1
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya.,The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA. .,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA. .,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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2
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome 2021; 9:132. [PMID: 34103074 PMCID: PMC8186369 DOI: 10.1186/s40168-021-01083-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. METHODS We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. RESULTS Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. CONCLUSIONS These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mac Kenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | | | - Laxmi Parida
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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3
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Lutz H, Vangelatos A, Gottel N, Osculati A, Visona S, Finley SJ, Gilbert JA, Javan GT. Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver. Front Microbiol 2020; 11:569630. [PMID: 33363519 PMCID: PMC7752770 DOI: 10.3389/fmicb.2020.569630] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/04/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.
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Affiliation(s)
- Holly Lutz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | | | - Neil Gottel
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Antonio Osculati
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia Visona
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Sheree J Finley
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
| | - Jack A Gilbert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Gulnaz T Javan
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
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4
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. medRxiv 2020:2020.11.19.20234229. [PMID: 33236030 PMCID: PMC7685343 DOI: 10.1101/2020.11.19.20234229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, California, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | | | - Laxmi Parida
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, California, USA
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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5
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Zhao D, Cardona C, Gottel N, Winton VJ, Thomas PM, Raba DA, Kelley ST, Henry C, Gilbert JA, Stephens B. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials. Sci Rep 2020; 10:14500. [PMID: 32879425 PMCID: PMC7467922 DOI: 10.1038/s41598-020-71560-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 08/18/2020] [Indexed: 11/12/2022] Open
Abstract
The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).
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Affiliation(s)
- Dan Zhao
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Neil Gottel
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Valerie J Winton
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel A Raba
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Christopher Henry
- Mathematics and Computer Science, Argonne National Laboratory, Lemont, IL, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA.
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6
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Hampton-Marcell JT, Larsen P, Anton T, Cralle L, Sangwan N, Lax S, Gottel N, Salas-Garcia M, Young C, Duncan G, Lopez JV, Gilbert JA. Detecting personal microbiota signatures at artificial crime scenes. Forensic Sci Int 2020; 313:110351. [PMID: 32559614 DOI: 10.1016/j.forsciint.2020.110351] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/16/2020] [Revised: 05/13/2020] [Accepted: 05/26/2020] [Indexed: 01/16/2023]
Abstract
When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real residences. We demonstrate that humans (n = 30) leave behind microbial signatures that can be used to track interaction with various surfaces within a building, but the likelihood of accurately detecting the specific burglar for a given home was between 20-25%. Also, the human microbiome contains rare microbial taxa that can be combined to create a unique microbial profile, which when compared to 600 other individuals can improve our ability to link an individual 'burglar' to a residence. In total, 5512 discriminating, non-singleton unique exact sequence variants (uESVs) were identified as unique to an individual, with a minimum of 1 and a maximum of 568, suggesting some people maintain a greater degree of unique taxa compared to our population of 600. Approximate 60-77% of the unique exact sequence variants originated from the hands of participants, and these microbial discriminators spanned 36 phyla but were dominated by the Proteobacteria (34%). A fitted regression generated to determine whether an intruder's uESVs found on door handles in an office decayed over time in the presence or absence of office workers, found no significant shift in proportion of uESVs over time irrespective of the presence of office workers. While it was possible to detect the correct burglars' microbiota as having contributed to the invaded space, the predictions were very weak in comparison to accepted forensic standards. This suggests that at this time 16S rRNA amplicon sequencing of the built environment microbiota cannot be used as a reliable trace evidence standard for criminal investigations.
