Holo-omics for deciphering plant-microbiome interactions

Xu, Ling; Pierroz, Grady; Wipf, Heidi M.-L.; Gao, Cheng; Taylor, John W.; Lemaux, Peggy G.; Coleman-Derr, Devin

doi:10.1186/s40168-021-01014-z

Holo-omics for deciphering plant-microbiome interactions

Journal Article · Wed Mar 24 00:00:00 EDT 2021 · Microbiome

DOI:https://doi.org/10.1186/s40168-021-01014-z· OSTI ID:1783198

^[1]; Pierroz, Grady ^[2]; Wipf, Heidi M.-L. ^[2]; Gao, Cheng ^[2]; Taylor, John W. ^[2]; Lemaux, Peggy G. ^[2]; Coleman-Derr, Devin ^[3]

Univ. of California, Berkeley, CA (United States); UC Berkeley
Univ. of California, Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States); US Dept. of Agriculture (USDA), Albany, CA (United States). Agricultural Research Service

Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets—referred to here as holo-omics—provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

Sponsoring Organization:: USDA; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0014081

OSTI ID:: 1783198

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 9; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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