401
|
Simon JC, Marchesi JR, Mougel C, Selosse MA. Host-microbiota interactions: from holobiont theory to analysis. MICROBIOME 2019; 7:5. [PMID: 30635058 PMCID: PMC6330386 DOI: 10.1186/s40168-019-0619-4] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 05/13/2023]
Abstract
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. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.
Collapse
Affiliation(s)
- Jean-Christophe Simon
- UMR 1349, IGEPP (Institut de Génétique, Environnement et Protection des Plantes), INRA, Agrocampus Ouest, Université Rennes 1, Domaine de la Motte, 35653, Le Rheu Cedex, France.
| | - Julian R Marchesi
- Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, UK
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Christophe Mougel
- UMR 1349, IGEPP (Institut de Génétique, Environnement et Protection des Plantes), INRA, Agrocampus Ouest, Université Rennes 1, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Marc-André Selosse
- Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, 57 Rue Cuvier-CP39, F-75005, Paris, France
- Faculty of Biology, University of Gdansk, Ul. Wita Stwosza 59, 80-308, Gdansk, Poland
| |
Collapse
|
402
|
Microbial embryonal colonization during pipefish male pregnancy. Sci Rep 2019; 9:3. [PMID: 30626884 PMCID: PMC6327025 DOI: 10.1038/s41598-018-37026-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 11/08/2018] [Indexed: 02/06/2023] Open
Abstract
While originally acquired from the environment, a fraction of the microbiota is transferred from parents to offspring. The immune system shapes the microbial colonization, while commensal microbes may boost host immune defences. Parental transfer of microbes in viviparous animals remains ambiguous, as the two transfer routes (transovarial vs. pregnancy) are intermingled within the maternal body. Pipefishes and seahorses (syngnathids) are ideally suited to disentangle transovarial microbial transfer from a contribution during pregnancy due to their maternal egg production and their unique male pregnancy. We assessed the persistency and the changes in the microbial communities of the maternal and paternal reproductive tracts over proceeding male pregnancy by sequencing microbial 16S rRNA genes of swabs from maternal gonads and brood pouches of non-pregnant and pregnant fathers. Applying parental immunological activation with heat-killed bacteria, we evaluated the impact of parental immunological status on microbial development. Our data indicate that maternal gonads and paternal brood pouches harbor distinct microbial communities, which could affect embryonal development in a sex-specific manner. Upon activation of the immune system, a shift of the microbial community was observed. The activation of the immune system induced the expansion of microbiota richness during late pregnancy, which corresponds to the time point of larval mouth opening, when initial microbial colonization must take place.
Collapse
|
403
|
Patrignani F, Siroli L, Parolin C, Serrazanetti DI, Vitali B, Lanciotti R. Use of Lactobacillus crispatus to produce a probiotic cheese as potential gender food for preventing gynaecological infections. PLoS One 2019; 14:e0208906. [PMID: 30625157 PMCID: PMC6326422 DOI: 10.1371/journal.pone.0208906] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 11/17/2018] [Indexed: 01/01/2023] Open
Abstract
This research is aimed to evaluate the suitability of Squacquerone cheese to support the viability of Lactobacillus crispatus BC4, a vaginal strain endowed with a strong antimicrobial activity against urogenital pathogens and foodborne microorganisms, in order to recommend a gender food for woman wellbeing. The viability of L. crispatus BC4, used as adjunct culture, was evaluated during the refrigerated storage of Squacquerone cheese, as well as when the cheese was subjected to simulated stomach-duodenum passage tested by the patented Simulator of the Human Intestinal Microbial Ecosystem (SHIME). Moreover, the effects of L. crispatus BC4 addition were evaluated on product hydrolytic patterns, in terms of proteolysis, lipolysis and volatile molecule profiles. The data showed that L. crispatus BC4 maintained high viability, also in presence of physiological stress conditions, until the end of the refrigerated storage. Moreover, the inclusion of L. crispatus BC4 gave rise to cheese product with higher score of overall acceptability when compared to control cheese. In addition, the survival of L. crispatus BC4, carried in test cheese, in gastro intestinal conditions was confirmed by SHIME. The results showed that the vaginal Lactobacillus strain was more affected by the low pH of the stomach, simulated by the SHIME reactor, rather than to bile salts and pancreatic juices. Although only in vivo trials will be able to confirm the functionality of the cheese in the vaginal environment, these data represent a first step towards the employment of the Squacquerone cheese as probiotic food able to promote the woman’s health by preventing gynaecological infections.
Collapse
Affiliation(s)
- Francesca Patrignani
- Department of Agricultural and Food Sciences, Alma Mater Studiorum—University of Bologna, Cesena, Italy
- * E-mail:
| | - Lorenzo Siroli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum—University of Bologna, Cesena, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Diana I. Serrazanetti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum—University of Bologna, Cesena, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum—University of Bologna, Cesena, Italy
| |
Collapse
|
404
|
Bastiaanssen TFS, Cowan CSM, Claesson MJ, Dinan TG, Cryan JF. Making Sense of … the Microbiome in Psychiatry. Int J Neuropsychopharmacol 2019; 22:37-52. [PMID: 30099552 PMCID: PMC6313131 DOI: 10.1093/ijnp/pyy067] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/10/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022] Open
Abstract
Microorganisms can be found almost anywhere, including in and on the human body. The collection of microorganisms associated with a certain location is called a microbiota, with its collective genetic material referred to as the microbiome. The largest population of microorganisms on the human body resides in the gastrointestinal tract; thus, it is not surprising that the most investigated human microbiome is the human gut microbiome. On average, the gut hosts microbes from more than 60 genera and contains more cells than the human body. The human gut microbiome has been shown to influence many aspects of host health, including more recently the brain.Several modes of interaction between the gut and the brain have been discovered, including via the synthesis of metabolites and neurotransmitters, activation of the vagus nerve, and activation of the immune system. A growing body of work is implicating the microbiome in a variety of psychological processes and neuropsychiatric disorders. These include mood and anxiety disorders, neurodevelopmental disorders such as autism spectrum disorder and schizophrenia, and even neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Moreover, it is probable that most psychotropic medications have an impact on the microbiome.Here, an overview will be provided for the bidirectional role of the microbiome in brain health, age-associated cognitive decline, and neurological and psychiatric disorders. Furthermore, a primer on the common microbiological and bioinformatics techniques used to interrogate the microbiome will be provided. This review is meant to equip the reader with a primer to this exciting research area that is permeating all areas of biological psychiatry research.