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Affiliation(s)
- Jarrad T Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States; Department of Surgery, University of Chicago, Chicago, IL, United States.
| | - Peter Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Tifani Anton
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Lauren Cralle
- Department of Surgery, University of Chicago, Chicago, IL, United States
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Simon Lax
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Neil Gottel
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Mariana Salas-Garcia
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Candace Young
- Department of Chemistry, Physics and Engineering Studies, Chicago State University, Chicago, IL, United States
| | - George Duncan
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jose V Lopez
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States; Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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7
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Shojaee S, Sharma A, Gottel N, Sanchez T, Gilbert JA, Rahman NM. Microbiome profile associated with malignant pleural effusion. PLoS One 2020; 15:e0232181. [PMID: 32384089 PMCID: PMC7209204 DOI: 10.1371/journal.pone.0232181] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/08/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction There is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases. Method From a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V4 region amplicon sequencing was performed. Exact Sequence Variants (ESVs) were used for diversity analyses. The Shannon and Richness indices of alpha diversity and UniFrac beta diversity measures were tested for significance using permutational multivariate analysis of variance. Analyses of Composition of Microbiome was used to identify differentially abundant bacterial ESVs between the groups controlled for multiple hypothesis testing. Results 38 patients with MPE and 9 with non-MPE were included. A subgroup of patients with metastatic adenocarcinoma histology were identified among MPE group (adenocarcinoma of lung origin (LA-MPE) = 11, breast origin (BA-MPE) = 11). MPE presented with significantly greater alpha diversity compared to non-MPE group. Within the MPE group, BA-MPE was more diverse compared to LA-MPE group. In multivariable analysis, ESVs belonging to family S24-7 and genera Allobaculum, Stenotrophomonas, and Epulopiscium were significantly enriched in the malignant group compared to the non-malignant group. Conclusion Our results are the first to demonstrate a microbiome signature according to MPE and non-MPE. The role of microbiome in pleural effusion pathogenesis needs further exploration.
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Affiliation(s)
- Samira Shojaee
- Division of Pulmonary and Critical Care Medicine, Virginia Commonwealth University Medical Center, Richmond, VA, United States of America
- * E-mail:
| | - Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
| | - Neil Gottel
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
- Scripps Institution of Oceanography, UCSD, San Diego, CA, United States of America
| | - Trinidad Sanchez
- Division of Pulmonary and Critical Care Medicine, Virginia Commonwealth University Medical Center, Richmond, VA, United States of America
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
- Scripps Institution of Oceanography, UCSD, San Diego, CA, United States of America
| | - Najib M. Rahman
- Oxford Respiratory Trials Unit, Oxford Centre for Respiratory Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
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8
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Hyoju SK, Adriaansens C, Wienholts K, Sharma A, Keskey R, Arnold W, van Dalen D, Gottel N, Hyman N, Zaborin A, Gilbert J, van Goor H, Zaborina O, Alverdy JC. Low-fat/high-fibre diet prehabilitation improves anastomotic healing via the microbiome: an experimental model. Br J Surg 2019; 107:743-755. [PMID: 31879948 DOI: 10.1002/bjs.11388] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/20/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Both obesity and the presence of collagenolytic bacterial strains (Enterococcus faecalis) can increase the risk of anastomotic leak. The aim of this study was to determine whether mice chronically fed a high-fat Western-type diet (WD) develop anastomotic leak in association with altered microbiota, and whether this can be mitigated by a short course of standard chow diet (SD; low fat/high fibre) before surgery. METHODS Male C57BL/6 mice were assigned to either SD or an obesogenic WD for 6 weeks followed by preoperative antibiotics and colonic anastomosis. Microbiota were analysed longitudinally after operation and correlated with healing using an established anastomotic healing score. In reiterative experiments, mice fed a WD for 6 weeks were exposed to a SD for 2, 4 and 6 days before colonic surgery, and anastomotic healing and colonic microbiota analysed. RESULTS Compared with SD-fed mice, WD-fed mice demonstrated an increased risk of anastomotic leak, with a bloom in the abundance of Enterococcus in lumen and expelled stool (65-90 per cent for WD versus 4-15 per cent for SD; P = 0·010 for lumen, P = 0·013 for stool). Microbiota of SD-fed mice, but not those fed WD, were restored to their preoperative composition after surgery. Anastomotic healing was significantly improved when WD-fed mice were exposed to a SD diet for 2 days before antibiotics and surgery (P < 0·001). CONCLUSION The adverse effects of chronic feeding of a WD on the microbiota and anastomotic healing can be prevented by a short course of SD in mice. Surgical relevance Worldwide, enhanced recovery programmes have developed into standards of care that reduce major complications after surgery, such as surgical-site infections and anastomotic leak. A complementary effort termed prehabilitation includes preoperative approaches such as smoking cessation, exercise and dietary modification. This study investigated whether a short course of dietary prehabilitation in the form of a low-fat/high-fibre composition can reverse the adverse effect of a high-fat Western-type diet on anastomotic healing in mice. Intake of a Western-type diet had a major adverse effect on both the intestinal microbiome and anastomotic healing following colonic anastomosis in mice. This could be reversed when mice received a low-fat/high-fibre diet before operation. Taken together, these data suggest that dietary modifications before major surgery can improve surgical outcomes via their effects on the intestinal microbiome.
