Journal Articles, BioMed Central and SpringerOpen

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AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
Bioelectrochemical production of hydrogen in an innovative pressure-retarded osmosis/microbial electrolysis cell system: experiments and modeling
Yuan, Heyang; Lu, Yaobin; Abu-Reesh, Ibrahim M.; He, Zhen (Biomed Central, 2015-08-14)
Background While microbial electrolysis cells (MECs) can simultaneously produce bioelectrochemical hydrogen and treat wastewater, they consume considerable energy to overcome the unfavorable thermodynamics, which is not sustainable and economically feasible in practical applications. This study presents a proof-of-concept system in which hydrogen can be produced in an MEC powered by theoretically predicated energy from pressure-retarded osmosis (PRO). The system consists of a PRO unit that extracts high-quality water and generates electricity from water osmosis, and an MEC for organic removal and hydrogen production. The feasibility of the system was demonstrated using simulated PRO performance (in terms of energy production and effluent quality) and experimental MEC results (e.g., hydrogen production and organic removal). Results The PRO and MEC models were proven to be valid. The model predicted that the PRO unit could produce 485 mL of clean water and 579 J of energy with 600 mL of draw solution (0.8 M of NaCl). The amount of the predicated energy was applied to the MEC by a power supply, which drove the MEC to remove 93.7 % of the organic compounds and produce 32.8 mL of H2 experimentally. Increasing the PRO influent volume and draw concentration could produce more energy for the MEC operation, and correspondingly increase the MEC hydraulic retention time (HRT) and total hydrogen production. The models predicted that at an external voltage of 0.9 V, the MEC energy consumption reached the maximum PRO energy production. With a higher external voltage, the MEC energy consumption would exceed the PRO energy production, leading to negative effects on both organic removal and hydrogen production. Conclusions The PRO-MEC system holds great promise in addressing water-energy nexus through organic removal, hydrogen production, and water recovery: (1) the PRO unit can reduce the volume of wastewater and extract clean water; (2) the PRO effluents can be further treated by the MEC; and (3) the osmotic energy harvested from the PRO unit can be applied to the MEC for sustainable bioelectrochemical hydrogen production.
CNT@TiO2 nanohybrids for high-performance anode of lithium-ion batteries
Wen, Zhenhai; Ci, Suqin; Mao, Shun; Cui, Shumao; He, Zhen; Chen, Junhong (Springer, 2013-11-22)
This work describes a potential anode material for lithium-ion batteries (LIBs), namely, anatase TiO2 nanoparticle-decorated carbon nanotubes (CNTs@TiO2). The electrochemical properties of CNTs@TiO2 were thoroughly investigated using various electrochemical techniques, including cyclic voltammetry, electrochemical impedance spectroscopy, galvanostatic cycling, and rate experiments. It was revealed that compared with pure TiO2 nanoparticles and CNTs alone, the CNT@TiO2 nanohybrids offered superior rate capability and achieved better cycling performance when used as anodes of LIBs. The CNT@TiO2 nanohybrids exhibited a cycling stability with high reversible capacity of about 190 mAh g-1 after 120-cycles at a current density of 100-mA-g-1 and an excellent rate capability (up to 100 mAh g-1 at a current density of 1,000-mA-g-1).
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes
Keenum, Ishi M.; Williams, Robert K.; Ray, Partha P.; Garner, Emily; Knowlton, Katharine F.; Pruden, Amy (2021-04-01)
Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.
Experimental determination of the oral bioavailability and bioaccessibility of lead particles
Deshommes, Elise; Tardif, Robert; Edwards, Marc A.; Sauvé, Sébastien; Prévost, Michèle (2012-11-22)
In vivo estimations of Pb particle bioavailability are costly and variable, because of the nature of animal assays. The most feasible alternative for increasing the number of investigations carried out on Pb particle bioavailability is in vitro testing. This testing method requires calibration using in vivo data on an adapted animal model, so that the results will be valid for childhood exposure assessment. Also, the test results must be reproducible within and between laboratories. The Relative Bioaccessibility Leaching Procedure, which is calibrated with in vivo data on soils, presents the highest degree of validation and simplicity. This method could be applied to Pb particles, including those in paint and dust, and those in drinking water systems, which although relevant, have been poorly investigated up to now for childhood exposure assessment.
Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems
Proctor, Caitlin R.; Dai, Dongjuan; Edwards, Marc A.; Pruden, Amy (2017-10-04)
Background Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been systematically evaluated. Here, we utilize simulated household water heaters to examine the effects of stepwise increases in temperature (32–53 °C), pipe material (copper vs. cross-linked polyethylene (PEX)), and influent assimilable organic carbon (0–700 μg/L) on opportunistic pathogen gene copy numbers and the microbiota composition, as determined by quantitative polymerase chain reaction and 16S rRNA gene amplicon sequencing. Results Temperature had an overarching influence on both the microbiota composition and L. pneumophila numbers. L. pneumophila peaked at 41 °C in the presence of PEX (1.58 × 105 gene copies/mL). At 53 °C, L. pneumophila was not detected. Several operational taxonomic units (OTUs) persisted across all conditions, accounting for 50% of the microbiota composition from 32 to 49 °C and 20% at 53 °C. Pipe material most strongly influenced microbiota composition at lower temperatures, driven by five to six OTUs enriched with each material. Copper pipes supported less L. pneumophila than PEX pipes (mean 2.5 log10 lower) at temperatures ≤ 41 °C, but showed no difference in total bacterial numbers. Differences between pipe materials diminished with elevated temperature, probably resulting from decreased release of copper ions. At temperatures ≤ 45 °C, influent assimilable organic carbon correlated well with total bacterial numbers, but not with L. pneumophila numbers. At 53 °C, PEX pipes leached organic carbon, reducing the importance of dosed organic carbon. L. pneumophila numbers correlated with a Legionella OTU and a Methylophilus OTU identified by amplicon sequencing. Conclusions Temperature was the most effective factor for the control of L. pneumophila, while microbiota composition shifted with each stepwise temperature increase. While copper pipe may also help shape the microbiota composition and limit L. pneumophila proliferation, its benefits might be constrained at higher temperatures. Influent assimilable organic carbon affected total bacterial numbers, but had minimal influence on opportunistic pathogen gene numbers or microbiota composition. These findings provide guidance among multiple control measures for the growth of opportunistic pathogens in hot water plumbing and insight into the mediating role of microbial ecological factors.
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes
Arango-Argoty, Gustavo; Dai, Dongjuan; Pruden, Amy; Vikesland, Peter J.; Heath, Lenwood S.; Zhang, Liqing (2019-06-07)
Background Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes. Results Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates. Conclusions NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .
Nanomaterial enabled sensors for environmental contaminants
Willner, Marjorie R.; Vikesland, Peter J. (2018-11-22)
The need and desire to understand the environment, especially the quality of one’s local water and air, has continued to expand with the emergence of the digital age. The bottleneck in understanding the environment has switched from being able to store all of the data collected to collecting enough data on a broad range of contaminants of environmental concern. Nanomaterial enabled sensors represent a suite of technologies developed over the last 15 years for the highly specific and sensitive detection of environmental contaminants. With the promise of facile, low cost, field-deployable technology, the ability to quantitatively understand nature in a systematic way will soon be a reality. In this review, we first introduce nanosensor design before exploring the application of nanosensors for the detection of three classes of environmental contaminants: pesticides, heavy metals, and pathogens.
Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs
Zhang, Husen; Wang, Haifeng; Shepherd, Megan L.; Wen, Ke; Li, Guohua; Yang, Xingdong; Kocher, Jacob; Giri-Rachman, Ernawati; Dickerman, Allan W.; Settlage, Robert E.; Yuan, Lijuan (2014-09-09)
We generated a neonatal pig model with human infant gut microbiota (HGM) to study the effect of a probiotic on the composition of the transplanted microbiota following rotavirus vaccination and challenge. All the HGM-transplanted pigs received two doses of an oral attenuated rotavirus vaccine. The gut microbiota of vaccinated pigs were investigated for effects of Lactobacillus rhamnosus GG (LGG) supplement and homotypic virulent human rotavirus (HRV) challenge. High-throughput sequencing of V4 region of 16S rRNA genes demonstrated that HGM-transplanted pigs carried microbiota similar to that of the C-section delivered baby. Firmicutes and Proteobacteria represented over 98% of total bacteria in the human donor and the recipient pigs. HRV challenge caused a phylum-level shift from Firmicutes to Proteobacteria. LGG supplement prevented the changes in microbial communities caused by HRV challenge. In particular, members of Enterococcus in LGG-supplemented pigs were kept at the baseline level, while they were enriched in HRV challenged pigs. Taken together, our results suggested that HGM pigs are valuable for testing the microbiota’s response to probiotic interventions for treating infantile HRV infection.