Collapse
Affiliation(s)
- Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| | | | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Ireland
- Department of Psychiatry, University College Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| |
Collapse
|
405
|
Kranabetter JM, Harman-Denhoed R, Hawkins BJ. Saprotrophic and ectomycorrhizal fungal sporocarp stoichiometry (C : N : P) across temperate rainforests as evidence of shared nutrient constraints among symbionts. THE NEW PHYTOLOGIST 2019; 221:482-492. [PMID: 30084239 DOI: 10.1111/nph.15380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/07/2018] [Indexed: 06/08/2023]
Abstract
Quantifying nutritional dynamics of free-living saprotrophs and symbiotic ectomycorrhizal fungi in the field is challenging, but the stoichiometry of fruiting bodies (sporocarps) may be an effective methodology for this purpose. Carbon (C), nitrogen (N) and phosphorus (P) concentrations of soils, foliage and 146 sporocarp collections were analyzed from 14 Pseudotsuga menziesii var. menziesii stands across a podzolization gradient on Vancouver Island (Canada). N and P concentrations were considerably higher in saprotrophic fungi. Fungal N% increased with soil N content at a greater rate for saprotrophs than ectomycorrhizal fungi, while fungal P% of saprotrophs was more constrained. Fungal N : P was more responsive to soil N : P for ectomycorrhizal fungi (homeostatic regulation coefficient 'H' = 2.9) than saprotrophs (H = 5.9), while N : P of ectomycorrhizal fungi and host tree foliage scaled almost identically. Results underscore the role of ectomycorrhizal fungi as nutrient conduits, supporting host trees, whereas saprotrophs maintain a greater degree of nutritional homeostasis. Site nutrient constraints were shared in equal measure between ectomycorrhizal fungi and host trees, particularly for P, suggesting neither partner benefits from enhanced nutrition at the expense of the other. Sporocarp stoichiometry provides new insights into mycorrhizal relationships and illustrates pervasive P deficiencies across temperate rainforests of the Pacific Northwest.
Collapse
Affiliation(s)
- J Marty Kranabetter
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, PO Box 9536, Stn Prov Govt, Victoria, BC, V8W 9C4, Canada
| | - Rachael Harman-Denhoed
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, Victoria, BC, V8W 3N5, Canada
| | - Barbara J Hawkins
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, Victoria, BC, V8W 3N5, Canada
| |
Collapse
|
406
|
Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
Collapse
Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| |
Collapse
|
407
|
Abstract
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.
Collapse
|
408
|
Keller A, Brandel A, Becker MC, Balles R, Abdelmohsen UR, Ankenbrand MJ, Sickel W. Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. MICROBIOME 2018; 6:229. [PMID: 30579360 PMCID: PMC6303958 DOI: 10.1186/s40168-018-0614-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/13/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either secondary invaders of European foulbrood or considered a threat to honey bees. We thus investigated whether Paenibacillus is a common bacterium associated with various wild bees and hence poses a latent threat to honey bees visiting the same flowers. RESULTS We collected 202 samples from 82 individuals or nests of 13 bee species at the same location and screened each for Paenibacillus using high-throughput sequencing-based 16S metabarcoding. We then isolated the identified strain Paenibacillus MBD-MB06 from a solitary bee nest and sequenced its genome. We did find conserved toxin genes and such encoding for chitin-binding proteins, yet none specifically related to foulbrood virulence or chitinases. Phylogenomic analysis revealed a closer relationship to strains of root-associated Paenibacillus rather than strains causing foulbrood or other accompanying diseases. We found anti-microbial evidence within the genome, confirmed by experimental bioassays with strong growth inhibition of selected fungi as well as gram-positive and gram-negative bacteria. CONCLUSIONS The isolated wild bee associate Paenibacillus MBD-MB06 is a common, but irregularly occurring part of wild bee microbiomes, present on adult body surfaces and guts and within nests especially in megachilids. It was phylogenetically and functionally distinct from harmful members causing honey bee colony diseases, although it shared few conserved proteins putatively toxic to insects that might indicate ancestral predisposition for the evolution of insect pathogens within the group. By contrast, our strain showed anti-microbial capabilities and the genome further indicates abilities for chitin-binding and biofilm-forming, suggesting it is likely a useful associate to avoid fungal penetration of the bee cuticula and a beneficial inhabitant of nests to repress fungal threats in humid and nutrient-rich environments of wild bee nests.
Collapse
Affiliation(s)
- Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
- Present Address: Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074, Würzburg, Germany.
- Present Address: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Annette Brandel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Present Address: BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Mira C Becker
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Department of Behavioral Physiology & Sociobiology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Rebecca Balles
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082, Würzburg, Germany
- Present Address: Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074, Würzburg, Germany
- Present Address: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Wiebke Sickel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Present Address: Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, Nussallee 13, 53115, Bonn, Germany
| |
Collapse
|
409
|
Huitzil S, Sandoval-Motta S, Frank A, Aldana M. Modeling the Role of the Microbiome in Evolution. Front Physiol 2018; 9:1836. [PMID: 30618841 PMCID: PMC6307544 DOI: 10.3389/fphys.2018.01836] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/06/2018] [Indexed: 12/17/2022] Open
Abstract
There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.
Collapse
Affiliation(s)
- Saúl Huitzil
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Consejo Nacional de Ciencia y Tecnología, Cátedras CONACyT, Mexico City, Mexico
| | - Alejandro Frank
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Member of El Colegio Nacional, Mexico City, Mexico
| | - Maximino Aldana
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
410
|
Abstract
Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.