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Affiliation(s)
- S K Hyoju
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - C Adriaansens
- Department of Surgery, University of Chicago, Chicago, Illinois, USA.,Department of Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - K Wienholts
- Department of Surgery, University of Chicago, Chicago, Illinois, USA.,Department of Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - A Sharma
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - R Keskey
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - W Arnold
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - D van Dalen
- Department of Surgery, University of Chicago, Chicago, Illinois, USA.,Department of Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - N Gottel
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - N Hyman
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - A Zaborin
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - J Gilbert
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - H van Goor
- Department of Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - O Zaborina
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - J C Alverdy
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
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9
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Fei N, Bernabé BP, Lie L, Baghdan D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Gottel N, Riesen W, Korte W, Luke A, Kliethermes SA, Layden BT, Gilbert JA, Dugas LR. The human microbiota is associated with cardiometabolic risk across the epidemiologic transition. PLoS One 2019; 14:e0215262. [PMID: 31339887 PMCID: PMC6656343 DOI: 10.1371/journal.pone.0215262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 03/26/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023] Open
Abstract
Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions. We characterized gut- and oral-associated microbiota and CM risk in 655 participants of African-origin, aged 25-45, from Ghana, South Africa, Jamaica, and the United States (US). CM risk was classified using the CM risk cut-points for elevated waist circumference, elevated blood pressure and elevated fasted blood glucose, low high-density lipoprotein (HDL), and elevated triglycerides. Gut-associated bacterial alpha diversity negatively correlated with elevated blood pressure and elevated fasted blood glucose. Similarly, gut bacterial beta diversity was also significantly differentiated by waist circumference, blood pressure, triglyceridemia and HDL-cholesterolemia. Notably, differences in inter- and intra-personal gut microbial diversity were geographic-region specific. Participants meeting the cut-points for 3 out of the 5 CM risk factors were significantly more enriched with Lachnospiraceae, and were significantly depleted of Clostridiaceae, Peptostreptococcaceae, and Prevotella. The predicted relative proportions of the genes involved in the pathways for lipopolysaccharides (LPS) and butyrate synthesis were also significantly differentiated by the CM risk phenotype, whereby genes involved in the butyrate synthesis via lysine, glutarate and 4-aminobutyrate/succinate pathways and LPS synthesis pathway were enriched in participants with greater CM risk. Furthermore, inter-individual oral microbiota diversity was also significantly associated with the CM risk factors, and oral-associated Streptococcus, Prevotella, and Veillonella were enriched in participants with 3 out of the 5 CM risk factors. We demonstrate that in a diverse cohort of African-origin adults, CM risk is significantly associated with reduced microbial diversity, and the enrichment of specific bacterial taxa and predicted functional traits in both gut and oral environments. As well as providing new insights into the associations between the gut and oral microbiota and CM risk, this study also highlights the potential for novel therapeutic discoveries which target the oral and gut microbiota in CM risk.
