451
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Exploring the diversity-stability paradigm using sponge microbial communities. Sci Rep 2018; 8:8425. [PMID: 29849034 PMCID: PMC5976656 DOI: 10.1038/s41598-018-26641-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.
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452
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In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. ISME JOURNAL 2018; 12:2024-2038. [PMID: 29849170 DOI: 10.1038/s41396-018-0152-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/21/2018] [Accepted: 04/29/2018] [Indexed: 12/21/2022]
Abstract
A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root-associated and leaf-associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in southwest of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota operational taxonomic units. This result suggests that the potential biomarkers controlling pathogen's invasion are highly dynamic.
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453
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Abstract
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.
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Affiliation(s)
- Eric Bapteste
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
- CNRS, UMR7138, Institut de Biologie Paris-Seine, F-75005 Paris, France
| | - Philippe Huneman
- Institut d’Histoire et de Philosophie des Sciences et des Techniques (CNRS / Paris I Sorbonne), F-75006 Paris, France
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454
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Bourrat P, Griffiths PE. Multispecies individuals. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:33. [PMID: 29761370 DOI: 10.1007/s40656-018-0194-1] [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: 05/09/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called 'holobionts'. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of ecological dependence between separate individuals. Some widely used arguments in support of the 'holobiont' concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality.
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Affiliation(s)
- Pierrick Bourrat
- Department of Philosophy, Macquarie University, North Ryde, NSW, 2109, Australia.
- School of History and Philosophy of Science, University of Sydney, Main Quadrangle A14, Sydney, NSW, 2006, Australia.
- Department of Philosophy and Charles Perkins Centre, University of Sydney, Main Quadrangle A14, Sydney, NSW, 2006, Australia.
| | - Paul E Griffiths
- Department of Philosophy and Charles Perkins Centre, University of Sydney, Main Quadrangle A14, Sydney, NSW, 2006, Australia
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455
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Benjamino J, Lincoln S, Srivastava R, Graf J. Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration. MICROBIOME 2018; 6:86. [PMID: 29747692 PMCID: PMC5944116 DOI: 10.1186/s40168-018-0469-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/26/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions. RESULTS Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut. CONCLUSIONS This combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.
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Affiliation(s)
- Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT, 06269, USA
| | - Stephen Lincoln
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Ranjan Srivastava
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT, 06269, USA.
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456
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Diversity and antimicrobial potential in sea anemone and holothurian microbiomes. PLoS One 2018; 13:e0196178. [PMID: 29742123 PMCID: PMC5942802 DOI: 10.1371/journal.pone.0196178] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
Marine invertebrates, as holobionts, contain symbiotic bacteria that coevolve and develop antimicrobial substances. These symbiotic bacteria are an underexplored source of new bioactive molecules to face the emerging antibiotic resistance in pathogens. Here, we explored the antimicrobial activity of bacteria retrieved from the microbiota of two sea anemones (Anemonia sulcata, Actinia equina) and two holothurians (Holothuria tubulosa, Holothuria forskali). We tested the antimicrobial activity of the isolated bacteria against pathogens with interest for human health, agriculture and aquaculture. We isolated 27 strains with antibacterial activity and 12 of these isolates also showed antifungal activity. We taxonomically identified these strains being Bacillus and Vibrio species the most representative producers of antimicrobial substances. Microbiome species composition of the two sea anemones was similar between them but differed substantially of seawater bacteria. In contrast, microbiome species composition of the two holothurian species was different between them and in comparison with the bacteria in holothurian feces and seawater. In all the holobiont microbiomes Bacteroidetes was the predominant phylum. For each microbiome, we determined diversity and the rank-abundance dominance using five fitted models (null, pre-emption, log-Normal, Zipf and Zipf-Mandelbrot). The models with less evenness (i.e. Zipf and Zipf-Mandelblot) showed the best fits in all the microbiomes. Finally, we tracked (using the V4 hypervariable region of 16S rRNA gene) the relative abundance of these 27 isolates with antibacterial activity in the total pool of sequences obtained for the microbiome of each holobiont. Coincidences, although with extremely low frequencies, were detected only in the microbiome of H. forskali. This fact suggests that these isolated bacteria belong to the long tail of rare symbiotic bacteria. Therefore, more and more sophisticated culture techniques are necessary to explore this apparently vast pool of rare symbiontic bacteria and to determine their biotechnological potentiality.
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457
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Grieneisen LE, Livermore J, Alberts S, Tung J, Archie EA. Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons. Integr Comp Biol 2018; 57:770-785. [PMID: 29048537 DOI: 10.1093/icb/icx046] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.
