The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

Kelliher, Julia M.; Robinson, Aaron J.; Longley, Reid; Johnson, Leah Y. D.; Hanson, Buck T.; Morales, Demosthenes P.; Cailleau, Guillaume; Junier, Pilar; Bonito, Gregory; Chain, Patrick S. G.

doi:10.1186/s40168-023-01634-7

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

Journal Article · Sat Aug 26 00:00:00 EDT 2023 · Microbiome

DOI:https://doi.org/10.1186/s40168-023-01634-7· OSTI ID:1996873

Kelliher, Julia M.; Robinson, Aaron J.; Longley, Reid; Johnson, Leah Y. D.; Hanson, Buck T.; Morales, Demosthenes P.; Cailleau, Guillaume; Junier, Pilar; Bonito, Gregory; Chain, Patrick S. G.

Abstract

As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how “microbiomes within microbiomes” affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales.

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Sponsoring Organization:: USDOE

OSTI ID:: 1996873

Alternate ID(s):: OSTI ID: 1998129

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 11; ISSN 2049-2618

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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