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Affiliation(s)
- Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Beatriz Peñalver Bernabé
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Louise Lie
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
| | - Danny Baghdan
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
| | - Kweku Bedu-Addo
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacob Plange-Rhule
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Pascal Bovet
- Institute of Social & Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
- Ministry of Health, Mahé, Victoria, Republic of Seychelles
| | - Neil Gottel
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Walter Riesen
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Wolfgang Korte
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Amy Luke
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
| | - Stephanie A. Kliethermes
- Department of Orthopedics and Rehabilitation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Lara R. Dugas
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States of America
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10
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Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R. Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. Biotechniques 2019; 67:29-32. [PMID: 31124709 PMCID: PMC7030937 DOI: 10.2144/btn-2018-0192] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conventional wisdom holds that PCR amplification for sequencing should employ pooled replicate reactions to reduce bias due to jackpot effects and chimera formation. However, modern amplicon data analysis employs methods that may be less sensitive to such artifacts. Here we directly compare results from single versus triplicate reactions for 16S amplicon sequencing and find no significant impact of adopting a less labor-intensive single-reaction protocol.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Division of Bioscience, Argonne National Laboratory University of Chicago, Chicago, IL, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neil Gottel
- Division of Bioscience, Argonne National Laboratory University of Chicago, Chicago, IL, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jack A Gilbert
- Division of Bioscience, Argonne National Laboratory University of Chicago, Chicago, IL, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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11
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Hu J, Ben Maamar S, Glawe AJ, Gottel N, Gilbert JA, Hartmann EM. Impacts of indoor surface finishes on bacterial viability. Indoor Air 2019; 29:551-562. [PMID: 30980566 PMCID: PMC6851865 DOI: 10.1111/ina.12558] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 01/03/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 05/21/2023]
Abstract
Microbes in indoor environments are constantly being exposed to antimicrobial surface finishes. Many are rendered non-viable after spending extended periods of time under low-moisture, low-nutrient surface conditions, regardless of whether those surfaces have been amended with antimicrobial chemicals. However, some microorganisms remain viable even after prolonged exposure to these hostile conditions. Work with specific model pathogens makes it difficult to draw general conclusions about how chemical and physical properties of surfaces affect microbes. Here, we explore the survival of a synthetic community of non-model microorganisms isolated from built environments following exposure to three chemically and physically distinct surface finishes. Our findings demonstrated the differences in bacterial survival associated with three chemically and physically distinct materials. Alkaline clay surfaces select for an alkaliphilic bacterium, Kocuria rosea, whereas acidic mold-resistant paint favors Bacillus timonensis, a Gram-negative spore-forming bacterium that also survives on antimicrobial surfaces after 24 hours of exposure. Additionally, antibiotic-resistant Pantoea allii did not exhibit prolonged retention on antimicrobial surfaces. Our controlled microcosm experiment integrates measurement of indoor chemistry and microbiology to elucidate the complex biochemical interactions that influence the indoor microbiome.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Sarah Ben Maamar
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Adam J. Glawe
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Neil Gottel
- Department of SurgeryThe University of ChicagoChicagoIllinois
| | - Jack A. Gilbert
- Department of SurgeryThe University of ChicagoChicagoIllinois
| | - Erica M. Hartmann
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
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12
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Richardson M, Gottel N, Gilbert JA, Gordon J, Gandhi P, Reboulet R, Hampton-Marcell JT. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area. Microbiome 2019; 7:82. [PMID: 31159879 PMCID: PMC6547563 DOI: 10.1186/s40168-019-0695-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/09/2019] [Indexed: 05/05/2023]