Sources of airborne microorganisms in the built environment
Prussin, Aaron J. II; Marr, Linsey C. (Biomed Central, 2015-12-22)
Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the built environment is characterizing the various sources of airborne microorganisms and the relative contribution of each. We have identified the following eight major categories of sources of airborne bacteria, viruses, and fungi in the built environment: humans; pets; plants; plumbing systems; heating, ventilation, and air-conditioning systems; mold; dust resuspension; and the outdoor environment. Certain species are associated with certain sources, but the full potential of source characterization and source apportionment has not yet been realized. Ideally, future studies will quantify detailed emission rates of microorganisms from each source and will identify the relative contribution of each source to the indoor air microbiome. This information could then be used to probe fundamental relationships between specific sources and human health, to design interventions to improve building health and human health, or even to provide evidence for forensic investigations.
Translating research to policy at the NCSE 2017 symposium “Microbiology of the Built Environment: Implications for Health and Design”
Bope, Ashleigh; Weir, Mark H.; Pruden, Amy; Morowitz, Michael; Mitchell, Jade; Dannemiller, Karen C. (2018-09-15)
Here, we summarize a symposium entitled “Microbiology of the Built Environment: Implications for Health and Design” that was presented at the National Council for Science and the Environment (NCSE) 17th National Conference and Global Forum in January 2017. We covered topics including indoor microbial exposures and childhood asthma, the influence of hospital design on neonatal development, the role of the microbiome in our premise (i.e., building) plumbing systems, antibiotic resistance, and quantitative microbial risk assessment. This symposium engaged the broader scientific and policy communities in a discussion to increase awareness of this critical research area and translate findings to practice.
Viruses in the Built Environment (VIBE) meeting report
Prussin, Aaron J. II; Belser, Jessica A.; Bischoff, Werner; Kelley, Scott T.; Lin, Kaisen; Lindsley, William G.; Nshimyimana, Jean P.; Schuit, Michael; Wu, Zhenyu; Bibby, Kyle J.; Marr, Linsey C. (2020-01-04)
Background During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled “Viruses in the Built Environment (VIBE),” at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. Results Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. Conclusions We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi. Video abstract.
Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap
Rhoads, William J.; Ji, Pan; Pruden, Amy; Edwards, Marc A. (Biomed Central, 2015-12-01)
Background Lowering water heater temperature set points and using less drinking water are common approaches to conserving water and energy; yet, there are discrepancies in past literature regarding the effects of water heater temperature and water use patterns on the occurrence of opportunistic pathogens, in particular Legionella pneumophila. Our objective was to conduct a controlled, replicated pilot-scale investigation to address this knowledge gap using continuously recirculating water heaters to examine five water heater set points (39–58 °C) under three water use conditions. We hypothesized that L. pneumophila levels at the tap depend on the collective influence of water heater temperature, flow frequency, and the resident plumbing ecology. Results We confirmed temperature setting to be a critical factor in suppressing L. pneumophila growth both in continuously recirculating hot water lines and at distal taps. For example, at 51 °C, planktonic L. pneumophila in recirculating lines was reduced by a factor of 28.7 compared to 39 °C and was prevented from re-colonizing biofilm. However, L. pneumophila still persisted up to 58 °C, with evidence that it was growing under the conditions of this study. Further, exposure to 51 °C water in a low-use tap appeared to optimally select for L. pneumophila (e.g., 125 times greater numbers than in high-use taps). We subsequently explored relationships among L. pneumophila and other ecologically relevant microbes, noting that elevated temperature did not have a general disinfecting effect in terms of total bacterial numbers. We documented the relationship between L. pneumophila and Legionella spp., and noted several instances of correlations with Vermamoeba vermiformis, and generally found that there is a dynamic relationship with this amoeba host over the range of temperatures and water use frequencies examined. Conclusions Our study provides a new window of understanding into the microbial ecology of potable hot water systems and helps to resolve past discrepancies in the literature regarding the influence of water temperature and stagnation on L. pneumophila, which is the cause of a growing number of outbreaks. This work is especially timely, given society’s movement towards “green” buildings and the need to reconcile innovations in building design with public health.

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