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Affiliation(s)
- Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Josh Livermore
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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458
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Dearing MD, Kohl KD. Beyond Fermentation: Other Important Services Provided to Endothermic Herbivores by their Gut Microbiota. Integr Comp Biol 2018; 57:723-731. [PMID: 28662572 DOI: 10.1093/icb/icx020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
For decades, comparative biologists have recognized the importance of microbial partners in facilitating herbivory as a successful feeding strategy. Most of this success is attributed to the ability of gut microbes to digest recalcitrant dietary fiber and provides usable nutrients to their hosts. Gut microbes can also provide numerous other functions, such as vitamin synthesis, nitrogen recycling, and the detoxification of plant secondary compounds. Here, we review these microbial functions in herbivorous mammals and birds, highlighting studies that utilize recently developed metagenomic techniques. Several of these studies emphasize that microbial services are the product of interactions and exchanges within a complex microbial community, rather than the product of an individual member. Additionally, a number of these microbial functions are interdependent. For example, levels of dietary nitrogen or plant toxins can influence fiber digestibility. Further studies into the variety of microbial services provided to herbivorous hosts, and how these services might interact will broaden our understanding of host-microbe interactions.
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Affiliation(s)
- M Denise Dearing
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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459
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Parfrey LW, Moreau CS, Russell JA. Introduction: The host-associated microbiome: Pattern, process and function. Mol Ecol 2018; 27:1749-1765. [DOI: 10.1111/mec.14706] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Laura Wegener Parfrey
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada
- Department of Zoology; University of British Columbia; Vancouver British Columbia Canada
| | - Corrie S. Moreau
- Department of Science and Education; Field Museum of Natural History; Chicago IL USA
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460
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Dysbiotic drift and biopsychosocial medicine: how the microbiome links personal, public and planetary health. Biopsychosoc Med 2018; 12:7. [PMID: 29743938 PMCID: PMC5932796 DOI: 10.1186/s13030-018-0126-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023] Open
Abstract
The emerging concept of planetary health emphasizes that the health of human civilization is intricately connected to the health of natural systems within the Earth’s biosphere; here, we focus on the rapidly progressing microbiome science - the microbiota-mental health research in particular - as a way to illustrate the pathways by which exposure to biodiversity supports health. Microbiome science is illuminating the ways in which stress, socioeconomic disadvantage and social polices interact with lifestyle and behaviour to influence the micro and macro-level biodiversity that otherwise mediates health. Although the unfolding microbiome and mental health research is dominated by optimism in biomedical solutions (e.g. probiotics, prebiotics), we focus on the upstream psychosocial and ecological factors implicated in dysbiosis; we connect grand scale biodiversity in the external environment with differences in human-associated microbiota, and, by extension, differences in immune function and mental outlook. We argue that the success of planetary health as a new concept will be strengthened by a more sophisticated understanding of the ways in which individuals develop emotional connections to nature (nature relatedness) and the social policies and practices which facilitate or inhibit the pro-environmental values that otherwise support personal, public and planetary health.
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461
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Fietz K, Rye Hintze CO, Skovrind M, Kjærgaard Nielsen T, Limborg MT, Krag MA, Palsbøll PJ, Hestbjerg Hansen L, Rask Møller P, Gilbert MTP. Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. MICROBIOME 2018; 6:82. [PMID: 29720271 PMCID: PMC5932900 DOI: 10.1186/s40168-018-0467-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/26/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it has recently been argued that their microbiomes may also contribute to population genetic divergence. We explored whether this might be plausible along the well-described environmental gradient of the Baltic Sea in two species of sand lance (Ammodytes tobianus and Hyperoplus lanceolatus). Specifically, we assessed both their population genetic and gut microbial composition variation and investigated not only which environmental parameters correlate with the observed variation, but whether host genome also correlates with microbiome variation. RESULTS We found a clear genetic structure separating the high-salinity North Sea from the low-salinity Baltic Sea sand lances. The observed genetic divergence was not simply a function of isolation by distance, but correlated with environmental parameters, such as salinity, sea surface temperature, and, in the case of A. tobianus, possibly water microbiota. Furthermore, we detected two distinct genetic groups in Baltic A. tobianus that might represent sympatric spawning types. Investigation of possible drivers of gut microbiome composition variation revealed that host species identity was significantly correlated with the microbial community composition of the gut. A potential influence of host genetic factors on gut microbiome composition was further confirmed by the results of a constrained analysis of principal coordinates. The host genetic component was among the parameters that best explain observed variation in gut microbiome composition. CONCLUSIONS Our findings have relevance for the population structure of two commercial species but also provide insights into potentially relevant genomic and microbial factors with regards to sand lance adaptation across the North Sea-Baltic Sea environmental gradient. Furthermore, our findings support the hypothesis that host genetics may play a role in regulating the gut microbiome at both the interspecific and intraspecific levels. As sequencing costs continue to drop, we anticipate that future studies that include full genome and microbiome sequencing will be able to explore the full relationship and its potential adaptive implications for these species.
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Affiliation(s)
- Katharina Fietz
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
- Marine Evolution and Conservation, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Christian Olaf Rye Hintze
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Mikkel Skovrind
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Morten T Limborg
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Marcus A Krag
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Per J Palsbøll
- Marine Evolution and Conservation, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Peter Rask Møller
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
- NTNU University Museum, 7491, Trondheim, Norway.