Abstract
The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens, the microbial community, and the indoor living environment, we sampled the bedrooms of 65 homes in the Chicago area using 23the patient-friendly Inspirotec electrokinetic air sampling device, which collects airborne particles for characterization of both allergens and microbial DNA. The sampling device captured sufficient microbial material to enable 16S rRNA amplicon sequencing data to be generated for every sample in the study. Neither the presence of HEPA filters nor the height at which the air sampling device was placed had any influence on the microbial community profile. A core microbiota of 31 OTUs was present in more than three quarters of the samples, comprising around 45% of the relative sequence counts in each bedroom. The most abundant single organisms were Staphylococcus, with other core taxa both human and outdoor-associated. Bacterial alpha diversity was significantly increased in bedrooms that reported having open windows, those with flowering plants in the vicinity, and those in homes occupied by dogs. Porphyromonas, Moraxella, Sutterella, and Clostridium, along with family Neisseraceae, were significantly enriched in homes with dogs; interestingly, cats did not show a significant impact on microbial diversity or relative abundance. While dog allergen load was significantly correlated with bacterial alpha diversity, the taxa that significantly correlated with allergen burden did not exclusively overlap with those enriched in homes with dogs. Alternaria allergen load was positively correlated with bacterial alpha diversity, while Aspergillus allergen load was negatively correlated. The Alternaria allergen load was also significantly correlated with open windows. Microbial communities were significantly differentiated between rural, suburban, and urban homes and houses that were physically closer to each other maintained significantly more similar microbiota. We have demonstrated that it is possible to determine significant associations between allergen burden and the microbiota in air from the same sample and that these associations relate to the characteristics of the home and neighborhoods.
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Affiliation(s)
- Miles Richardson
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, 10032, USA.
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, 60637, USA.
| | - Neil Gottel
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- BioScience Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- BioScience Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Julian Gordon
- Inspirotec Inc, 332 S. Michigan Avenue, Suite 10 32 #1248, Chicago, IL, 60604, USA
| | - Prasanthi Gandhi
- Inspirotec Inc, 332 S. Michigan Avenue, Suite 10 32 #1248, Chicago, IL, 60604, USA
| | - Rachel Reboulet
- Inspirotec Inc, 332 S. Michigan Avenue, Suite 10 32 #1248, Chicago, IL, 60604, USA
| | - Jarrad T Hampton-Marcell
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
- BioScience Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
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13
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Dodiya HB, Kuntz T, Shaik SM, Baufeld C, Leibowitz J, Zhang X, Gottel N, Zhang X, Butovsky O, Gilbert JA, Sisodia SS. Sex-specific effects of microbiome perturbations on cerebral Aβ amyloidosis and microglia phenotypes. J Exp Med 2019; 216:1542-1560. [PMID: 31097468 PMCID: PMC6605759 DOI: 10.1084/jem.20182386] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/26/2019] [Accepted: 04/16/2019] [Indexed: 12/12/2022] Open
Abstract
We demonstrated that an antibiotic cocktail (ABX)-perturbed gut microbiome is associated with reduced amyloid-β (Aβ) plaque pathology and astrogliosis in the male amyloid precursor protein (APP)SWE /presenilin 1 (PS1)ΔE9 transgenic model of Aβ amyloidosis. We now show that in an independent, aggressive APPSWE/PS1L166P (APPPS1-21) mouse model of Aβ amyloidosis, an ABX-perturbed gut microbiome is associated with a reduction in Aβ pathology and alterations in microglial morphology, thus establishing the generality of the phenomenon. Most importantly, these latter alterations occur only in brains of male mice, not in the brains of female mice. Furthermore, ABX treatment lead to alterations in levels of selected microglial expressed transcripts indicative of the "M0" homeostatic state in male but not in female mice. Finally, we found that transplants of fecal microbiota from age-matched APPPS1-21 male mice into ABX-treated APPPS1-21 male restores the gut microbiome and partially restores Aβ pathology and microglial morphology, thus demonstrating a causal role of the microbiome in the modulation of Aβ amyloidosis and microglial physiology in mouse models of Aβ amyloidosis.
