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Host-microbiota interactions: from holobiont theory to analysis

Follow-up of the First International Conference on Holobionts

(Paris, April 19-21, 2017)

It is becoming increasingly clear that the development, nutrition, physiology and health of most macro-organisms are influenced by the complex microbial communities they host, that shape their ecology and evolution. Biology is indeed undergoing a paradigm shift, where individual phenotypes are seen as a result of the combined expression of the host and associated microbe genomes, leading to the popularization of notions of the holobiont (the host and its microbiota) and the hologenome (the collective genomes of a holobiont). Holobiont research is now an imperative across numerous fields of the life and medical sciences, including aspects of (bio)informatics. This pushed the scientific community to organize the first International Conference on Holobionts in Paris, April 19-21, 2017.

In this special series in Microbiome, we highlight articles that show, use or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants, to sponges and insects.

Guest editors:
Julian Marchesi (Imperial College London)
Christophe Mougel (Institut National de la Recherche Agronomique)
Marc-André Selosse (Muséum National d’Histoire Naturelle Paris ; University of Gdansk)
Jean-Christophe Simon (Institut National de la Recherche Agronomique)

  1. The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ...

    Authors: Limei Lin, Fei Xie, Daming Sun, Junhua Liu, Weiyun Zhu and Shengyong Mao
    Citation: Microbiome 2019 7:83
  2. In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems....

    Authors: Jean-Christophe Simon, Julian R. Marchesi, Christophe Mougel and Marc-André Selosse
    Citation: Microbiome 2019 7:5
  3. Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunitie...

    Authors: Cervin Guyomar, Fabrice Legeai, Emmanuelle Jousselin, Christophe Mougel, Claire Lemaitre and Jean-Christophe Simon
    Citation: Microbiome 2018 6:181
  4. Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the e...

    Authors: Marius Bredon, Jessica Dittmer, Cyril Noël, Bouziane Moumen and Didier Bouchon
    Citation: Microbiome 2018 6:162
  5. Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the seque...

    Authors: Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Eric Pelletier, Ian Probert, Johan Decelle, Stéphane Le Crom, Fabrice Not and Lucie Bittner
    Citation: Microbiome 2018 6:105
  6. All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the inter...

    Authors: Michal Sorek, Yisrael Schnytzer, Hiba Waldman Ben-Asher, Vered Chalifa Caspi, Chii-Shiarng Chen, David J. Miller and Oren Levy
    Citation: Microbiome 2018 6:83
  7. The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relat...

    Authors: Maarten van de Guchte, Hervé M. Blottière and Joël Doré
    Citation: Microbiome 2018 6:81
  8. Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer l...

    Authors: Nathan Vannier, Cendrine Mony, Anne-Kristel Bittebiere, Sophie Michon-Coudouel, Marine Biget and Philippe Vandenkoornhuyse
    Citation: Microbiome 2018 6:79
  9. The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selectio...

    Authors: Eugene Rosenberg and Ilana Zilber-Rosenberg
    Citation: Microbiome 2018 6:78
  10. Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often refe...

    Authors: M. Amine Hassani, Paloma Durán and Stéphane Hacquard
    Citation: Microbiome 2018 6:58
  11. The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants ...

    Authors: Mohammadhossein Ravanbakhsh, Rashmi Sasidharan, Laurentius A. C. J. Voesenek, George A. Kowalchuk and Alexandre Jousset
    Citation: Microbiome 2018 6:52
  12. The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced ...

    Authors: Morgane Guégan, Karima Zouache, Colin Démichel, Guillaume Minard, Van Tran Van, Patrick Potier, Patrick Mavingui and Claire Valiente Moro
    Citation: Microbiome 2018 6:49
  13. Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant ...

    Authors: Ellen Young, Manus Carey, Andrew A. Meharg and Caroline Meharg
    Citation: Microbiome 2018 6:48
  14. Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host...

    Authors: Kelly Brener-Raffalli, Camille Clerissi, Jeremie Vidal-Dupiol, Mehdi Adjeroud, François Bonhomme, Marine Pratlong, Didier Aurelle, Guillaume Mitta and Eve Toulza
    Citation: Microbiome 2018 6:39
  15. Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperativ...

    Authors: M. A. Cregger, A. M. Veach, Z. K. Yang, M. J. Crouch, R. Vilgalys, G. A. Tuskan and C. W. Schadt
    Citation: Microbiome 2018 6:31