Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data
Abstract
Modulation of interspecies interactions in the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method that enables predicting the effect of new species on pairwise interactions among existing members and termed it the Minimal Interspecies Interaction Adjustment (MIIA). The theoretical basis for MIIA has been validated in the condition where all member species can grow solely as well as with partners. While useful, this development becomes highly constrained in cases that species have not been mono-cultured (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients – basic parameters required for implementing the MIIA – are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only axenic data are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, inmore »
- Authors:
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1592781
- Alternate Identifier(s):
- OSTI ID: 1600521
- Report Number(s):
- PNNL-SA-144026
Journal ID: ISSN 1664-302X; 3049
- Grant/Contract Number:
- AC05-76RL01830; 18K19364; PJ01334605
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Name: Frontiers in Microbiology Journal Volume: 10; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; microbial communities; microbial ecology; context dependence; network inference; interspecies interactions
Citation Formats
Lee, Joon-Yong, Haruta, Shin, Kato, Souichiro, Bernstein, Hans C., Lindemann, Stephen R., Lee, Dong-Yup, Fredrickson, Jim K., and Song, Hyun-Seob. Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data. Switzerland: N. p., 2020.
Web. doi:10.3389/fmicb.2019.03049.
Lee, Joon-Yong, Haruta, Shin, Kato, Souichiro, Bernstein, Hans C., Lindemann, Stephen R., Lee, Dong-Yup, Fredrickson, Jim K., & Song, Hyun-Seob. Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data. Switzerland. https://doi.org/10.3389/fmicb.2019.03049
Lee, Joon-Yong, Haruta, Shin, Kato, Souichiro, Bernstein, Hans C., Lindemann, Stephen R., Lee, Dong-Yup, Fredrickson, Jim K., and Song, Hyun-Seob. Tue .
"Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data". Switzerland. https://doi.org/10.3389/fmicb.2019.03049.
@article{osti_1592781,
title = {Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data},
author = {Lee, Joon-Yong and Haruta, Shin and Kato, Souichiro and Bernstein, Hans C. and Lindemann, Stephen R. and Lee, Dong-Yup and Fredrickson, Jim K. and Song, Hyun-Seob},
abstractNote = {Modulation of interspecies interactions in the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method that enables predicting the effect of new species on pairwise interactions among existing members and termed it the Minimal Interspecies Interaction Adjustment (MIIA). The theoretical basis for MIIA has been validated in the condition where all member species can grow solely as well as with partners. While useful, this development becomes highly constrained in cases that species have not been mono-cultured (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients – basic parameters required for implementing the MIIA – are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only axenic data are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. In the case study of a four-member, multispecies community that provides data with respect to each case mentioned, we were able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.},
doi = {10.3389/fmicb.2019.03049},
journal = {Frontiers in Microbiology},
number = ,
volume = 10,
place = {Switzerland},
year = {Tue Jan 21 00:00:00 EST 2020},
month = {Tue Jan 21 00:00:00 EST 2020}
}
https://doi.org/10.3389/fmicb.2019.03049
Web of Science
Works referenced in this record:
Spatial determinants of quorum signaling in a Pseudomonas aeruginosa infection model
journal, April 2018
- Darch, Sophie E.; Simoska, Olja; Fitzpatrick, Mignon
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 18
Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria
journal, December 2004
- Kato, Souichiro; Haruta, Shin; Cui, Zong Jun
- FEMS Microbiology Ecology, Vol. 51, Issue 1
Network Relationships of Bacteria in a Stable Mixed Culture
journal, January 2008
- Kato, Souichiro; Haruta, Shin; Cui, Zong Jun
- Microbial Ecology, Vol. 56, Issue 3
Microbial interactions: from networks to models
journal, July 2012
- Faust, Karoline; Raes, Jeroen
- Nature Reviews Microbiology, Vol. 10, Issue 8
Lotka-Volterra Population Models
journal, November 1978
- Wangersky, P. J.
