Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
Abstract
To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( > 55%) of the community is composed of poorly characterized low abundance (individually < 1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.
- Authors:
-
- Univ. of Oklahoma, Norman, OK (United States); The Univ. of Rhode Island, Kingston, RI (United States)
- Univ. of Oklahoma, Norman, OK (United States)
- Arizona State Univ., Tempe, AZ (United States)
- Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences (CAS), Beijing (China)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Montana State Univ., Bozeman, MT (United States)
- Michigan State Univ., East Lansing, MI (United States)
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1327637
- Alternate Identifier(s):
- OSTI ID: 1255538; OSTI ID: 1407297
- Grant/Contract Number:
- AC05-00OR22725; FG02-07ER64398; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; metagenomics; bioremediation; groundwater microbiology
Citation Formats
Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., and Zhou, Jizhong. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. United States: N. p., 2015.
Web. doi:10.3389/fmicb.2015.01205.
Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., & Zhou, Jizhong. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. United States. https://doi.org/10.3389/fmicb.2015.01205
Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., and Zhou, Jizhong. Sat .
"Comparative metagenomics reveals impact of contaminants on groundwater microbiomes". United States. https://doi.org/10.3389/fmicb.2015.01205. https://www.osti.gov/servlets/purl/1327637.
@article{osti_1327637,
title = {Comparative metagenomics reveals impact of contaminants on groundwater microbiomes},
author = {Hemme, Christopher L. and Tu, Qichao and Shi, Zhou and Qin, Yujia and Gao, Weimin and Deng, Ye and Nostrand, Joy D. Van and Wu, Liyou and He, Zhili and Chain, Patrick S. G. and Tringe, Susannah G. and Fields, Matthew W. and Rubin, Edward M. and Tiedje, James M. and Hazen, Terry C. and Arkin, Adam P. and Zhou, Jizhong},
abstractNote = {To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( > 55%) of the community is composed of poorly characterized low abundance (individually < 1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.},
doi = {10.3389/fmicb.2015.01205},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {Sat Oct 31 00:00:00 EDT 2015},
month = {Sat Oct 31 00:00:00 EDT 2015}
}
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Works referenced in this record:
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
journal, August 2011
- Kong, Yong
- Genomics, Vol. 98, Issue 2
UCHIME improves sensitivity and speed of chimera detection
journal, June 2011
- Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C.
- Bioinformatics, Vol. 27, Issue 16
Metagenomic analysis of a stable trichloroethene-degrading microbial community
journal, March 2012
- Brisson, Vanessa L.; West, Kimberlee A.; Lee, Patrick KH
- The ISME Journal, Vol. 6, Issue 9
The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem
journal, January 2013
- Inskeep, William
- Frontiers in Microbiology, Vol. 4
Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat
journal, January 2008
- Kunin, Victor; Raes, Jeroen; Harris, J. Kirk
- Molecular Systems Biology, Vol. 4, Issue 1
Comparative Metagenomics of Microbial Communities
journal, April 2005
- Tringe, S. G.
- Science, Vol. 308, Issue 5721
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007
- Wang, Q.; Garrity, G. M.; Tiedje, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 16
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010
- Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
journal, March 2010
- DeAngelis, Kristen M.; Gladden, John M.; Allgaier, Martin
- BioEnergy Research, Vol. 3, Issue 2
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
The integrated microbial genomes system: an expanding comparative analysis resource
journal, October 2009
- Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 38, Issue suppl_1
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011
- Magoc, T.; Salzberg, S. L.
- Bioinformatics, Vol. 27, Issue 21
Phylogenetic and Functional Biomakers as Indicators of Bacterial Community Responses to Mixed-Waste Contamination
journal, April 2006
- Fields, M. W.; Bagwell, C. E.; Carroll, S. L.
- Environmental Science & Technology, Vol. 40, Issue 8
Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer
journal, April 2011
- Van Nostrand, Joy D.; Wu, Liyou; Wu, Wei-Min
- Applied and Environmental Microbiology, Vol. 77, Issue 11
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
journal, February 2010
- Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.
- The ISME Journal, Vol. 4, Issue 5
Mineralogical characterization of saprolite at the FRC background site in Oak Ridge, Tennessee
journal, December 2008
- Kim, Young-Jin; Moon, Ji-Won; Roh, Yul
- Environmental Geology, Vol. 58, Issue 6
Horizontal Gene Transfer of PIB-Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils
journal, May 2006
- Martinez, R. J.; Wang, Y.; Raimondo, M. A.
- Applied and Environmental Microbiology, Vol. 72, Issue 5
IMG/M: a data management and analysis system for metagenomes
journal, December 2007
- Markowitz, V. M.; Ivanova, N. N.; Szeto, E.
