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Coevolution of Hosts and their Microbiome
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Coevolution of Hosts and their Microbiome

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (31 May 2018) | Viewed by 29217

Special Issue Editors

Dr. Philipp Heeb

E-Mail Website
Guest Editor
Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, Toulouse, France
Interests: host-microbiota interactions; social foraging and competition; parent-offspring communication; host-parasite interactions and host-life history traits
Dr. Alexandre Jousset

E-Mail Website
Guest Editor
Ecology and Biodiversity, Department of Biology, Utrecht University, Utrecht, The Netherlands
Interests: biodiversity; plant-microbe interactions; microbiology; soil ecology; sustainable agriculture; disease ecology
Dr. Ville-Petri Friman

E-Mail Website
Guest Editor
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Interests: evolution; experimental evolution; coevolution; ecology; microbiology; microbiomes; pathogens; phages; bacteria; protists; plants; eco-evolutionary dynamics; plant-microbe interactions
Special Issues, Collections and Topics in MDPI journals
Dr. Morten Tønsberg Limborg

E-Mail Website
Guest Editor
National History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
Interests: population genomics; speciation; host-microbe interactions; applied hologenomics

Special Issue Information

Dear Colleagues,

The evolution of life-history traits in plants and animals has taken place in the midst of complex microbial communities. Biology is undergoing a fundamental reshaping where the phenotypic expression of individuals needs to be considered as the combined expression of the host and its associated microbial genomes, defined as the "holobiont” (i.e., the host and its microbiota). These concepts have wide ranging implications and have led to the realization that multicellular organisms coevolve with their microbial symbionts. Although host-microbe interactions can be understood by ecological processes, much less is known about the significance of evolutionary and eco-evolutionary processes. Given its complex structure, understanding the specific roles, adaptability, and functions provided by the microbiome is a new scientific frontier. This Special Issue will reflect recent developments in molecular and statistical techniques to discuss theoretical concepts and empirical evidences on the role of the microbiota in holobiont evolution.

Dr. Philipp Heeb
Dr. Alexandre Jousset
Dr. Ville-Petri Friman
Dr. Morten Tønsberg Limborg
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Host-microbe interactions
  • co-evolution
  • holobiont
  • microbiota
  • adaptation

Published Papers (6 papers)

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Editorial

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3 pages, 169 KiB  
Editorial
Special Issue: Coevolution of Hosts and Their Microbiome
by Morten T. Limborg and Philipp Heeb
Genes 2018, 9(11), 549; https://doi.org/10.3390/genes9110549 - 13 Nov 2018
Cited by 11 | Viewed by 3528
Abstract
The evolution of life-history traits in plants and animals has taken place in the midst of complex microbial communities. [...] Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)

Research

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18 pages, 2378 KiB  
Article
Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion
by Sonia M. Rodríguez-Ruano, Manuel Martín-Vivaldi, Juan M. Peralta-Sánchez, Ana B. García-Martín, Ángela Martínez-García, Juan J. Soler, Eva Valdivia and Manuel Martínez-Bueno
Genes 2018, 9(8), 407; https://doi.org/10.3390/genes9080407 - 11 Aug 2018
Cited by 10 | Viewed by 3794
Abstract
The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the [...] Read more.
The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the high infection risk experienced during the stay in the hole-nests. However, the knowledge on hoopoes uropygial gland microbial community dynamics is quite limited and based so far on culture-dependent and molecular fingerprinting studies. In this work, we sampled wild and captive hoopoes of different sex, age, and reproductive status, and studied their microbiota using quantitative polymerase chain reaction (qPCR), fluorescence in situ hybridization (FISH) and pyrosequencing. Surprisingly, we found a complex bacterial community in all individuals (including non-nesting ones) during the breeding season. Nevertheless, dark secretions from nesting hoopoes harbored significantly higher bacterial density than white secretions from breeding males and both sexes in winter. We hypothesize that bacterial proliferation may be host-regulated in phases of high infection risk (i.e., nesting). We also highlight the importance of specific antimicrobial-producing bacteria present only in dark secretions that may be key in this defensive symbiosis. Finally, we discuss the possible role of environmental conditions in shaping the uropygial microbiota, based on differences found between wild and captive hoopoes. Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)
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16 pages, 1674 KiB  
Article
Gut Microbiota of Great Spotted Cuckoo Nestlings is a Mixture of Those of Their Foster Magpie Siblings and of Cuckoo Adults
by Magdalena Ruiz-Rodríguez, Manuel Martín-Vivaldi, Manuel Martínez-Bueno and Juan José Soler
Genes 2018, 9(8), 381; https://doi.org/10.3390/genes9080381 - 27 Jul 2018
Cited by 18 | Viewed by 3832 | Correction
Abstract
Diet and host genetic or evolutionary history are considered the two main factors determining gut microbiota of animals, although studies are scarce in natural populations. The system of great spotted cuckoos (Clamator glandarius) parasitizing magpies (Pica pica) is ideal [...] Read more.
Diet and host genetic or evolutionary history are considered the two main factors determining gut microbiota of animals, although studies are scarce in natural populations. The system of great spotted cuckoos (Clamator glandarius) parasitizing magpies (Pica pica) is ideal to study both effects since magpie adults feed cuckoo and magpie nestlings with the same diet and, consequently, differences in gut microbiota of nestlings of these two species will mainly reflect the importance of genetic components. Moreover, the diet of adults and of nestling cuckoos drastically differ from each other and, thus, differences and similarities in their microbiotas would respectively reflect the effect of environmental and genetic factors. We used next-generation sequencing technologies to analyze the gut microbiota of cuckoo adults and nestlings and of magpie nestlings. The highest α-diversity estimates appeared in nestling cuckoos and the lowest in nestling magpies. Moreover, despite the greatest differences in the microbiome composition of magpies and cuckoos of both ages, cuckoo nestlings harbored a mixture of the Operational Taxonomic Units (OTUs) present in adult cuckoos and nestling magpies. We identified the bacterial taxa responsible for such results. These results suggest important phylogenetic components determining gut microbiome of nestlings, and that diet might be responsible for similarities between gut microbiome of cuckoo and magpie nestlings that allow cuckoos to digest food provided by magpie adults. Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)
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Review

