pages or to other free pages, so it’s a shame that we have to pay $38 for a non-peer-reviewed list of links. I have a better and free list called Archaeological Microbiology on my website MicrobiomeDigest for free.


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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.