Collapse
|
411
|
Nakatsuji T, Gallo RL. The role of the skin microbiome in atopic dermatitis. Ann Allergy Asthma Immunol 2018; 122:263-269. [PMID: 30550810 DOI: 10.1016/j.anai.2018.12.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, California
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, California.
| |
Collapse
|
412
|
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev 2018; 42:335-352. [PMID: 29471481 DOI: 10.1093/femsre/fuy008] [Citation(s) in RCA: 329] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
Collapse
Affiliation(s)
- Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27705, USA.,Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095 CNRS et Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
| | - Matthias Becker
- IGZ, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.,Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sophie Mieszkin
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Larry J Millet
- Joint Institute for Biological Science, University of Tennessee, and the Biosciences Division of Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, 10125 Torino, Italy
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry, G. Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Jan Dirk van Elsas
- Microbial Ecology group, GELIFES, University of Groningen, 9747 Groningen, The Netherlands
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
| |
Collapse
|
413
|
Abstract
All animals have associated microbial communities called microbiomes that influence the physiology and fitness of their host. It is unclear to what extent individual microbial species versus interactions between them influence the host. Here, we mapped all possible interactions between individual species of bacteria against Drosophila melanogaster fruit fly fitness traits. Our approach revealed that the same bacterial interactions that shape microbiome abundances also shape host fitness traits. The fitness traits of lifespan and fecundity showed a life history tradeoff, where equal total fitness can be gotten by either high fecundity over a short life or low fecundity over a long life. The microbiome interactions are as important as the individual species in shaping these fundamental aspects of fly physiology. Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits, including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which, in turn, accelerated development, reproduction, and aging: Flies that reproduced more died sooner. From these measurements, we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Development and fecundity converged with higher diversity, suggesting minimal dependence on interactions. However, host lifespan and microbiome abundances were highly dependent on interactions between bacterial species. Higher-order interactions (involving three, four, and five species) occurred in 13–44% of possible cases depending on the trait, with the same interactions affecting multiple traits, a reflection of the life history tradeoff. Overall, we found these interactions were frequently context-dependent and often had the same magnitude as individual species themselves, indicating that the interactions can be as important as the individual species in gut microbiomes.
Collapse
|
414
|
Amedei A, Boem F. I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine. Int J Mol Sci 2018; 19:E3756. [PMID: 30486338 PMCID: PMC6321351 DOI: 10.3390/ijms19123756] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call "health" and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as "health" and "individual," do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.
Collapse
Affiliation(s)
- Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, 03 50134, Firenze, Italy.
- Department of Biomedicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Largo Brambilla, 03 50134, Firenze, Italy.
| | - Federico Boem
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, 03 50134, Firenze, Italy.
| |
Collapse
|
415
|
Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T. Binning enables efficient host genome reconstruction in cnidarian holobionts. Gigascience 2018; 7:5039706. [PMID: 29917104 PMCID: PMC6049006 DOI: 10.1093/gigascience/giy075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches. Results Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity. Conclusions Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.
Collapse
Affiliation(s)
- Juan Sebastián Celis
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Corporation Center of Excellence in Marine Sciences, Cra 54 No 106-18, Bogotá, Colombia
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Catalina Ramírez-Portilla
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Evolutionary Biology and Ecology, Université libre de Bruxelles, Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University Giessen. Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.,Corporation Center of Excellence in Marine Sciences, Cra 54 No 106-18, Bogotá, Colombia
| |
Collapse
|
416
|
Antwis RE, Lea JMD, Unwin B, Shultz S. Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies. MICROBIOME 2018; 6:207. [PMID: 30466491 PMCID: PMC6251106 DOI: 10.1186/s40168-018-0593-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/07/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbiome composition is linked to host functional traits including metabolism and immune function. Drivers of microbiome composition are increasingly well-characterised; however, evidence of group-level microbiome convergence is limited and may represent a multi-level trait (i.e. across individuals and groups), whereby heritable phenotypes are influenced by social interactions. Here, we investigate the influence of spatial structuring and social interactions on the gut microbiome composition of Welsh mountain ponies. RESULTS We show that semi-feral ponies exhibit variation in microbiome composition according to band (group) membership, in addition to considerable within-individual variation. Spatial structuring was also identified within bands, suggesting that despite communal living, social behaviours still influence microbiome composition. Indeed, we show that specific interactions (i.e. mother-offspring and stallion-mare) lead to more similar microbiomes, further supporting the notion that individuals influence the microbiome composition of one another and ultimately the group. Foals exhibited different microbiome composition to sub-adults and adults, most likely related to differences in diet. CONCLUSIONS We provide novel evidence that microbiome composition is structured at multiple levels within populations of social mammals and thus may form a unit on which selection can act. High levels of within-individual variation in microbiome composition, combined with the potential for social interactions to influence microbiome composition, suggest the direction of microbiome selection may be influenced by the individual members present in the group. Although the functional implications of this require further research, these results lend support to the idea that multi-level selection can act on microbiomes.
Collapse
Affiliation(s)
- Rachael E. Antwis
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Jessica M. D. Lea
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Bryony Unwin
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Susanne Shultz
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| |
Collapse
|
417
|
Kokou F, Sasson G, Nitzan T, Doron-Faigenboim A, Harpaz S, Cnaani A, Mizrahi I. Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature. eLife 2018; 7:e36398. [PMID: 30454554 PMCID: PMC6277203 DOI: 10.7554/elife.36398] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023] Open
Abstract
The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.