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13 pages, 936 KiB  
Review
Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition
by Cristian Pasquaretta, Tamara Gómez-Moracho, Philipp Heeb and Mathieu Lihoreau
Genes 2018, 9(11), 534; https://doi.org/10.3390/genes9110534 - 06 Nov 2018
Cited by 22 | Viewed by 4962
Abstract
Microbes influence a wide range of host social behaviors and vice versa. So far, however, the mechanisms underpinning these complex interactions remain poorly understood. In social animals, where individuals share microbes and interact around foods, the gut microbiota may have considerable consequences on [...] Read more.
Microbes influence a wide range of host social behaviors and vice versa. So far, however, the mechanisms underpinning these complex interactions remain poorly understood. In social animals, where individuals share microbes and interact around foods, the gut microbiota may have considerable consequences on host social interactions by acting upon the nutritional behavior of individual animals. Here we illustrate how conceptual advances in nutritional ecology can help the study of these processes and allow the formulation of new empirically testable predictions. First, we review key evidence showing that gut microbes influence the nutrition of individual animals, through modifications of their nutritional state and feeding decisions. Next, we describe how these microbial influences and their social consequences can be studied by modelling populations of hosts and their gut microbiota into a single conceptual framework derived from nutritional geometry. Our approach raises new perspectives for the study of holobiont nutrition and will facilitate theoretical and experimental research on the role of the gut microbiota in the mechanisms and evolution of social behavior. Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)
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17 pages, 725 KiB  
Review
Olfactory Communication via Microbiota: What Is Known in Birds?
by Öncü Maraci, Kathrin Engel and Barbara A. Caspers
Genes 2018, 9(8), 387; https://doi.org/10.3390/genes9080387 - 31 Jul 2018
Cited by 34 | Viewed by 10370
Abstract
Animal bodies harbour a complex and diverse community of microorganisms and accumulating evidence has revealed that microbes can influence the hosts’ behaviour, for example by altering body odours. Microbial communities produce odorant molecules as metabolic by-products and thereby modulate the biochemical signalling profiles [...] Read more.
Animal bodies harbour a complex and diverse community of microorganisms and accumulating evidence has revealed that microbes can influence the hosts’ behaviour, for example by altering body odours. Microbial communities produce odorant molecules as metabolic by-products and thereby modulate the biochemical signalling profiles of their animal hosts. As the diversity and the relative abundance of microbial species are influenced by several factors including host-specific factors, environmental factors and social interactions, there are substantial individual variations in the composition of microbial communities. In turn, the variations in microbial communities would consequently affect social and communicative behaviour by influencing recognition cues of the hosts. Therefore, microbiota studies have a great potential to expand our understanding of recognition of conspecifics, group members and kin. In this review, we aim to summarize existing knowledge of the factors influencing the microbial communities and the effect of microbiota on olfactory cue production and social and communicative behaviour. We concentrate on avian taxa, yet we also include recent research performed on non-avian species when necessary. Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)
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Other

3 pages, 193 KiB  
Correction
Correction: Ruiz-Rodríguez et al. Gut Microbiota of Great Spotted Cuckoo Nestlings Is a Mixture of Those of Their Foster Magpie Siblings and of Cuckoo Adults. Genes 2018, 9, 381
by Magdalena Ruiz-Rodríguez, Manuel Martín-Vivaldi, Manuel Martínez-Bueno and Juan José Soler
Genes 2018, 9(11), 530; https://doi.org/10.3390/genes9110530 - 31 Oct 2018
Cited by 2 | Viewed by 2031
Abstract
The authors wish to make the following changes in their paper [...] Full article
(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)
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