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Affiliation(s)
- Hemraj B Dodiya
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Thomas Kuntz
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Shabana M Shaik
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Caroline Baufeld
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jeffrey Leibowitz
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Xulun Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Neil Gottel
- Department of Pediatrics and Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA
| | - Xiaoqiong Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Oleg Butovsky
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA
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Dugas LR, Bernabé BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X, Dong Q, Sun J, Kliethermes S, Gottel N, Luke A, Gilbert JA, Layden BT. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Sci Rep 2018; 8:17135. [PMID: 30459320 PMCID: PMC6244201 DOI: 10.1038/s41598-018-35230-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI < 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value < 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p < 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value < 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity.
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Affiliation(s)
- Lara R Dugas
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | | | - Medha Priyadarshini
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Seo Jin Park
- Department of Microbiology-Immunology, Northwestern University, Chicago, Illinois, USA
| | - Laquita Brown
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | | | - David Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Evelyn C Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Xiang Gao
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Qunfeng Dong
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jun Sun
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie Kliethermes
- Department of Orthopedics and Rehabilitation, University of Wisconsin School of Medicine and Public Health, Wisconsin, USA
| | - Neil Gottel
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Amy Luke
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jack A Gilbert
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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15
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Cason CA, Kuntz TM, Gottel N, Xiong L, Jiang Q, Chang EB, Gilbert JA, Ho KJ. Abstract 318: Modulation of Neointimal Hyperplasia Severity in Rats by Commensal Microbial Transfer. Arterioscler Thromb Vasc Biol 2017. [DOI: 10.1161/atvb.37.suppl_1.318] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neointimal hyperplasia is a major contributor to restenosis after arterial interventions. The genetic and environmental mechanisms underlying the variable propensity for neointimal hyperplasia between individuals are not well understood. One possible modulator could be commensal gut microbes. To address whether microbes mediate neointimal hyperplasia, we cohoused genetically different rats (Lewis [LE] and Sprague-Dawley [SD]) which harbor different commensal microbes and compared neointimal hyperplasia 2 weeks after carotid angioplasty in the cohoused and non-cohoused cohorts. Cohousing is a means of microbial transfer between cage inhabitants. We observed that differences in neointimal hyperplasia between non-cohoused LE and SD rats (median intima+media [I+M] area 0.12 mm
2
LE vs. 0.26 mm
2
SD, P<.0001;Mann-Whitney) were mitigated when rats are cohoused for 1 month (Figure 1A), suggesting an environmental effect that outweighs the genetic influence. Specifically, I+M area decreased by 23% in SD rats that were cohoused with LE rats (P<.0001;Mann-Whitney), and there was a trend towards a 10% increase in I+M area in cohoused LE rats. To identify specific bacteria associated with the change in neointimal hyperplasia, we monitored fecal bacteria over time using 16S rRNA sequencing. Principal component analysis revealed that fecal samples from cohoused rats diverged from non-cohoused rats in both strains (P<.001 SD, P=.008 LE;PERMANOVA) (Figure 1B). The greatest change was cohoused SD samples becoming similar to non-cohoused LE samples over time, which correlates with the carotid morphometric data. Comparative analysis showed that abundance of the bacterial genera Peptococcus and Blautia negatively correlated with I+M area in both strains (P<.001;Fisher z transform, Bonferroni corrected, Spearman’s ρ -0.8 for both). Ongoing studies will further delineate the potential causative relationship between these microbes and neointimal hyperplasia.
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16
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Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, Podar M, Schadt CW. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS One 2013; 8:e76382. [PMID: 24146861 PMCID: PMC3797799 DOI: 10.1371/journal.pone.0076382] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/21/2013] [Indexed: 12/24/2022] Open
Abstract
Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects.
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Affiliation(s)
- Migun Shakya
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Genome Science and Technology Program, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Neil Gottel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Hector Castro
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Lee Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Gregory Bonito
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Gerald Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Genome Science and Technology Program, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Genome Science and Technology Program, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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