Collapse
Affiliation(s)
- Fotini Kokou
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Goor Sasson
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
| | - Tali Nitzan
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Institute of Plant ScienceAgricultural Research OrganizationRishon LeZionIsrael
| | - Sheenan Harpaz
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
| |
Collapse
|
418
|
Dual-stressor selection alters eco-evolutionary dynamics in experimental communities. Nat Ecol Evol 2018; 2:1974-1981. [DOI: 10.1038/s41559-018-0701-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/24/2018] [Indexed: 11/08/2022]
|
419
|
Special Issue: Coevolution of Hosts and Their Microbiome. Genes (Basel) 2018; 9:genes9110549. [PMID: 30428546 PMCID: PMC6266481 DOI: 10.3390/genes9110549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
|
420
|
Randall JM, Mceachern K, Knapp J, Power P, Junak S, Gill K, Knapp D, Guilliams M. Informing Our Successors: What Botanical Information for Santa Cruz Island will Researchers and Conservation Managers in the Century Ahead Need the Most? WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John M. Randall
- The Nature Conservancy, California Chapter, 201 Mission Street, San Francisco, CA 94105
| | - Kathryn Mceachern
- U.S. Geological Survey, WERC, Channel Islands Field Station, 1901 Spinnaker Drive, Ventura, CA 93001
| | - John Knapp
- The Nature Conservancy, California Chapter, 201 Mission Street, San Francisco, CA 94105
| | - Paula Power
- National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001
| | - Steve Junak
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Kristina Gill
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Denise Knapp
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Matt Guilliams
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| |
Collapse
|
421
|
Hubert J, Nesvorna M, Sopko B, Smrz J, Klimov P, Erban T. Two Populations of Mites ( Tyrophagus putrescentiae) Differ in Response to Feeding on Feces-Containing Diets. Front Microbiol 2018; 9:2590. [PMID: 30425700 PMCID: PMC6218854 DOI: 10.3389/fmicb.2018.02590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023] Open
Abstract
Background:Tyrophagus putrescentiae is a ubiquitous mite species in soil, stored products and house dust and infests food and causes allergies in people. T. putrescentiae populations harbor different bacterial communities, including intracellular symbionts and gut bacteria. The spread of microorganisms via the fecal pellets of T. putrescentiae is a possibility that has not been studied in detail but may be an important means by which gut bacteria colonize subsequent generations of mites. Feces in soil may be a vector for the spread of microorganisms. Methods: Extracts from used mite culture medium (i.e., residual food, mite feces, and dead mite bodies) were used as a source of feces-inhabiting microorganisms as food for the mites. Two T. putrescentiae populations (L and P) were used for experiments, and they hosted the intracellular bacteria Cardinium and Wolbachia, respectively. The effects of the fecal fraction on respiration in a mite microcosm, mite nutrient contents, population growth and microbiome composition were evaluated. Results: Feces from the P population comprised more than 90% Bartonella-like sequences. Feces from the L population feces hosted Staphylococcus, Virgibacillus, Brevibacterium, Enterobacteriaceae, and Bacillus. The mites from the P population, but not the L population, exhibited increased bacterial respiration in the microcosms in comparison to no-mite controls. Both L- and P-feces extracts had an inhibitory effect on the respiration of the microcosms, indicating antagonistic interactions within feces-associated bacteria. The mite microbiomes were resistant to the acquisition of new bacterial species from the feces, but their bacterial profiles were affected. Feeding of P mites on P-feces-enriched diets resulted in an increase in Bartonella abundance from 6 to 20% of the total bacterial sequences and a decrease in Bacillus abundance. The population growth was fivefold accelerated on P-feces extracts in comparison to the control. Conclusion: The mite microbiome, to a certain extent, resists the acquisition of new bacteria when mites are fed on feces of the same species. However, a Bartonella-like bacteria-feces-enriched diet seems to be beneficial for mite populations with symbiotic Bartonella-like bacteria. Coprophagy on the feces of its own population may be a mechanism of bacterial acquisition in T. putrescentiae.
Collapse
Affiliation(s)
- Jan Hubert
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
| | - Marta Nesvorna
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
| | - Bruno Sopko
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia.,Department of Medical Chemistry and Clinical Biochemistry, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czechia
| | - Jaroslav Smrz
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Pavel Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States.,Institute of Biology, University of Tyumen, Tyumen, Russia
| | - Tomas Erban
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
| |
Collapse
|
422
|
Bourrat P. Have Causal Claims About the Gut Microbiome Been Over-Hyped? Bioessays 2018; 40:e1800178. [DOI: 10.1002/bies.201800178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Pierrick Bourrat
- Department of Philosophy; Macquarie University; Building W6A North Ryde New South Wales Australia 2109
- Department of Philosophy; HPS School & Charles Perkins Centre; The University of Sydney; Camperdown New South Wales Australia 2006
| |
Collapse
|
423
|
Alcaraz JP, Cinquin P, Martin DK. Tackling the Concept of Symbiotic Implantable Medical Devices with Nanobiotechnologies. Biotechnol J 2018; 13:e1800102. [PMID: 30367543 DOI: 10.1002/biot.201800102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/17/2018] [Indexed: 12/21/2022]
Abstract
This review takes an approach to implanted medical devices that considers whether the intention of the implanted device is to have any communication of energy or materials with the body. The first part describes some specific examples of three different classes of implants, analyzed with regards to the type of signal sent to cells. Through several examples, the authors describe that a one way signaling to the body leads to encapsulation or degradation. In most cases, those phenomena do not lead to major problems. However, encapsulation or degradation are critical for new kinds of medical devices capable of duplex communication, which are defined in this review as symbiotic devices. The concept the authors propose is that implanted medical devices that need to be symbiotic with the body also need to be designed with an intended duplex communication of energy and materials with the body. This extends the definition of a biocompatible system to one that requires stable exchange of materials between the implanted device and the body. Having this novel concept in mind will guide research in a new field between medical implant and regenerative medicine to create actual symbiotic devices.
Collapse
Affiliation(s)
- Jean-Pierre Alcaraz
- Univverity Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,SyNaBi, Pavillon Taillefer, Domaine de la Merci, La Tronche 38706, Grenoble, France
| | - Philippe Cinquin
- Univverity Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,SyNaBi, Pavillon Taillefer, Domaine de la Merci, La Tronche 38706, Grenoble, France
| | - Donald K Martin
- Univverity Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,SyNaBi, Pavillon Taillefer, Domaine de la Merci, La Tronche 38706, Grenoble, France
| |
Collapse
|
424
|
Osmanovic D, Kessler DA, Rabin Y, Soen Y. Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole. Biol Direct 2018; 13:24. [PMID: 30621755 PMCID: PMC6889200 DOI: 10.1186/s13062-018-0224-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023] Open
Abstract
Background The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts. Results To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (“detox”). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host’s offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria). Conclusions These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system. Reviewers This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman. Electronic supplementary material The online version of this article (10.1186/s13062-018-0224-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dino Osmanovic
- Department of Physics, Bar-Ilan University, 52900, Ramat Gan, Israel
| | - David A Kessler
- Department of Physics, Bar-Ilan University, 52900, Ramat Gan, Israel
| | - Yitzhak Rabin
- Department of Physics, Bar-Ilan University, 52900, Ramat Gan, Israel.,NYU-ECNU Institute of Physics at NYU, Shanghai, 200062, China
| | - Yoav Soen
- Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel. .,Department of Physics, Massachusetts Institute of Technology (MIT), MA, 02139, Cambridge, USA.
