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Puce L, Hampton-Marcell J, Trabelsi K, Ammar A, Chtourou H, Boulares A, Marinelli L, Mori L, Cotellessa F, Currà A, Trompetto C, Bragazzi NL. Swimming and the human microbiome at the intersection of sports, clinical, and environmental sciences: A scoping review of the literature. Front Microbiol 2022; 13:984867. [PMID: 35992695 PMCID: PMC9382026 DOI: 10.3389/fmicb.2022.984867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
The human microbiota is comprised of more than 10–100 trillion microbial taxa and symbiotic cells. Two major human sites that are host to microbial communities are the gut and the skin. Physical exercise has favorable effects on the structure of human microbiota and metabolite production in sedentary subjects. Recently, the concept of “athletic microbiome” has been introduced. To the best of our knowledge, there exists no review specifically addressing the potential role of microbiomics for swimmers, since each sports discipline requires a specific set of techniques, training protocols, and interactions with the athletic infrastructure/facility. Therefore, to fill in this gap, the present scoping review was undertaken. Four studies were included, three focusing on the gut microbiome, and one addressing the skin microbiome. It was found that several exercise-related variables, such as training volume/intensity, impact the athlete’s microbiome, and specifically the non-core/peripheral microbiome, in terms of its architecture/composition, richness, and diversity. Swimming-related power-/sprint- and endurance-oriented activities, acute bouts and chronic exercise, anaerobic/aerobic energy systems have a differential impact on the athlete’s microbiome. Therefore, their microbiome can be utilized for different purposes, including talent identification, monitoring the effects of training methodologies, and devising ad hoc conditioning protocols, including dietary supplementation. Microbiomics can be exploited also for clinical purposes, assessing the effects of exposure to swimming pools and developing potential pharmacological strategies to counteract the insurgence of skin infections/inflammation, including acne. In conclusion, microbiomics appears to be a promising tool, even though current research is still limited, warranting, as such, further studies.
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Affiliation(s)
- Luca Puce
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Jarrad Hampton-Marcell
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Khaled Trabelsi
- Institut Supérieur du Sport et de l’Éducation Physique de Sfax, Université de Sfax, Sfax, Tunisia
- Research Laboratory: Education, Motricité, Sport et Santé, EM2S, Sfax University, Sfax, Tunisia
| | - Achraf Ammar
- Department of Training and Movement Science, Institute of Sport Science, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Sport Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Interdisciplinary Laboratory in Neurosciences, Physiology and Psychology: Physical Activity, Health and Learning (LINP2), Université Paris Lumières, Paris Nanterre University, Nanterre, France
| | - Hamdi Chtourou
- Institut Supérieur du Sport et de l’Éducation Physique de Sfax, Université de Sfax, Sfax, Tunisia
- Activité Physique, Sport et Santé, UR18JS01, Observatoire National du Sport, Tunis, Tunisia
| | - Ayoub Boulares
- Higher Institute of Sports and Physical Education of Ksar-Said, University of Manouba, Tunis, Tunisia
| | - Lucio Marinelli
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Laura Mori
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Filippo Cotellessa
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Antonio Currà
- Department of Medical-Surgical Sciences and Biotechnologies, A. Fiorini Hospital, Sapienza University of Rome, Latina, Italy
| | - Carlo Trompetto
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University, Toronto, ON, Canada
- *Correspondence: Nicola Luigi Bragazzi,
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Zumpf C, Cacho J, Grasse N, Quinn J, Hampton-Marcell J, Armstrong A, Campbell P, Negri MC, Lee DK. Influence of shrub willow buffers strategically integrated in an Illinois corn-soybean field on soil health and microbial community composition. Sci Total Environ 2021; 772:145674. [PMID: 33663956 DOI: 10.1016/j.scitotenv.2021.145674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Soil serves many important ecological functions and is an integral part of our existence as a society. However, concerns for soil health are growing globally, in part due to the negative impacts of agricultural management on soil resources. The production of perennial bioenergy crops on marginal land in row-crop production systems is one solution that could improve land-use efficiency and address the sustainability of cropland management. Because the relationship between crop management and the environment is complex, more research is needed to evaluate the potential benefits perennial bioenergy crop production has on soil health, as well as other ecosystem services. In this study, shrub willow buffers were strategically integrated into a corn-soybean cropping system with the main objective of reducing nitrate-N leaching from grain crop production while producing biomass for bioenergy. Two buffer systems (defined by landscape positions) were included for comparison, one on marginal land with exposure to nitrate-N leaching from upslope grain (southern plots) and one on fertile soils with less nitrate-N leaching potential (northern plots). Evaluation of soil (chemistry, bulk density, microbial community) and shrub willow vegetation properties (fine roots, leaf litter decomposition, and nutrient uptake dynamics), showed that landscape position plays an important role in (1) the dynamics of soil chemical properties, (2) shrub willow's influence and productivity, and (3) the provision of additional ecosystem services such as reductions in nitrous oxide emissions and nitrate-N leaching. In addition, the combination of crop type and landscape position (N-grain, N-willow, S-grain, and S-willow) influenced the species composition of the soil microbial community, resulting in unique and identifiable communities. These results highlight the potential application of shrub willow buffers for ecosystem service provision and support of ecosystem processes; however, understanding the relationship between the microbial community, crop type, and landscape is important for understanding the sustainability of the design.