- Nucleic Acids Research, Vol. 36, Issue Database
Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments
journal, December 1988
- Lovley, Derek R.; Goodwin, Steve
- Geochimica et Cosmochimica Acta, Vol. 52, Issue 12
Global modeling of withdrawal, allocation and consumptive use of surface water and groundwater resources
journal, January 2014
- Wada, Y.; Wisser, D.; Bierkens, M. F. P.
- Earth System Dynamics, Vol. 5, Issue 1
GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer
journal, October 2009
- Van Nostrand, Joy D.; Wu, Wei-Min; Wu, Liyou
- Environmental Microbiology, Vol. 11, Issue 10
Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure
journal, August 2008
- Moreels, David; Crosson, Garry; Garafola, Craig
- Environmental Science and Pollution Research, Vol. 15, Issue 6
Potential for In Situ Bioremediation of a Low-pH, High-Nitrate Uranium-Contaminated Groundwater
journal, November 2003
- Shelobolina, Evgenya S.; O'Neill, Kathleen; Finneran, Kevin T.
- Soil and Sediment Contamination: An International Journal, Vol. 12, Issue 6
Short read fragment assembly of bacterial genomes
journal, February 2008
- Chaisson, M. J.; Pevzner, P. A.
- Genome Research, Vol. 18, Issue 2
Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate
journal, August 2004
- North, N. N.; Dollhopf, S. L.; Petrie, L.
- Applied and Environmental Microbiology, Vol. 70, Issue 8
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine
journal, August 2009
- Claesson, Marcus J.; O'Sullivan, Orla; Wang, Qiong
- PLoS ONE, Vol. 4, Issue 8
Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems: Aquifer metagenomics
journal, October 2011
- Smith, Renee J.; Jeffries, Thomas C.; Roudnew, Ben
- Environmental Microbiology, Vol. 14, Issue 1
Hydrologic Significance of Carbon Monoxide Concentrations in Ground Water
journal, May 2007
- Chapelle, Francis H.; Bradley, Paul M.
- Ground Water, Vol. 45, Issue 3
Community structure and metabolism through reconstruction of microbial genomes from the environment
journal, February 2004
- Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip
- Nature, Vol. 428, Issue 6978
Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface
journal, March 2004
- Coombs, J. M.; Barkay, T.
- Applied and Environmental Microbiology, Vol. 70, Issue 3
Using Hydrochemical Fades to Delineate Ground Water Flowpaths in Fractured Shale
journal, February 1999
- Schreiber, M. E.; Moline, G. R.; Bahr, J. M.
- Groundwater Monitoring & Remediation, Vol. 19, Issue 1
Groundwater: the processes and global significance of aquifer degradation
journal, November 2003
- Foster, S. S. D.; Chilton, P. J.
- Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 358, Issue 1440
Scaffolding pre-assembled contigs using SSPACE
journal, December 2010
- Boetzer, Marten; Henkel, Christiaan V.; Jansen, Hans J.
- Bioinformatics, Vol. 27, Issue 4
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels
journal, May 2008
- Cardenas, E.; Wu, W. -M.; Leigh, M. B.
- Applied and Environmental Microbiology, Vol. 74, Issue 12
IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009
- Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.
- Bioinformatics, Vol. 25, Issue 17
Identifying biologically relevant differences between metagenomic communities
journal, February 2010
- Parks, Donovan H.; Beiko, Robert G.
- Bioinformatics, Vol. 26, Issue 6
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
journal, June 2011
- Martinez-Garcia, Manuel; Swan, Brandon K.; Poulton, Nicole J.
- The ISME Journal, Vol. 6, Issue 1
Mineralogical characterization of saprolite at the FRC background site in Oak Ridge, Tennessee
journal, December 2008
- Kim, Young-Jin; Moon, Ji-Won; Roh, Yul
- Environmental Geology, Vol. 58, Issue 6
Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure
journal, August 2008
- Moreels, David; Crosson, Garry; Garafola, Craig
- Environmental Science and Pollution Research, Vol. 15, Issue 6
Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
journal, March 2010
- DeAngelis, Kristen M.; Gladden, John M.; Allgaier, Martin
- BioEnergy Research, Vol. 3, Issue 2
Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments
journal, December 1988
- Lovley, Derek R.; Goodwin, Steve
- Geochimica et Cosmochimica Acta, Vol. 52, Issue 12
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
journal, August 2011
- Kong, Yong
- Genomics, Vol. 98, Issue 2
Phylogenetic and Functional Biomakers as Indicators of Bacterial Community Responses to Mixed-Waste Contamination
journal, April 2006
- Fields, M. W.; Bagwell, C. E.; Carroll, S. L.