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462
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Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye. Prog Retin Eye Res 2018; 64:84-95. [DOI: 10.1016/j.preteyeres.2018.01.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 01/07/2018] [Accepted: 01/11/2018] [Indexed: 01/15/2023]
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463
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Endosymbiosis as a source of immune innovation. C R Biol 2018; 341:290-296. [DOI: 10.1016/j.crvi.2018.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 03/13/2018] [Indexed: 02/07/2023]
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464
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van de Guchte M, Blottière HM, Doré J. Humans as holobionts: implications for prevention and therapy. MICROBIOME 2018; 6:81. [PMID: 29716650 PMCID: PMC5928587 DOI: 10.1186/s40168-018-0466-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/23/2018] [Indexed: 05/27/2023]
Abstract
The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maintained and serves health, but signs are that perturbation of this equilibrium beyond the limits of resilience can propel the system into an alternative stable state, a pre-disease state, more susceptible to the development of chronic diseases. The microbiota-host equilibrium of a large and growing proportion of individuals in Western society may represent such a pre-disease state and explain the explosive development of chronic diseases such as inflammatory bowel disease, obesity, and other inflammatory diseases. These diseases themselves represent other alternative stable states again and are therefore hard to cure. The holistic view of the microbiota-host association where feedback loops between microbiota and host are thought to maintain the system in a stable state-be it a healthy, pre-disease, or disease state-implies that integrated approaches, addressing host processes and microbiota, should be used to treat or prevent (pre-)disease.
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Affiliation(s)
- Maarten van de Guchte
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Hervé M Blottière
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- MetaGenoPolis, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- MetaGenoPolis, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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465
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Abstract
PURPOSE OF REVIEW This review focuses on the recent discoveries about the impact of intestinal microbiota on mammalian host juvenile growth. RECENT FINDINGS Intestinal microbiota is a powerful modulator of many facets of multicellular host's physiology. Recent results from human field studies and animal research have clearly shown that not only the nutrition, but also the intestinal microbiota impacts host postnatal growth kinetics. Absence of microbiome leads to stunted growth in mammalian gnotobiotic models and changes in the composition of the intestinal microbiota can impact the postnatal growth kinetics both positively and negatively under normal nutritional conditions as well as in undernutrition. Strikingly, specific bacterial strains are able to interact with GH/IGF-1 somatotropic axis activity, thus directly impacting host juvenile development. SUMMARY Intestinal microbiota dictates the pace of host postnatal growth. This newly described role envisages that therapy with specific bacterial strains, together with re-nutritional strategies, might successfully alleviate the long-term sequelae of undernutrition during childhood in humans.
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Affiliation(s)
- Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
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466
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Wang J, Chen L, Zhao N, Xu X, Xu Y, Zhu B. Of genes and microbes: solving the intricacies in host genomes. Protein Cell 2018; 9:446-461. [PMID: 29611114 PMCID: PMC5960464 DOI: 10.1007/s13238-018-0532-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Xizhan Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yakun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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467
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‘The importance of symbiosis in philosophy of biology: an analysis of the current debate on biological individuality and its historical roots’. Symbiosis 2018. [DOI: 10.1007/s13199-018-0556-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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468
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Vannier N, Mony C, Bittebiere AK, Michon-Coudouel S, Biget M, Vandenkoornhuyse P. A microorganisms' journey between plant generations. MICROBIOME 2018; 6:79. [PMID: 29695286 PMCID: PMC5918900 DOI: 10.1186/s40168-018-0459-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/09/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network. METHODS We used the clonal plant Glechoma hederacea as plant model and forced newly emitted clonal progeny to root in separated pots while controlling the presence of microorganisms. We used an amplicon sequencing approach of 16S and 18S rRNA targeting bacteria/archaea and fungi respectively to describe the root microbiota of mother and clonal-plant offspring. RESULTS We demonstrated the vertical transmission of a significant proportion of the mother plants' symbiotic bacteria and fungi to the daughters. Interestingly, archaea were not transmitted to the daughter plants. Transmitted communities had lower richness, suggesting a filtration during transmission. We found that the transmitted pool of microorganisms was similar among daughters, constituting the heritability of a specific cohort of microorganisms, opening a new understanding of the plant holobiont. We also found significant effects of distance to the mother plant and of growth time on the richness of the microbiota transmitted. CONCLUSIONS In this clonal plant, microorganisms are transmitted between individuals through connections, thereby ensuring the availability of microbe partners for the newborn plants as well as the dispersion between hosts for the microorganisms. This previously undescribed ecological process allows the dispersal of microorganisms in space and across plant generations. As the vast majority of plants are clonal, this process might be therefore a strong driver of ecosystem functioning and assembly of plant and microorganism communities in a wide range of ecosystems.
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Affiliation(s)
- Nathan Vannier
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France.