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Affiliation(s)
- Colleen Zumpf
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA.
| | - Jules Cacho
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Nora Grasse
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - John Quinn
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, Bioscience Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Abigail Armstrong
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Patty Campbell
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - M Cristina Negri
- Argonne National Laboratory, Environmental Science Division, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - D K Lee
- University of Illinois Urbana-Champaign, Crop Science Department, 1102 S. Goodwin Ave., Urbana, IL, USA
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3
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Cook MD, Hampton-Marcell J, Brown M. Differential Gut Scfa Microbial Taxa Correlated With Blood Pressure Status In African American Collegiate Athletes. Med Sci Sports Exerc 2020. [DOI: 10.1249/01.mss.0000679064.42955.5c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ 2020; 8:e9235. [PMID: 32551196 PMCID: PMC7292020 DOI: 10.7717/peerj.9235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
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Affiliation(s)
- David A Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Russell Y Neches
- Genome Center, University of California, Davis, CA, United States of America
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Wendy E Brown
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.,Science Cheerleaders, Inc., Philadelphia, PA, United States of America
| | - Darlene Cavalier
- Science Cheerleaders, Inc., Philadelphia, PA, United States of America.,SciStarter.org, Philadelphia, PA, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, University of Chicago, Lemont, IL, United States of America
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UC San Diego School of Medicine, San Diego, CA, United States of America
| | - Jonathan A Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
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5
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1219] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol 2016; 18:2039-51. [PMID: 26914164 DOI: 10.1111/1462-2920.13231] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/17/2016] [Indexed: 01/16/2023]
Abstract
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.
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Affiliation(s)
- Sarah L O'Brien
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Sean M Gibbons
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Graduate Program in Biophysical Sciences, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA
| | - Eric R Johnston
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Julie D Jastrow
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
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7
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Gordon J, Gandhi P, Shekhawat G, Frazier A, Hampton-Marcell J, Gilbert JA. A simple novel device for air sampling by electrokinetic capture. Microbiome 2015; 3:79. [PMID: 26715467 PMCID: PMC4696304 DOI: 10.1186/s40168-015-0141-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/02/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. RESULTS An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as "gold standard." Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. CONCLUSIONS This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
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Affiliation(s)
- Julian Gordon
- Inspirotec LLC, 3307 Meadow Lane, Glenview, IL, 60025, USA.
| | | | - Gajendra Shekhawat
- Department of Materials Science and Engineering, McCormick School of Engineering and Applied Science, Northwestern University, 2220 Campus Drive, #2036, Evanston, IL, 60208, USA.
| | - Angel Frazier
- Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Jarrad Hampton-Marcell
- Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Jack A Gilbert
- Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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8
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Van Bonn W, LaPointe A, Gibbons SM, Frazier A, Hampton-Marcell J, Gilbert J. Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management. Zoo Biol 2015; 34:360-7. [PMID: 26031788 DOI: 10.1002/zoo.21220] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/22/2015] [Accepted: 04/28/2015] [Indexed: 12/19/2022]
Abstract
The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health.
