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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. The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assem...

    Authors: Vinicius S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. Chiriac, Michaela M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujčić, Maliheh Mehrshad, Vojtěch Kasalický, Adrian-Stefan Andrei, Jitka Jezberová, Jaromir Seďa, Pavel Rychtecký, Petr Znachor, Karel Šimek and Rohit Ghai
    Citation: Microbiome 2023 11:15
  2. It is well-known that the microbiome produces a myriad of specialised metabolites with diverse functions. To better characterise their structures and identify their producers in complex samples, integrative ge...

    Authors: Joris J. R. Louwen, Marnix H. Medema and Justin J. J. van der Hooft
    Citation: Microbiome 2023 11:13
  3. Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior st...

    Authors: Jonathan P. Jacobs, Venu Lagishetty, Megan C. Hauer, Jennifer S. Labus, Tien S. Dong, Ryan Toma, Momchilo Vuyisich, Bruce D. Naliboff, Jeffrey M. Lackner, Arpana Gupta, Kirsten Tillisch and Emeran A. Mayer
    Citation: Microbiome 2023 11:5
  4. Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous fact...

    Authors: B. J. Kunath, O. Hickl, P. Queirós, C. Martin-Gallausiaux, L. A. Lebrun, R. Halder, C. C. Laczny, T. S. B. Schmidt, M. R. Hayward, D. Becher, A. Heintz-Buschart, C. de Beaufort, P. Bork, P. May and P. Wilmes
    Citation: Microbiome 2022 10:243
  5. The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome, has been associated with the development ...

    Authors: Patrick G. Gavin, Ki Wook Kim, Maria E. Craig, Michelle M. Hill and Emma E. Hamilton-Williams
    Citation: Microbiome 2022 10:230
  6. Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome f...

    Authors: Jiakang Yin, Ziliang Zhang, Chengcheng Zhu, Taotao Wang, Ruihong Wang and Lifang Ruan
    Citation: Microbiome 2022 10:227
  7. The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datas...

    Authors: Stephanie D. Jurburg, François Buscot, Antonis Chatzinotas, Narendrakumar M. Chaudhari, Adam T. Clark, Magda Garbowski, Matthias Grenié, Erik F. Y. Hom, Canan Karakoç, Susanne Marr, Steffen Neumann, Mika Tarkka, Nicole M. van Dam, Alexander Weinhold and Anna Heintz-Buschart
    Citation: Microbiome 2022 10:225
  8. The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that oc...

    Authors: Xiaoting Yan, Huazhe Si, Yuhang Zhu, Songze Li, Yu Han, Hanlu Liu, Rui Du, Phillip B. Pope, Qiang Qiu and Zhipeng Li
    Citation: Microbiome 2022 10:222
  9. Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope pro...

    Authors: Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone and Jennifer Pett-Ridge
    Citation: Microbiome 2022 10:199
  10. Most previous studies attempting to prove the phenomenon of mother-to-infant microbiota transmission were observational, performed only at genus/species-level resolution, and relied entirely on non-culture-bas...

    Authors: Zhi Zhong, Hai Tang, Tingting Shen, Xinwei Ma, Feiyan Zhao, Lai-Yu Kwok, Zhihong Sun, Menghe Bilige and Heping Zhang
    Citation: Microbiome 2022 10:197
  11. Dioecious plants have coevolved with diverse plant microbiomes, which are crucial for the fitness and productivity of their host. Sexual dimorphism in morphology, physiology, or gene expression may relate to d...

    Authors: Qingxue Guo, Lin Liu, Jiantong Liu, Helena Korpelainen and Chunyang Li
    Citation: Microbiome 2022 10:191
  12. Comparisons of the gut microbiome of lean and obese humans have revealed that obesity is associated with the gut microbiome plus changes in numerous environmental factors, including high-fat diet (HFD). Here, ...

    Authors: Gihyeon Kim, Youngmin Yoon, Jin Ho Park, Jae Won Park, Myung-guin Noh, Hyun Kim, Changho Park, Hyuktae Kwon, Jeong-hyeon Park, Yena Kim, Jinyoung Sohn, Shinyoung Park, Hyeonhui Kim, Sun-Kyoung Im, Yeongmin Kim, Ha Yung Chung…
    Citation: Microbiome 2022 10:188
  13. Chinese Lunar Palace 1 (LP1) is a ground-based bio-regenerative life support system (BLSS) test bed integrating highly efficient plant cultivation, animal protein production, urine nitrogen recycling, and bioc...

    Authors: Jianlou Yang, Zikai Hao, Lantao Zhang, Yuming Fu and Hong Liu
    Citation: Microbiome 2022 10:169
  14. DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in c...

    Authors: Hoon Je Seong, Simon Roux, Chung Yeon Hwang and Woo Jun Sul
    Citation: Microbiome 2022 10:157
  15. 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