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Title: Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

Abstract

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offeringmore » new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.« less

Authors:
 [1];  [2];  [2];  [3];  [4];  [3];  [4];  [5];  [5]
+ Show Author Affiliations
  1. Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology; Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry
  2. Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
  5. Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry; Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
OSTI Identifier:
1400161
Alternate Identifier(s):
OSTI ID: 1550118
Grant/Contract Number:  
AC05-00OR22725; SC0006654; DEB1134877; 2015066:MNL:11/19/2015
Resource Type:
Accepted Manuscript
Journal Name:
Biochimica et Biophysica Acta - General Subjects
Additional Journal Information:
Journal Volume: 1861; Journal Issue: 9; Journal ID: ISSN 0304-4165
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Rawle, Rachel A., Hamerly, Timothy, Tripet, Brian P., Giannone, Richard J., Wurch, Louie, Hettich, Robert L., Podar, Mircea, Copié, Valerie, and Bothner, Brian. Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association. United States: N. p., 2017. Web. doi:10.1016/j.bbagen.2017.06.001.
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Rawle, Rachel A., Hamerly, Timothy, Tripet, Brian P., Giannone, Richard J., Wurch, Louie, Hettich, Robert L., Podar, Mircea, Copié, Valerie, & Bothner, Brian. Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association. United States. https://doi.org/10.1016/j.bbagen.2017.06.001
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Rawle, Rachel A., Hamerly, Timothy, Tripet, Brian P., Giannone, Richard J., Wurch, Louie, Hettich, Robert L., Podar, Mircea, Copié, Valerie, and Bothner, Brian. Sun . "Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association". United States. https://doi.org/10.1016/j.bbagen.2017.06.001. https://www.osti.gov/servlets/purl/1400161.
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@article{osti_1400161,
title = {Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association},
author = {Rawle, Rachel A. and Hamerly, Timothy and Tripet, Brian P. and Giannone, Richard J. and Wurch, Louie and Hettich, Robert L. and Podar, Mircea and Copié, Valerie and Bothner, Brian},
abstractNote = {Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.},
doi = {10.1016/j.bbagen.2017.06.001},
journal = {Biochimica et Biophysica Acta - General Subjects},
number = 9,
volume = 1861,
place = {United States},
year = {Sun Jun 04 00:00:00 EDT 2017},
month = {Sun Jun 04 00:00:00 EDT 2017}
}
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https://doi.org/10.1016/j.bbagen.2017.06.001
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    • DOI: 10.1111/1758-2229.12740

    Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges
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