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Affiliation(s)
- William Van Bonn
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois
| | - Allen LaPointe
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois
| | - Sean M Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois.,Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois
| | - Angel Frazier
- Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois
| | - Jarrad Hampton-Marcell
- Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois.,Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, Illinois
| | - Jack Gilbert
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois.,Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois.,Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, Illinois.,Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, Illinois.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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9
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Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA. The soil microbiome influences grapevine-associated microbiota. mBio 2015; 6:mBio.02527-14. [PMID: 25805735 DOI: 10.1128/mbio.02527-14.editor] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
UNLABELLED Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g., Rhizobiaceae and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management. IMPORTANCE Vine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.
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Affiliation(s)
| | | | - Pamela Weisenhorn
- Computation Institute, University of Chicago, Chicago, Illinois, USA
| | - Kristin West
- Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA
| | | | - Simon Lax
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Nicholas A Bokulich
- Departments of Viticulture and Enology; Food Science and Technology; Foods for Health Institute, University of California, Davis, California, USA
| | - David A Mills
- Departments of Viticulture and Enology; Food Science and Technology; Foods for Health Institute, University of California, Davis, California, USA
| | | | - Safiyh Taghavi
- Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA
| | - Daniel van der Lelie
- Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA
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10
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Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 2014; 345:1048-52. [PMID: 25170151 DOI: 10.1126/science.1254529] [Citation(s) in RCA: 575] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.
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Affiliation(s)
- Simon Lax
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Daniel P Smith
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jarrad Hampton-Marcell
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Sarah M Owens
- Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Computation Institute, University of Chicago, Chicago, IL 60637, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Nicole M Scott
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Sean M Gibbons
- Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Peter Larsen
- Department of Bioscience, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Benjamin D Shogan
- Department of Surgery, University of Chicago Medicine, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Sophie Weiss
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80304, USA
| | - Jessica L Metcalf
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA
| | - Luke K Ursell
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA
| | - Yoshiki Vázquez-Baeza
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA. Department of Computer Science, University of Colorado at Boulder, Boulder, CO 80304, USA
| | - Will Van Treuren
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA
| | - Nur A Hasan
- CosmosID, 387 Technology Drive, Suite 3119, College Park, MD 20742, USA. Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland College Park, College Park, MD 20742, USA
| | - Molly K Gibson
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Rita Colwell
- CosmosID, 387 Technology Drive, Suite 3119, College Park, MD 20742, USA. Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland College Park, College Park, MD 20742, USA
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA
| | - Rob Knight
- Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA. Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA.
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11
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Rubin BER, Sanders JG, Hampton-Marcell J, Owens SM, Gilbert JA, Moreau CS. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. Microbiologyopen 2014; 3:910-21. [PMID: 25257543 PMCID: PMC4263514 DOI: 10.1002/mbo3.216] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 08/20/2014] [Accepted: 08/28/2014] [Indexed: 01/13/2023] Open
Abstract
The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.
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Affiliation(s)
- Benjamin E R Rubin
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois; Department of Science and Education, Field Museum of Natural History, Chicago, Illinois
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12
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Winston ME, Hampton-Marcell J, Zarraonaindia I, Owens SM, Moreau CS, Gilbert JA, Hartsel J, Kennedy SJ, Gibbons SM. Understanding cultivar-specificity and soil determinants of the cannabis microbiome. PLoS One 2014; 9:e99641. [PMID: 24932479 PMCID: PMC4059704 DOI: 10.1371/journal.pone.0099641] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/17/2014] [Indexed: 11/19/2022] Open
Abstract
Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. The influence of soil type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.
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Affiliation(s)
- Max E. Winston
- The Field Museum, Department of Science and Education, Chicago, Illinois, United States of America
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Lemont, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Iratxe Zarraonaindia
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Lemont, Illinois, United States of America
- Basque Country Government, Bilbao, Spain
| | - Sarah M. Owens
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Lemont, Illinois, United States of America
- Computation Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Corrie S. Moreau
- The Field Museum, Department of Science and Education, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Lemont, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Josh Hartsel
- Cannavest, San Diego, California, United States of America
| | | | - S. M. Gibbons
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Lemont, Illinois, United States of America
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Chicago, Illinois, United States of America
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