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Anne-Kristel Bittebiere
- Université de Lyon 1, CNRS, UMR 5023 LEHNA, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Sophie Michon-Coudouel
- Université de Rennes 1, CNRS, UMS3343 OSUR, campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Marine Biget
- Université de Rennes 1, CNRS, UMS3343 OSUR, campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
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469
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Doolittle WF, Inkpen SA. Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking. Proc Natl Acad Sci U S A 2018; 115:4006-4014. [PMID: 29581311 PMCID: PMC5910863 DOI: 10.1073/pnas.1722232115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution's principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider-as "units of selection" in their own right-the processes implemented by genes, cells, species, or communities. "It's the song not the singer" (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that "holobionts" (microbes and their animal or plant hosts) are aggregate "units of selection," claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.
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Affiliation(s)
- W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada;
| | - S Andrew Inkpen
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Philosophy, Dalhousie University, Halifax, NS B3H 4R2, Canada
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470
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Abstract
The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.
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471
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Chagas FO, Pessotti RDC, Caraballo-Rodríguez AM, Pupo MT. Chemical signaling involved in plant-microbe interactions. Chem Soc Rev 2018; 47:1652-1704. [PMID: 29218336 DOI: 10.1039/c7cs00343a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.
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Affiliation(s)
- Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Avenida do Café, s/n, 14040-903, Ribeirão Preto-SP, Brazil.
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472
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Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Thézé J, Streicker D, Frank HK, Loza-Rubio E, Liu S, Ryder OA, Samaniego Castruita JA, Katzourakis A, Pacheco G, Taboada B, Löber U, Pybus OG, Li Y, Rojas-Anaya E, Bohmann K, Carmona Baez A, Arias CF, Liu S, Greenwood AD, Bertelsen MF, White NE, Bunce M, Zhang G, Sicheritz-Pontén T, Gilbert MPT. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nat Ecol Evol 2018; 2:659-668. [PMID: 29459707 PMCID: PMC5868727 DOI: 10.1038/s41559-018-0476-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
Abstract
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.
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Affiliation(s)
- M Lisandra Zepeda Mendoza
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anne Kathrine Runge
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Daniel Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine & MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Hannah K Frank
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Shengmao Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - George Pacheco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | - Yang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Edith Rojas-Anaya
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Kristine Bohmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aldo Carmona Baez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Undergraduate Program for Genomic Sciences, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nicole E White
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Michael Bunce
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - M P Thomas Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia.
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway.
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473
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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474
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Guivier E, Martin JF, Pech N, Ungaro A, Chappaz R, Gilles A. Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species. MICROBIAL ECOLOGY 2018; 75:799-810. [PMID: 28956100 DOI: 10.1007/s00248-017-1077-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Understanding the role of microbiota as reproductive barriers or sources of adaptive novelty in the fundamental biological phenomenon of speciation is an exciting new challenge necessitating exploration of microbiota variation in wild interbreeding species. We focused on two interbreeding cyprinid species, Chondrostoma nasus and Parachondrostoma toxostoma, which have geographic distributions characterized by a mosaic of hybrid zones. We described microbiota diversity and composition in the three main teleost mucosal tissues, the skin, gills and gut, in the parental parapatric populations. We found that tissue type was the principal determinant of bacterial community composition. In particular, there was strong microbiota differentiation between external and internal tissues, with secondary discrimination between the two species. These findings suggest that specific environmental and genetic filters associated with each species have shaped the bacterial communities, potentially reflecting deterministic assemblages of bacteria. We defined the core microbiota common to both Chondrostoma species for each tissue, highlighting the occurrence of microbe-host genome interactions at this critical level for studies of the functional consequences of hybridization. Further investigations will explore to what extend these specific tissue-associated microbiota signatures could be profoundly altered in hybrids, with functional consequences for post-mating reproductive isolation in relation to environmental constraints.
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Affiliation(s)
- Emmanuel Guivier
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France.
| | | | - Nicolas Pech
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
| | - Arnaud Ungaro
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
| | - Rémi Chappaz
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
| | - André Gilles
- IMBE, Aix Marseille Université, CNRS, IRD, Avignon Université, Centre Saint-Charles, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
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475
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 516] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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476
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Wei N, Ashman TL. The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ. Sci Rep 2018; 8:5195. [PMID: 29581521 PMCID: PMC5979953 DOI: 10.1038/s41598-018-23518-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/14/2018] [Indexed: 01/18/2023] Open
Abstract
Plant-associated microbiomes profoundly influence host interactions with below- and aboveground environments. Characterizing plant-associated microbiomes in experimental settings have revealed important drivers of microbiota assemblies within host species. However, it remains unclear how important these individual drivers (e.g., organ type, host species, host sexual phenotype) are in structuring the patterns of plant-microbiota association in the wild. Using 16s rRNA sequencing, we characterized root, leaf and flower microbiomes in three closely related, sexually polymorphic Fragaria species, in the broadly sympatric portion of their native ranges in Oregon, USA. Taking into account the potential influence of broad-scale abiotic environments, we found that organ type explained the largest variation of compositional and phylogenetic α- and β-diversity of bacterial communities in these wild populations, and its overall effect exceeded that of host species and host sex. Yet, the influence of host species increased from root to leaf to flower microbiomes. We detected strong sexual dimorphism in flower and leaf microbiomes, especially in host species with the most complete separation of sexes. Our results provide the first demonstration of enhanced influence of host species and sexual dimorphism from root to flower microbiomes, which may be applicable to many other plants in the wild.