- Environmental Science & Technology, Vol. 40, Issue 8
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
journal, February 2010
- Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.
- The ISME Journal, Vol. 4, Issue 5
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
journal, June 2011
- Martinez-Garcia, Manuel; Swan, Brandon K.; Poulton, Nicole J.
- The ISME Journal, Vol. 6, Issue 1
Metagenomic analysis of a stable trichloroethene-degrading microbial community
journal, March 2012
- Brisson, Vanessa L.; West, Kimberlee A.; Lee, Patrick KH
- The ISME Journal, Vol. 6, Issue 9
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat
journal, January 2008
- Kunin, Victor; Raes, Jeroen; Harris, J. Kirk
- Molecular Systems Biology, Vol. 4, Issue 1
Horizontal gene transfer enables programmable gene stability in synthetic microbiota
journal, September 2022
- Wang, Teng; Weiss, Andrea; Aqeel, Ammara
- Nature Chemical Biology, Vol. 18, Issue 11
Potential for In Situ Bioremediation of a Low-pH, High-Nitrate Uranium-Contaminated Groundwater
journal, November 2003
- Shelobolina, Evgenya S.; O'Neill, Kathleen; Finneran, Kevin T.
- Soil and Sediment Contamination: An International Journal, Vol. 12, Issue 6
Identifying biologically relevant differences between metagenomic communities
journal, February 2010
- Parks, Donovan H.; Beiko, Robert G.
- Bioinformatics, Vol. 26, Issue 6
Scaffolding pre-assembled contigs using SSPACE
journal, December 2010
- Boetzer, Marten; Henkel, Christiaan V.; Jansen, Hans J.
- Bioinformatics, Vol. 27, Issue 4
UCHIME improves sensitivity and speed of chimera detection
journal, June 2011
- Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C.
- Bioinformatics, Vol. 27, Issue 16
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
IMG/M: a data management and analysis system for metagenomes
journal, December 2007
- Markowitz, V. M.; Ivanova, N. N.; Szeto, E.
- Nucleic Acids Research, Vol. 36, Issue Database
The integrated microbial genomes system: an expanding comparative analysis resource
journal, October 2009
- Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 38, Issue suppl_1
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
Short read fragment assembly of bacterial genomes
journal, February 2008
- Chaisson, M. J.; Pevzner, P. A.
- Genome Research, Vol. 18, Issue 2
GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer
journal, October 2009
- Van Nostrand, Joy D.; Wu, Wei-Min; Wu, Liyou
- Environmental Microbiology, Vol. 11, Issue 10
Hydrologic Significance of Carbon Monoxide Concentrations in Ground Water
journal, May 2007
- Chapelle, Francis H.; Bradley, Paul M.
- Ground Water, Vol. 45, Issue 3
Using Hydrochemical Fades to Delineate Ground Water Flowpaths in Fractured Shale
journal, February 1999
- Schreiber, M. E.; Moline, G. R.; Bahr, J. M.
- Groundwater Monitoring & Remediation, Vol. 19, Issue 1
Comparative Metagenomics of Microbial Communities
journal, April 2005
- Tringe, S. G.
- Science, Vol. 308, Issue 5721
DNA recovery from soils of diverse composition.
journal, January 1996
- Zhou, J.; Bruns, M. A.; Tiedje, J. M.
- Applied and environmental microbiology, Vol. 62, Issue 2
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine
journal, August 2009
- Claesson, Marcus J.; O'Sullivan, Orla; Wang, Qiong
- PLoS ONE, Vol. 4, Issue 8
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- Tipayno, Sherlyn C.; Truu, Jaak; Samaddar, Sandipan
- Ecology and Evolution, Vol. 8, Issue 12
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- Techtmann, Stephen M.; Hazen, Terry C.
- Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 10
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- Smith, H. J.; Zelaya, A. J.; De León, K. B.
- FEMS Microbiology Ecology, Vol. 94, Issue 12
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journal, March 2018
- Wang, Z. G.; You, Y. M.; Xu, W. H.
- European Journal of Soil Science, Vol. 69, Issue 3
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- BMC Genomics, Vol. 19, Issue 1
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- PLOS ONE, Vol. 11, Issue 9
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- Christensen, Geoff A.; Moon, JiWon; Veach, Allison M.
- PLOS ONE, Vol. 13, Issue 3
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journal, September 2018
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- PLOS ONE, Vol. 13, Issue 9
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- Genes, Vol. 10, Issue 5
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