| |
Collapse
|
425
|
Correa MA, Matusovsky B, Brackney DE, Steven B. Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development. Nat Commun 2018; 9:4464. [PMID: 30367055 PMCID: PMC6203775 DOI: 10.1038/s41467-018-07014-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
The mosquito gut microbiome plays an important role in mosquito development and fitness, providing a promising avenue for novel mosquito control strategies. Here we present a method for rearing axenic (bacteria free) Aedes aegypti mosquitoes, consisting of feeding sterilized larvae on agar plugs containing a high concentration of liver and yeast extract. This approach allows for the complete development to adulthood while maintaining sterility; however, axenic mosquito's exhibit delayed development time and stunted growth in comparison to their bacterially colonized cohorts. These data challenge the notion that live microorganisms are required for mosquito development, and suggest that the microbiota's main role is nutritional. Furthermore, we colonize axenic mosquitoes with simplified microbial communities ranging from a single bacterial species to a three-member community, demonstrating the ability to control the composition of the microbiota. This axenic system will allow the systematic manipulation of the mosquito microbiome for a deeper understanding of microbiota-host interactions.
Collapse
Affiliation(s)
- Maria A Correa
- Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, 06511, CT, USA
| | - Brian Matusovsky
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 06511, CT, USA
| | - Doug E Brackney
- Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, 06511, CT, USA.
| | - Blaire Steven
- Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, 06511, CT, USA.
| |
Collapse
|
426
|
Caetano-Anollés G, Nasir A, Kim KM, Caetano-Anollés D. Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. Evol Bioinform Online 2018; 14:1176934318805101. [PMID: 30364468 PMCID: PMC6196624 DOI: 10.1177/1176934318805101] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022] Open
Abstract
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
Collapse
Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
| |
Collapse
|
427
|
Abstract
All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host–microbiome ecosystem as a “holobiont”. Because natural selection acts on an organism’s realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the “hologenome”, or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.
Collapse
Affiliation(s)
- J Jeffrey Morris
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
428
|
Leftwich PT, Hutchings MI, Chapman T. Diet, Gut Microbes and Host Mate Choice: Understanding the significance of microbiome effects on host mate choice requires a case by case evaluation. Bioessays 2018; 40:e1800053. [PMID: 30311675 DOI: 10.1002/bies.201800053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 09/06/2018] [Indexed: 12/22/2022]
Abstract
All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Recent reports that assortative mating of hosts by diet can be mediated by commensal gut microbes have attracted interest as a potential route to host reproductive isolation (RI). Here, the authors discuss logical problems with this line of argument. The authors briefly review how microbes can affect host mating preferences and evaluate recent findings from fruitflies. Endosymbionts can potentially influence host RI given stable and recurrent co-association of hosts and microbes over evolutionary time. However, observations of co-occurrence of microbes and hosts are ripe for misinterpretation and such associations will rarely represent a meaningful holobiont. A framework in which hosts and their microbes are independent evolutionary units provides the only satisfactory explanation for the observed range of effects and associations.
Collapse
Affiliation(s)
- Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
429
|
Guyomar C, Legeai F, Jousselin E, Mougel C, Lemaitre C, Simon JC. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches. MICROBIOME 2018; 6:181. [PMID: 30305166 PMCID: PMC6180509 DOI: 10.1186/s40168-018-0562-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/20/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND 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 opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. RESULTS We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. CONCLUSIONS We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.
Collapse
Affiliation(s)
- Cervin Guyomar
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Fabrice Legeai
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Emmanuelle Jousselin
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montpellier, France
| | - Christophe Mougel
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
| | - Claire Lemaitre
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Jean-Christophe Simon
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France.
| |
Collapse
|
430
|
Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee PA, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, Rubin EM, Lee SW, Kim JF. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat Biotechnol 2018; 36:nbt.4232. [PMID: 30295674 DOI: 10.1038/nbt.4232] [Citation(s) in RCA: 329] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/01/2018] [Indexed: 11/09/2022]
Abstract
Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant. We cultivated this flavobacterium, named TRM1, and found that it could suppress R. solanacearum-disease development in a susceptible plant in pot experiments. Our findings reveal a role for native microbiota in protecting plants from microbial pathogens, and our approach charts a path toward the development of probiotics to ameliorate plant diseases.
Collapse
Affiliation(s)
- Min-Jung Kwak
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Kihyuck Choi
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jidam Lee
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Pyeong An Lee
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Soo Yeon Choi
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | | | - Hyoung Ju Lee
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Eun Joo Jung
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Hyein Park
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Nazish Roy
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Heebal Kim
- C&K Genomics, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Myeong Min Lee
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Edward M Rubin
- Department of Energy Joint Genome Institute (DOE JGI) and Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Seon-Woo Lee
- Department of Applied Biology, Dong-A University, Busan, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Strategic Initiative for Microbiomes in Agriculture and Food (iMAF), Yonsei University, Seoul, Republic of Korea
| |
Collapse
|
431
|
Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biol Evol 2018; 10:707-715. [PMID: 29420719 PMCID: PMC5830969 DOI: 10.1093/gbe/evy031] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 02/07/2023] Open
Abstract
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.