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Affiliation(s)
- Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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477
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Callens M, Watanabe H, Kato Y, Miura J, Decaestecker E. Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. MICROBIOME 2018; 6:56. [PMID: 29566771 PMCID: PMC5863831 DOI: 10.1186/s40168-018-0444-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/13/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota. RESULTS Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth. CONCLUSIONS These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.
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Affiliation(s)
- Martijn Callens
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium
- Centre d'Ecologie Fonctionelle Evolutive, CNRS Montpellier, UMR 5175, 1919 route de Mende, 34293, Montpellier CEDEX 5, France
| | - Hajime Watanabe
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Yasuhiko Kato
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Jun Miura
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Ellen Decaestecker
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium.
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478
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Young E, Carey M, Meharg AA, Meharg C. Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing. MICROBIOME 2018; 6:48. [PMID: 29554982 PMCID: PMC5859661 DOI: 10.1186/s40168-018-0434-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/05/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant species with controlled microbiota inoculation treatments, molecular plant-microbiome interactions can be functionally investigated via RNA-Seq. Complex, natural plant-microbiome studies are limited, typically focusing on microbial rRNA and omitting functional microbiome investigations, presenting a fundamental knowledge gap. Here, root and shoot meta-transcriptome analyses, in tandem with shoot elemental content and root staining, were employed to investigate transcriptome responses in the wild grass Holcus lanatus and its associated natural multi-species eukaryotic microbiome. A full factorial reciprocal soil transplant experiment was employed, using plant ecotypes from two widely contrasting natural habitats, acid bog and limestone quarry soil, to investigate naturally occurring, and ecologically meaningful, edaphically driven molecular plant-microbiome interactions. RESULTS Arbuscular mycorrhizal (AM) and non-AM fungal colonization was detected in roots in both soils. Staining showed greater levels of non-AM fungi, and transcriptomics indicated a predominance of Ascomycota-annotated genes. Roots in acid bog soil were dominated by Phialocephala-annotated transcripts, a putative growth-promoting endophyte, potentially involved in N nutrition and ion homeostasis. Limestone roots in acid bog soil had greater expression of other Ascomycete genera and Oomycetes and lower expression of Phialocephala-annotated transcripts compared to acid ecotype roots, which corresponded with reduced induction of pathogen defense processes, particularly lignin biosynthesis in limestone ecotypes. Ascomycota dominated in shoots and limestone soil roots, but Phialocephala-annotated transcripts were insignificant, and no single Ascomycete genus dominated. Fusarium-annotated transcripts were the most common genus in shoots, with Colletotrichum and Rhizophagus (AM fungi) most numerous in limestone soil roots. The latter coincided with upregulation of plant genes involved in AM symbiosis initiation and AM-based P acquisition in an environment where P availability is low. CONCLUSIONS Meta-transcriptome analyses provided novel insights into H. lanatus transcriptome responses, associated eukaryotic microbiota functions and taxonomic community composition. Significant edaphic and plant ecotype effects were identified, demonstrating that meta-transcriptome-based functional analysis is a powerful tool for the study of natural plant-microbiome interactions.
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Affiliation(s)
- Ellen Young
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Manus Carey
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Andrew A. Meharg
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Caroline Meharg
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
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479
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Sevellec M, Derome N, Bernatchez L. Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs. MICROBIOME 2018; 6:47. [PMID: 29540239 PMCID: PMC5853090 DOI: 10.1186/s40168-018-0427-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/20/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND It is well established that symbionts have considerable impact on their host, yet the investigation of the possible role of the holobiont in the host's speciation process is still in its infancy. In this study, we compared the intestinal microbiota among five sympatric pairs of dwarf (limnetic) and normal (benthic) lake whitefish Coregonus clupeaformis representing a continuum in the early stage of ecological speciation. We sequenced the 16s rRNA gene V3-V4 regions of the intestinal microbiota present in a total of 108 wild sympatric dwarf and normal whitefish as well as the water bacterial community from five lakes to (i) test for differences between the whitefish intestinal microbiota and the water bacterial community and (ii) test for parallelism in the intestinal microbiota of dwarf and normal whitefish. RESULTS The water bacterial community was distinct from the intestinal microbiota, indicating that intestinal microbiota did not reflect the environment, but rather the intrinsic properties of the host microbiota. Our results revealed a strong influence of the host (dwarf or normal) on the intestinal microbiota with pronounced conservation of the core intestinal microbiota (mean ~ 44% of shared genera). However, no clear evidence for parallelism was observed, whereby non-parallel differences between dwarf and normal whitefish were observed in three of the lakes while similar taxonomic composition was observed for the two other species pairs. CONCLUSIONS This absence of parallelism across dwarf vs. normal whitefish microbiota highlighted the complexity of the holobiont and suggests that the direction of selection could be different between the host and its microbiota.
