New papers on microbiology of the built environment, October 30, 2015

The latest papers on microbiome of buildings and other objects used by humans. Today, we have microbiomes of water reservoirs and plumbing pipes, Brazilian money notes, an Italian cheese factory, and a brewery. For more microbiome papers from other sources (both human-associated or environmental), check out my daily blog MicrobiomeDigest.com.

Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome – Pan Ji, Jeffrey Parks, Marc A. Edwards, Amy Pruden  – PLOS ONE (Open Access)

Screen Shot 2015-10-29 at 03.20PM, Oct 29To examine its composition and the factors that shape it, standardized cold water plumbing rigs were deployed at the treatment plant and in the distribution system of five water utilities across the U.S. (…) High throughput Illumina sequencing of 16S rRNA gene amplicons was employed to profile and compare the resident bulk water bacteria and archaea. The utility, location of the pipe rig, pipe material and stagnation all had a significant influence on the plumbing microbiome composition, but the utility source water and treatment practices were dominant factors. (…) Data were examined across utilities to identify a true universal core, special core, and peripheral organisms to deepen insight into the physical and chemical factors that shape the building plumbing microbiome.

Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir – Xiao Yang, Tinglin Huang, and Haihan Zhang – Water (Open Access)

Screen Shot 2015-10-29 at 03.29PM, Oct 29The microbial communities within reservoir ecosystems are shaped by water quality and hydrological characteristics. However, there are few studies focused on the effects of thermal stratification on the bacterial community diversity in drinking water reservoirs. In this study, we collected water samples from the Jinpen Reservoir around the re-stratification period. To explore the functional diversity and bacterial community composition, we used the Biolog method and 16S rRNA-based 454 pyrosequencing combined with flow cytometry. The results indicated that stratification of the reservoir had great effects on temperature and oxygen profiles, and both the functional diversity and the composition of the bacterial community strongly reflected the significant vertical stratification in the reservoir.

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces – Tairacan Augusto Pereira da Fonseca – Int. J. Environ. Res. Public Health (Open Access)

Screen Shot 2015-10-29 at 03.17PM, Oct 29In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins.

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant – Maria Calasso, Danilo Ercolini, Leonardo Mancini, Giuseppina Stellato, Fabio Minervini, Raffaella Di Cagno, Maria De Angelis, Marco Gobbetti – Food Microbiology

Screen Shot 2015-10-29 at 03.23PM, Oct 29This study was aimed at establishing the relationships between house, rind and core microbiotas of cheese varieties manufactured at the same industrial dairy plant. Caciotta and Caciocavallo Pugliese cheeses were chosen as model systems. Mesophilic lactobacilli, cocci and, especially, thermophilic cocci were the most abundant cultivable bacteria found on equipment, which were located in the production area. According to cell counts, catabolic profiles of microbial communities deriving from equipment, and cheese core and rind differed. As shown by 16S rRNA targeted metagenomics, Streptococcus thermophilus dominated the communities from knife surface, brine tank, curds and core cheeses as well as it was the main colonizing bacterium from drain table, rinds and ripening room of Caciocavallo Pugliese cheeses. (…)

Brewery: DGGE: The Occurrence of Beer Spoilage Lactic Acid Bacteria in Craft Beer Production – Cristiana Garofalo, Andrea Osimani, Vesna Milanović, Manuela Taccari, Lucia Aquilanti and Francesca Clementi – Journal of Food Science

Screen Shot 2015-10-29 at 03.38PM, Oct 29The aim of this research study was to track beer spoilage lactic acid bacteria (LAB) inside a brewery and during the craft beer production process. To that end, indoor air and work surface samples, collected in the brewery under study, together with commercial active dry yeasts, exhausted yeasts, yeast pellet (obtained after mature beer centrifugation), and spoiled beers were analyzed through culture-dependent methods and PCR-DGGE in order to identify the contaminant LAB species and the source of contamination. Lactobacillus brevis was detected in a spoiled beer and in a commercial active dry yeast. Other LAB species and bacteria ascribed to Staphylococcus sp., Enterobaceriaceae, and Acetobacter sp. were found in the brewery. (…)

Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review – Patricia M. C. Huijbers, Hetty Blaak, Mart C. M. de Jong, Elisabeth A. M. Graat, Christina M. J. E. Vandenbroucke-Grauls, and Ana Maria de Roda Husman – Environmental Science & Technology

Screen Shot 2015-10-29 at 03.33PM, Oct 29To establish a possible role for the natural environment in the transmission of clinically relevant AMR bacteria to humans, a literature review was conducted to systematically collect and categorize evidence for human exposure to extended-spectrum β-lactamase-producing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus spp. in the environment. In total, 239 datasets adhered to inclusion criteria. AMR bacteria were detected at exposure-relevant sites (35/38), including recreational areas, drinking water, ambient air, and shellfish, and in fresh produce. (…)  The abundance of AMR bacteria at exposure-relevant sites suggests risk for human exposure. (…)  To what extent the environment, compared to the clinical and veterinary domains, contributes to human exposure needs to be quantified.

 

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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.