Collapse
Affiliation(s)
- Guillaume Bernard
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Jananan S Pathmanathan
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Romain Lannes
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Philippe Lopez
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Eric Bapteste
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| |
Collapse
|
432
|
Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S. Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire. THE ISME JOURNAL 2018; 12:2559-2574. [PMID: 29955140 PMCID: PMC6154966 DOI: 10.1038/s41396-018-0166-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 12/31/2022]
Abstract
Microbiomes impact a variety of processes including a host's ability to access nutrients and maintain health. While host species differences in microbiomes have been described across ecosystems, little is known about how microbiomes assemble, particularly in the ecological and social contexts in which they evolved. We examined gut microbiome composition in nine sympatric wild non-human primate (NHP) species. Despite sharing an environment and interspecific interactions, individuals harbored unique and persistent microbiomes influenced by host species, social group, and parentage, but surprisingly not by social relationships among members of a social group. We found a branching order of host-species networks constructed using the composition of their microbiomes as characters, which was incongruent with known NHP phylogenetic relationships, with chimpanzees (Pan troglodytes verus) sister to colobines, upon which they regularly prey. In contrast to phylogenetic clustering found in all monkey microbiomes, chimpanzee microbiomes were unique in that they exhibited patterns of phylogenetic overdispersion. This reflects unique ecological processes impacting microbiome composition in chimpanzees and future studies will elucidate the aspects of chimpanzee ecology, life history, and physiology that explain their unique microbiome community structure. Our study of contemporaneous microbiomes of all sympatric diurnal NHP in an ecosystem highlights the diverse dispersal routes shaping these complex communities.
Collapse
Affiliation(s)
- Jan F Gogarten
- Department of Biology, McGill University, 855 Sherbrooke Street West, Montreal, QC, H3A2T7, Canada
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - T Jonathan Davies
- Department of Biology, McGill University, 855 Sherbrooke Street West, Montreal, QC, H3A2T7, Canada
| | - Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Alexander Mielke
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Roger Mundry
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Michael C Nelson
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT, 06269-3125, USA
| | - Roman M Wittig
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, B.P. 1303, Abidjan 01, Côte d'Ivoire.
| | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Sébastien Calvignac-Spencer
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| |
Collapse
|
433
|
Difford GF, Plichta DR, Løvendahl P, Lassen J, Noel SJ, Højberg O, Wright ADG, Zhu Z, Kristensen L, Nielsen HB, Guldbrandtsen B, Sahana G. Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows. PLoS Genet 2018; 14:e1007580. [PMID: 30312316 PMCID: PMC6200390 DOI: 10.1371/journal.pgen.1007580] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 10/24/2018] [Accepted: 07/20/2018] [Indexed: 01/23/2023] Open
Abstract
Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.
Collapse
Affiliation(s)
- Gareth Frank Difford
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Wageningen University & Research, Animal Breeding & Genomics, AH Wageningen, Netherlands
| | - Damian Rafal Plichta
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Jan Lassen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Viking Genetics, Randers SØ, Denmark
| | | | - Ole Højberg
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - André-Denis G. Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
| | - Zhigang Zhu
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Lise Kristensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Henrik Bjørn Nielsen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| |
Collapse
|
434
|
Kim YC, Anderson AJ. Rhizosphere pseudomonads as probiotics improving plant health. MOLECULAR PLANT PATHOLOGY 2018; 19:2349-2359. [PMID: 29676842 PMCID: PMC6638116 DOI: 10.1111/mpp.12693] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/08/2018] [Accepted: 04/18/2018] [Indexed: 05/25/2023]
Abstract
Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.
Collapse
Affiliation(s)
- Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangju 61186South Korea
| | - Anne J. Anderson
- Department of Biological EngineeringUtah State UniversityLoganUT 84322‐4105USA
| |
Collapse
|
435
|
Björk JR, Diéz-vives C, Astudillo-garcía C, Archie EA, Montoya JM. Vertical transmission of sponge microbiota is inconsistent and unfaithful.. [PMID: 31285574 PMCID: PMC6914380 DOI: 10.1101/425009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Classic evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes, and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas for the first time in multiple host species with highly diverse microbiota, leveraging known-parent offspring pairs sampled from eight species of wild marine sponges (Porifera). Contrary to the hypothesis that vertical transmission is an adaptation that allows sponges to faithfully transmit intact microbial consortia to offspring, we found that vertical transmission is weak and incomplete. Further, we found no evidence that siblings consistently receive the same microbes from their parents, nor that vertically transmitted microbes show high degrees of host species fidelity. Finally, while we show that monophyletic groups of microbes with known symbiotic features and capabilities are more common among vertically transmitted microbes than in the consortia of horizontally acquired microbes, the signature of this vertical transmission is only detectable on the level of Porifera as a whole. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.
Collapse
|
436
|
Sitaraman R. Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities. MICROBIOME 2018; 6:163. [PMID: 30223892 PMCID: PMC6142633 DOI: 10.1186/s40168-018-0551-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/05/2018] [Indexed: 05/26/2023]
Abstract
The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.
Collapse
Affiliation(s)
- Ramakrishnan Sitaraman
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India.
| |
Collapse
|
437
|
Carthey AJR, Gillings MR, Blumstein DT. The Extended Genotype: Microbially Mediated Olfactory Communication. Trends Ecol Evol 2018; 33:885-894. [PMID: 30224089 DOI: 10.1016/j.tree.2018.08.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/19/2018] [Accepted: 08/26/2018] [Indexed: 12/26/2022]
Abstract
Microbes are now known to influence inter- and intraspecific olfactory signaling systems. They do so by producing metabolites that function as odorants. A unique attribute of such odorants is that they arise as a product of microbial-host interactions. These interactions need not be mutualistic, and indeed can be antagonistic. We develop an integrated ecoevolutionary model to explore microbially mediated olfactory communication and a process model that illustrates the various ways that microbial products might contribute to odorants. This novel approach generates testable predictions, including that selection to incorporate microbial products should be a common feature of infochemicals that communicate identity but not those that communicate fitness or quality. Microbes extend an individual's genotype, but also enhance vulnerability to environmental change.
