Title: Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

Abstract

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expectedmore » to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.« less

Authors:

Song, Hyun-Seob; Lee, Joon-Yong; Haruta, Shin; Nelson, William C.; Lee, Dong-Yup; Lindemann, Stephen R.; Fredrickson, Jim K.; Bernstein, Hans C.

Publication Date:

Tue Jun 11 00:00:00 EDT 2019

Research Org.:

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1525546

Alternate Identifier(s):

OSTI ID: 1544786

Report Number(s):

PNNL-SA-131990
Journal ID: ISSN 1664-302X; 1264

Grant/Contract Number:  

AC05-76RL01830

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 Media SA

Country of Publication:

Switzerland

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; context dependence; network inference; rule-based approach; microbiome modeling; microbialecology