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Integrative multi-omics approaches to elucidate microbiome dynamics and ecosystem processes

© credit: Jim Moran
(From left to right: Mushroom springs field site, Yellowstone National Park (credit: Jim Moran), Sequencing at the DOE Joint Genome Institute, organic matter analyses at the DOE Environmental Molecular Sciences Laboratory, samples of heterotrophic microbial mats (credit: Jim Moran).  

Microbiome research is cross-cutting in nature, spanning diverse, interdisciplinary fields in the environmental sciences, health, agriculture, energy, and natural and built environments. Advances and applications of novel experimental and computational approaches have driven microbiome research from a nascent field to a robust area of science. These advances include shotgun metagenomics, single-cell genomics, metatranscriptomics, metaproteomics, and applying targeted and non-targeted metabolomics to environmental and host-associated samples. Advances in assembly and binning of metagenomic data have enabled reconstruction of population-level draft genomes that provide the genomic blueprint for uncultivated bacteria and archaea. This blueprint can further be leveraged to integrate diverse measures of transcription, translation, and chemical exchange to infer dynamic processes in natural ecosystems. Ultimately, multi-omics approaches will drive innovation in systems biology and inform host-associated and Earth-system models.

In this collection Microbiome is looking for manuscripts on experimental multi-omics techniques and leading technologies that are transforming microbial ecology and microbiome research across diverse domains. The contributions should highlight the integrative approaches necessary to decode the molecular underpinnings of microbiome processes, ranging from single cells to complex ecosystem networks. In the study design, development, implementation, and analyses, each of the contributions should address the importance of data stewardship along with the utility of community-driven standards and best practices.

Guest Editors:
Emiley Eloe-Fadrosh JGI/Lawrence Berkeley National Laboratory, USA
Brian Hedlund, University of Nevada, USA
Jose Pablo Dundore-Arias, California State University Monterey Bay, USA
Maryam Goudarzi, Cleveland Clinic Lerner Research Institute, USA

  1. Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same s...

    Authors: Yujie Meng, Shuang Li, Chong Zhang and Hao Zheng
    Citation: Microbiome 2022 10:140