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Affiliation(s)
- Maelle Sevellec
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, Québec G1V 0A6 Canada
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480
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Tieleman BI. Understanding immune function as a pace of life trait requires environmental context. Behav Ecol Sociobiol 2018; 72:55. [PMID: 29563662 PMCID: PMC5843675 DOI: 10.1007/s00265-018-2464-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/09/2017] [Accepted: 02/07/2018] [Indexed: 02/07/2023]
Abstract
This article provides a brief historical perspective on the integration of physiology into the concept of the pace of life of birds, evaluates the fit of immune function into this framework, and asks what it will take to fruitfully understand immune functioning of birds in pace of life studies in the future. In the late 1970s, physiology started to seriously enter avian life history ecology, with energy as the main currency of interest, inspired by David Lack's work in the preceding decades emphasizing how food availability explained life history variation. In an effort to understand the trade-off between survival and reproduction, and specifically the mortality costs associated with hard work, in the 1980s and 1990s, other physiological phenomena entered the realm of animal ecologists, including endocrinology, oxidative stress, and immunology. Reviewing studies thus far to evaluate the role of immune function in a life history context and particularly to address the questions whether immune function (1) consistently varies with life history variation among free-living bird species and (2) mediates life history trade-offs in experiments with free-living bird species; I conclude that, unlike energy metabolism, the immune system does not closely covary with life history among species nor mediates the classical trade-offs within individuals. Instead, I propose that understanding the tremendous immunological variation uncovered among free-living birds over the past 25 years requires a paradigm shift. The paradigm should shift from viewing immune function as a costly trait involved in life history trade-offs to explicitly including the benefits of the immune system and placing it firmly in an environmental and ecological context. A first step forward will be to quantify the immunobiotic pressures presented by diverse environmental circumstances that both shape and challenge the immune system of free-living animals. Current developments in the fields of infectious wildlife diseases and host-microbe interactions provide promising steps in this direction.
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Affiliation(s)
- B. Irene Tieleman
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
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481
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Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. MICROBIOME 2018; 6:46. [PMID: 29523192 PMCID: PMC5845141 DOI: 10.1186/s40168-018-0428-1] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
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Affiliation(s)
- L. Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - L. Rix
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - B. M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A. Franke
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - U. Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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482
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Abstract
For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.
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483
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A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology. mSystems 2018; 3:mSystems00146-17. [PMID: 29556549 PMCID: PMC5853186 DOI: 10.1128/msystems.00146-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change. Addressing these challenges will require the use of a variety of animal models and the development of systems approaches that can integrate large, multiomic data sets from both microbial communities and animal hosts. Integrating host-microbe interactions into the established field of comparative physiology represents an exciting frontier for both fields.
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484
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Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes. Nat Commun 2018; 9:952. [PMID: 29507332 PMCID: PMC5838112 DOI: 10.1038/s41467-018-03383-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/08/2018] [Indexed: 02/02/2023] Open
Abstract
Morphological plasticity is a genotype-by-environment interaction that enables organisms to increase fitness across varying environments. Symbioses with diverse microbiota may aid in acclimating to this variation, but whether the associated bacteria community is phenotype specific remains understudied. Here we induce morphological plasticity in three species of sea urchin larvae and measure changes in the associated bacterial community. While each host species has unique bacterial communities, the expression of plasticity results in the convergence on a phenotype-specific microbiome that is, in part, driven by differential association with α- and γ-proteobacteria. Furthermore, these results suggest that phenotype-specific signatures are the product of the environment and are correlated with ingestive and digestive structures. By manipulating diet quantity over time, we also show that differentially associating with microbiota along a phenotypic continuum is bidirectional. Taken together, our data support the idea of a phenotype-specific microbial community and that phenotypic plasticity extends beyond a genotype-by-environment interaction.
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485
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Haag KL. Holobionts and their hologenomes: Evolution with mixed modes of inheritance. Genet Mol Biol 2018; 41:189-197. [PMID: 29505062 PMCID: PMC5913720 DOI: 10.1590/1678-4685-gmb-2017-0070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and its associated microbiota constitute a biological entity called holobiont, and that regarding it as a higher-level unit of selection is unavoidable to understand phenotypic evolution. Novel extended phenotypes are often built through symbiotic interactions, allowing the holobiont to explore and survive in distinct environmental conditions, and may evolve in a Lamarckian fashion.
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Affiliation(s)
- Karen Luisa Haag
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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486
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Yergeau E, Tremblay J, Joly S, Labrecque M, Maynard C, Pitre FE, St-Arnaud M, Greer CW. Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. THE ISME JOURNAL 2018; 12:869-884. [PMID: 29330533 PMCID: PMC5864237 DOI: 10.1038/s41396-017-0018-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/10/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022]
Abstract
Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.