Collapse
Affiliation(s)
- Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Daniel T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
438
|
Cremon C, Barbaro MR, Ventura M, Barbara G. Pre- and probiotic overview. Curr Opin Pharmacol 2018; 43:87-92. [PMID: 30219638 DOI: 10.1016/j.coph.2018.08.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/22/2018] [Indexed: 12/18/2022]
Abstract
The dynamic relationship between gut microbiota and its human host is also known as a trophic association that might range from commensalism, where only the microbe enjoys a positive effect from the relationship, to intestinal symbiosis where both host and microbe benefit from their interaction. In the last years, we have started to understand how alterations of the gut microbiota composition leading to the disruption of host-microbial interactions are associated and/or predispose individuals to disease conditions ranging from inflammatory bowel diseases to allergy and functional gastrointestinal disorders, such as irritable bowel syndrome. While we await important insights in this field, the microbiota is already a therapeutic target. Based on the actual definitions, prebiotics are defined as substrates that are selectively utilized by host microorganisms conferring a health benefit, while probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Although their health promoting activities encompasses numerous effects, including immunostimulation, competitive exclusion of pathogens, and gut barrier enhancement, the exact mechanism of action by which these compounds exert their beneficial actions in humans is only partially known. In this review, we highlight the current insights into the clinical applications of prebiotics and probiotics in gastroenterology.
Collapse
Affiliation(s)
- Cesare Cremon
- Department of Medical and Surgical Sciences, Centre for Applied Biomedical Research, University of Bologna, Bologna, Italy
| | - Maria Raffaella Barbaro
- Department of Medical and Surgical Sciences, Centre for Applied Biomedical Research, University of Bologna, Bologna, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, Centre for Applied Biomedical Research, University of Bologna, Bologna, Italy.
| |
Collapse
|
439
|
Correa‐García S, Pande P, Séguin A, St‐Arnaud M, Yergeau E. Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation. Microb Biotechnol 2018; 11:819-832. [PMID: 30066464 PMCID: PMC6116750 DOI: 10.1111/1751-7915.13303] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/18/2022] Open
Abstract
Phytoremediation is a green and sustainable alternative to physico-chemical methods for contaminated soil remediation. One of the flavours of phytoremediation is rhizoremediation, where plant roots stimulate soil microbes to degrade organic contaminants. This approach is particularly interesting as it takes advantage of naturally evolved interaction mechanisms between plant and microorganisms and often results in a complete mineralization of the contaminants (i.e. transformation to water and CO2 ). However, many biotic and abiotic factors influence the outcome of this interaction, resulting in variable efficiency of the remediation process. The difficulty to predict precisely the timeframe associated with rhizoremediation leads to low adoption rates of this green technology. Here, we review recent literature related to rhizoremediation, with a particular focus on soil organisms. We then expand on the potential of rhizoremediation to be a model plant-microbe interaction system for microbiome manipulation studies.
Collapse
Affiliation(s)
- Sara Correa‐García
- Centre INRS‐Institut Armand‐FrappierInstitut national de la recherche scientifiqueUniversité du QuébecLavalQCCanada
- Laurentian Forest CenterNatural Ressources CanadaQuébec CityQCCanada
| | - Pranav Pande
- Centre INRS‐Institut Armand‐FrappierInstitut national de la recherche scientifiqueUniversité du QuébecLavalQCCanada
- Institut de recherche en biologie végétaleUniversité de Montréal and Jardin Botanique de MontréalMontréalQCCanada
| | - Armand Séguin
- Laurentian Forest CenterNatural Ressources CanadaQuébec CityQCCanada
| | - Marc St‐Arnaud
- Institut de recherche en biologie végétaleUniversité de Montréal and Jardin Botanique de MontréalMontréalQCCanada
| | - Etienne Yergeau
- Centre INRS‐Institut Armand‐FrappierInstitut national de la recherche scientifiqueUniversité du QuébecLavalQCCanada
| |
Collapse
|
440
|
Kiran GS, Sekar S, Ramasamy P, Thinesh T, Hassan S, Lipton AN, Ninawe AS, Selvin J. Marine sponge microbial association: Towards disclosing unique symbiotic interactions. MARINE ENVIRONMENTAL RESEARCH 2018; 140:169-179. [PMID: 29935729 DOI: 10.1016/j.marenvres.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.
Collapse
Affiliation(s)
- G Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Sivasankari Sekar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pasiyappazham Ramasamy
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - A S Ninawe
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| |
Collapse
|
441
|
Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? mSystems 2018; 3:e00097-18. [PMID: 30417109 PMCID: PMC6208643 DOI: 10.1128/msystems.00097-18] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.
Collapse
Affiliation(s)
- Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine M. Davis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K. Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
442
|
Wenzel MA, Douglas A, Piertney SB. Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS One 2018; 13:e0202212. [PMID: 30157257 PMCID: PMC6114722 DOI: 10.1371/journal.pone.0202212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/29/2018] [Indexed: 02/05/2023] Open
Abstract
The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.
Collapse
Affiliation(s)
- Marius A. Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Stuart B. Piertney
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
443
|
Rodríguez-Ruano SM, Martín-Vivaldi M, Peralta-Sánchez JM, García-Martín AB, Martínez-García Á, Soler JJ, Valdivia E, Martínez-Bueno M. Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion. Genes (Basel) 2018; 9:genes9080407. [PMID: 30103505 PMCID: PMC6115775 DOI: 10.3390/genes9080407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/23/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
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 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.
Collapse
Affiliation(s)
- Sonia M Rodríguez-Ruano
- Departamento de Microbiología, Universidad de Granada, E-18071 Granada, Spain.
- Faculty of Science, University of South Bohemia, CZ-370 05 Ceske Budejovice, Czechia.
| | - Manuel Martín-Vivaldi
- Departamento de Zoología, Universidad de Granada, E-18071 Granada, Spain.
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
| | | | | | - Ángela Martínez-García
- Estación Experimental de Zonas Áridas (Consejo Superior de Investigaciones Científicas, CSIC), E-04120 Almeria, Spain.
| | - Juan J Soler
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Estación Experimental de Zonas Áridas (Consejo Superior de Investigaciones Científicas, CSIC), E-04120 Almeria, Spain.
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, E-18071 Granada, Spain.
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Instituto de Biotecnología, Universidad de Granada, E-18071 Granada, Spain.
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, E-18071 Granada, Spain.