- Annual Review of Ecology and Systematics, Vol. 9, Issue 1
Design Principles of Microbial Communities: From Understanding to Engineering
journal, October 2018
- Song, Hyun-Seob
- Current Genomics, Vol. 19, Issue 8
Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil
journal, February 2017
- Wang, Honggui; Wei, Zhong; Mei, Lijuan
- Soil Biology and Biochemistry, Vol. 105
Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions
book, January 2018
- Song, Hyun-Seob; Nelson, William C.; Lee, Joon-Yong
- Emerging Areas in Bioengineering
Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes
journal, August 2015
- Bordenstein, Seth R.; Theis, Kevin R.
- PLOS Biology, Vol. 13, Issue 8
Identification of metolachlor mineralizing bacteria in aerobic and anaerobic soils using DNA-stable isotope probing
journal, December 2017
- Kanissery, Ramdas G.; Welsh, Allana; Gomez, Andres
- Biodegradation, Vol. 29, Issue 2
Stable isotope probing — linking microbial identity to function
journal, May 2005
- Dumont, Marc G.; Murrell, J. Colin
- Nature Reviews Microbiology, Vol. 3, Issue 6
Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms
journal, December 2018
- Darch, Sophie E.; Koley, Dipankar
- Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 474, Issue 2220
Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities
journal, June 2019
- Song, Hyun-Seob; Lee, Joon-Yong; Haruta, Shin
- Frontiers in Microbiology, Vol. 10
Engineering microbial consortia for controllable outputs
journal, March 2016
- Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun-Seob
- The ISME Journal, Vol. 10, Issue 9
Mathematical Modeling of Microbial Community Dynamics: A Methodological Review
journal, October 2014
- Song, Hyun-Seob; Cannon, William; Beliaev, Alexander
- Processes, Vol. 2, Issue 4
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
journal, April 2010
- He, Zhili; Deng, Ye; Van Nostrand, Joy D.
- The ISME Journal, Vol. 4, Issue 9
A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria
journal, July 2017
- Sun, Weimin; Krumins, Valdis; Dong, Yiran
- Microbial Ecology, Vol. 75, Issue 1
Food-web analysis through field measurement of per capita interaction strength
journal, January 1992
- Paine, R. T.
- Nature, Vol. 355, Issue 6355
Model Microbial Consortia as Tools for Understanding Complex Microbial Communities
journal, October 2018
- Haruta, Shin; Yamamoto, Kyosuke
- Current Genomics, Vol. 19, Issue 8
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling
journal, April 2015
- Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra
- Nature Reviews Microbiology, Vol. 13, Issue 6
Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
journal, August 2018
- Coenen, Ashley R.; Weitz, Joshua S.
- mSystems, Vol. 3, Issue 4
Microbial interspecies interactions: recent findings in syntrophic consortia
journal, May 2015
- Kouzuma, Atsushi; Kato, Souichiro; Watanabe, Kazuya
- Frontiers in Microbiology, Vol. 6
Determinative Factors of Competitive Advantage between Aerobic Bacteria for Niches at the Air-Liquid Interface
journal, January 2010
- Yamamoto, Kyosuke; Haruta, Shin; Kato, Souichiro
- Microbes and Environments, Vol. 25, Issue 4
How context dependent are species interactions?
journal, April 2014
- Chamberlain, Scott A.; Bronstein, Judith L.; Rudgers, Jennifer A.
- Ecology Letters, Vol. 17, Issue 7
Microbial interactions within the plant holobiont
journal, March 2018
- Hassani, M. Amine; Durán, Paloma; Hacquard, Stéphane
- Microbiome, Vol. 6, Issue 1
The Microbial Engines That Drive Earth's Biogeochemical Cycles
journal, May 2008
- Falkowski, P. G.; Fenchel, T.; Delong, E. F.
- Science, Vol. 320, Issue 5879
Stable Coexistence of Five Bacterial Strains as a Cellulose-Degrading Community
journal, November 2005
- Kato, S.; Haruta, S.; Cui, Z. J.
- Applied and Environmental Microbiology, Vol. 71, Issue 11