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Affiliation(s)
- Etienne Yergeau
- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada.
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Christine Maynard
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
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487
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Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, Adjeroud M, Bonhomme F, Pratlong M, Aurelle D, Mitta G, Toulza E. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. MICROBIOME 2018; 6:39. [PMID: 29463295 PMCID: PMC5819220 DOI: 10.1186/s40168-018-0423-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/11/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues. RESULTS We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures. CONCLUSION Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.
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Affiliation(s)
- Kelly Brener-Raffalli
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Camille Clerissi
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Jeremie Vidal-Dupiol
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Mehdi Adjeroud
- ENTROPIE, UMR 9220 & Laboratoire d’Excellence CORAIL, IRD, University of Perpignan Via Domitia, Perpignan, France
| | - François Bonhomme
- ISEM, UMR 5554, CNRS, University of Montpellier, IRD, EPHE, Sète, France
| | - Marine Pratlong
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Didier Aurelle
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Guillaume Mitta
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Eve Toulza
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
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488
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Fulthorpe R, MacIvor JS, Jia P, Yasui SLE. The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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489
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Limborg MT, Alberdi A, Kodama M, Roggenbuck M, Kristiansen K, Gilbert MTP. Applied Hologenomics: Feasibility and Potential in Aquaculture. Trends Biotechnol 2018; 36:252-264. [PMID: 29395346 DOI: 10.1016/j.tibtech.2017.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/06/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022]
Abstract
Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.
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Affiliation(s)
- Morten T Limborg
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Antton Alberdi
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Miyako Kodama
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | | | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Institute of Metagenomics, BGI-Shenzhen, Shenzhen 518120, China
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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490
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Lo WS, Huang YY, Kuo CH. Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiol Rev 2018; 40:855-874. [PMID: 28204477 PMCID: PMC5091035 DOI: 10.1093/femsre/fuw028] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2016] [Accepted: 07/10/2016] [Indexed: 02/07/2023] Open
Abstract
Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect–bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer. This review synthesizes the recent progress in genome characterization of insect-symbiotic bacteria, the emphases include (i) patterns of genome organization, (ii) evolutionary models and trajectories, and (iii) comparisons between facultative and obligate symbionts.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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491
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Wiley NC, Dinan TG, Ross RP, Stanton C, Clarke G, Cryan JF. The microbiota-gut-brain axis as a key regulator of neural function and the stress response: Implications for human and animal health. J Anim Sci 2018; 95:3225-3246. [PMID: 28727115 DOI: 10.2527/jas.2016.1256] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The brain-gut-microbiota axis comprises an extensive communication network between the brain, the gut, and the microbiota residing there. Development of a diverse gut microbiota is vital for multiple features of behavior and physiology, as well as many fundamental aspects of brain structure and function. Appropriate early-life assembly of the gut microbiota is also believed to play a role in subsequent emotional and cognitive development. If the composition, diversity, or assembly of the gut microbiota is impaired, this impairment can have a negative impact on host health and lead to disorders such as obesity, diabetes, inflammatory diseases, and even potentially neuropsychiatric illnesses, including anxiety and depression. Therefore, much research effort in recent years has focused on understanding the potential of targeting the intestinal microbiota to prevent and treat such disorders. This review aims to explore the influence of the gut microbiota on host neural function and behavior, particularly those of relevance to stress-related disorders. The involvement of microbiota in diverse neural functions such as myelination, microglia function, neuronal morphology, and blood-brain barrier integrity across the life span, from early life to adolescence to old age, will also be discussed. Nurturing an optimal gut microbiome may also prove beneficial in animal science as a means to manage stressful situations and to increase productivity of farm animals. The implications of these observations are manifold, and researchers are hopeful that this promising body of preclinical work can be successfully translated to the clinic and beyond.
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492
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Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis. PLoS One 2018; 13:e0190352. [PMID: 29293631 PMCID: PMC5749803 DOI: 10.1371/journal.pone.0190352] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022] Open
Abstract
Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings.
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493
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Brunetti AE, Carnevale Neto F, Vera MC, Taboada C, Pavarini DP, Bauermeister A, Lopes NP. An integrative omics perspective for the analysis of chemical signals in ecological interactions. Chem Soc Rev 2018; 47:1574-1591. [DOI: 10.1039/c7cs00368d] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals.