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Instituto de Biotecnología, Universidad de Granada, E-18071 Granada, Spain.
| |
Collapse
|
444
|
Ziegler M, Stone E, Colman D, Takacs-Vesbach C, Shepherd U. Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island, Australia. JOURNAL OF PHYCOLOGY 2018; 54:447-460. [PMID: 29696650 PMCID: PMC6105428 DOI: 10.1111/jpy.12749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Large-scale environmental disturbances may impact both partners in coral host-Symbiodinium systems. Elucidation of the assembly patterns in such complex and interdependent communities may enable better prediction of environmental impacts across coral reef ecosystems. In this study, we investigated how the community composition and diversity of dinoflagellate symbionts in the genus Symbiodinium were distributed among 12 host species from six taxonomic orders (Actinaria, Alcyonacea, Miliolida, Porifera, Rhizostoma, Scleractinia) and in the reef water and sediments at Lizard Island, Great Barrier Reef before the 3rd Global Coral Bleaching Event. 454 pyrosequencing of the ITS2 region of Symbiodinium yielded 83 operational taxonomic units (OTUs) at a 97% similarity cut-off. Approximately half of the Symbiodinium OTUs from reef water or sediments were also present in symbio. OTUs belonged to six clades (A-D, F-G), but community structure was uneven. The two most abundant OTUs (100% matches to types C1 and A3) comprised 91% of reads and OTU C1 was shared by all species. However, sequence-based analysis of these dominant OTUs revealed host species specificity, suggesting that genetic similarity cut-offs of Symbiodinium ITS2 data sets need careful evaluation. Of the less abundant OTUs, roughly half occurred at only one site or in one species and the background Symbiodinium communities were distinct between individual samples. We conclude that sampling multiple host taxa with differing life history traits will be critical to fully understand the symbiont diversity of a given system and to predict coral ecosystem responses to environmental change and disturbance considering the differential stress response of the taxa within.
Collapse
Affiliation(s)
- Maren Ziegler
- Author for correspondence: Maren Ziegler, 4700 King Abdullah University of Science and Technology (KAUST), Building 2, Office 2227, 3955-6900 Thuwal, Saudi Arabia, Tel.: +966 12 808 2446,
| | - Elizabeth Stone
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Daniel Colman
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Cristina Takacs-Vesbach
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Ursula Shepherd
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA; Honors College, University of New Mexico, Student Health Center Building, MSCO6-3890 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| |
Collapse
|
445
|
Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
Collapse
Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| |
Collapse
|
446
|
Chialva M, Zhou Y, Spadaro D, Bonfante P. Not only priming: Soil microbiota may protect tomato from root pathogens. PLANT SIGNALING & BEHAVIOR 2018; 13:e1464855. [PMID: 29701498 PMCID: PMC6149515 DOI: 10.1080/15592324.2018.1464855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
An increasing number of studies have investigated soil microbial biodiversity. However, the mechanisms regulating plant responses to soil microbiota are largely unknown. A previous work tested the hypothesis that tomato plants grown on native soils with their complex microbiotas respond differently from tomato growing in a sterile substrate. Two soils, suppressive or conducive to Fusarium oxysporum f. sp. lycopersici (FOL), and two genotypes susceptible and resistant to the same pathogen were considered. The work highlighted that the two tested soil microbiotas, irrespectively of their taxonomic composition, elicit the PAMP-triggered Immunity Pathway, the first level of plant defence, as well as an increased lignin synthesis, leading to an active protection when FOL is present in the soil. Here, we tested the expression of a panel of genes involved in Effector-Triggered Immunity (ETI), demonstrating that soil microbiota, beside genotype, affects plant resistance to FOL also modulating this pathway.
Collapse
Affiliation(s)
- Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| | - Yang Zhou
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
- College of Horticulture, South China Agricultural University, No. 483, Wushan St., Tianhe Dist. Guangzhou, China PR, 510642
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DISAFA) and AGROINNOVA, Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Largo Braccini 2, I-10095 Grugliasco, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125 Torino, Italy
| |
Collapse
|
447
|
Ruiz-Rodríguez M, Martín-Vivaldi M, Martínez-Bueno M, Soler JJ. Gut Microbiota of Great Spotted Cuckoo Nestlings is a Mixture of Those of Their Foster Magpie Siblings and of Cuckoo Adults. Genes (Basel) 2018; 9:genes9080381. [PMID: 30060541 PMCID: PMC6115760 DOI: 10.3390/genes9080381] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023] Open
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 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.
Collapse
Affiliation(s)
- Magdalena Ruiz-Rodríguez
- Biologie Integrative des Organismes Marins, Observatoire Océanologique, Sorbonne Universités, Avenue du Fontaulé, 66650 Banyuls-Sur-Mer, France.
| | - Manuel Martín-Vivaldi
- Departamento de Zoología, Universidad de Granada, E-18071 Granada, Spain.
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
| | - Manuel Martínez-Bueno
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Departamento de Microbiología, Universidad de Granada, E-18071 Granada, Spain.
| | - Juan José Soler
- Unidad Asociada Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, E-18071 Granada, Spain.
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (EEZA-CSIC), Ctra. Sacramento s/n, La Cañada de San Urbano, E-04120 Almería, Spain.
| |
Collapse
|
448
|
Faure D, Simon JC, Heulin T. Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems. THE NEW PHYTOLOGIST 2018; 218:1321-1324. [PMID: 29738088 DOI: 10.1111/nph.15199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Denis Faure
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Saclay, Gif-sur-Yvette, 91 190, Gif-sur-Yvette, France
| | - Jean-Christophe Simon
- INRA/Agrocampus Ouest/Université Rennes 1, UMR 1349, IGEPP, Domaine de la Motte, B.P. 35327, F-35653, Le Rheu Cedex, France
| | - Thierry Heulin
- Aix Marseille University, CEA, CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108, Saint-Paul-lez-Durance, France
| |
Collapse
|
449
|
Orr MR, Kocurek KM, Young DL. Gut Microbiota and Human Health: Insights From Ecological Restoration. THE QUARTERLY REVIEW OF BIOLOGY 2018. [DOI: 10.1086/698021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
450
|
Oyserman BO, Medema MH, Raaijmakers JM. Road MAPs to engineer host microbiomes. Curr Opin Microbiol 2018; 43:46-54. [DOI: 10.1016/j.mib.2017.11.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023]
|