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Affiliation(s)
- A. E. Brunetti
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - F. Carnevale Neto
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - M. C. Vera
- Instituto de Herpetología
- Unidad Ejecutora Lillo
- CONICET
- Tucumán
- Argentina
| | - C. Taboada
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - D. P. Pavarini
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - A. Bauermeister
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - N. P. Lopes
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
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494
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Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle. Animal 2018; 12:s336-s349. [DOI: 10.1017/s1751731118002276] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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495
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Pérez-Brocal V, Moya A. The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain). PLoS One 2018; 13:e0191867. [PMID: 29420668 PMCID: PMC5805259 DOI: 10.1371/journal.pone.0191867] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/13/2018] [Indexed: 02/07/2023] Open
Abstract
We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families Siphoviridae and Myoviridae, and Streptococcus phages, as well as the eukaryotic viral family Herpesviridae amongst the most widespread viruses. No significant differences were found between females and males for either viruses and bacteria in abundance and alpha and beta diversity. The virome show similarities with other oral viromes previously reported for healthy individuals, suggesting the existence of a universal core of oral viruses, at least in the Western society, regardless of the geographical location.
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Affiliation(s)
- Vicente Pérez-Brocal
- Genomics and Health, FISABIO-Public Health, Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail:
| | - Andrés Moya
- Genomics and Health, FISABIO-Public Health, Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Integrative Systems Biology Institute (I2Sysbio) University of Valencia and Spanish Research Council (CSIC), Valencia, Spain
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496
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Gorkiewicz G, Moschen A. Gut microbiome: a new player in gastrointestinal disease. Virchows Arch 2018; 472:159-172. [PMID: 29243124 PMCID: PMC5849673 DOI: 10.1007/s00428-017-2277-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023]
Abstract
The gastrointestinal (GI) tract harbors a diverse and host-specific gut microbial community. Whereas host-microbe interactions are based on homeostasis and mutualism, the microbiome also contributes to disease development. In this review, we summarize recent findings connecting the GI microbiome with GI disease. Starting with a description of biochemical factors shaping microbial compositions in each gut segment along the longitudinal axis, improved histological techniques enabling high resolution visualization of the spatial microbiome structure are highlighted. Subsequently, inflammatory and neoplastic diseases of the esophagus, stomach, and small and large intestines are discussed and the respective changes in microbiome compositions summarized. Finally, approaches aiming to restore disturbed microbiome compositions thereby promoting health are discussed.
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Affiliation(s)
- Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Alexander Moschen
- Christian Doppler Laboratory for Mucosal Immunology & Division of Internal Medicine I, Department of Medicine, Medical University Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria
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497
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Kohl KD, Dearing MD, Bordenstein SR. Microbial communities exhibit host species distinguishability and phylosymbiosis along the length of the gastrointestinal tract. Mol Ecol 2017; 27:1874-1883. [PMID: 29230893 DOI: 10.1111/mec.14460] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
Abstract
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates, it has only been investigated using samples from faeces or the distal colon. Here, we collected the contents of five gut regions from seven rodent species and inventoried the bacterial communities by sequencing the 16S rRNA gene. We investigated how community structures varied across gut regions and whether the pattern of phylosymbiosis was present along the length of the gut. Gut communities varied by host species and gut region, with Oscillospira and Ruminococcus being more abundant in the stomach and hindgut regions. Gut microbial communities were highly distinguishable by host species across all gut regions, with the strength of the discrimination increasing along the length of the gut. Last, the pattern of phylosymbiosis was found in all five gut regions, as well as faeces. Aspects of the gut environment, such as oxygen levels, production of antimicrobials or other factors, may shift microbial communities across gut regions. However, regardless of these differences, host species maintain distinguishable, phylosymbiotic assemblages of microbes that may have functional impacts for the host.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
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498
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Abstract
The trillions of microbes living in the gut—the gut microbiota—play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity’s near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human–microbiome interactions.
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Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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499
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Gerardo N, Hurst G. Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes. BMC Biol 2017; 15:126. [PMID: 29282064 PMCID: PMC5744397 DOI: 10.1186/s12915-017-0455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).
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Affiliation(s)
- Nicole Gerardo
- Department of Biology, Emory University, 1510 Clifton RD, Atlanta, Georgia, 30322, USA.
| | - Gregory Hurst
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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500
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Colla G, Hoagland L, Ruzzi M, Cardarelli M, Bonini P, Canaguier R, Rouphael Y. Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome. FRONTIERS IN PLANT SCIENCE 2017; 8:2202. [PMID: 29312427 PMCID: PMC5744479 DOI: 10.3389/fpls.2017.02202] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/14/2017] [Indexed: 05/18/2023]
Abstract
Plant-derived protein hydrolysates (PHs) have gained prominence as plant biostimulants because of their potential to increase the germination, productivity and quality of a wide range of horticultural and agronomic crops. Application of PHs can also alleviate the negative effects of abiotic plant stress due to salinity, drought and heavy metals. Recent studies aimed at uncovering the mechanisms regulating these beneficial effects indicate that PHs could be directly affecting plants by stimulating carbon and nitrogen metabolism, and interfering with hormonal activity. Indirect effects could also play a role as PHs could enhance nutrient availability in plant growth substrates, and increase nutrient uptake and nutrient-use efficiency in plants. Moreover, the beneficial effects of PHs also could be due to the stimulation of plant microbiomes. Plants are colonized by an abundant and diverse assortment of microbial taxa that can help plants acquire nutrients and water and withstand biotic and abiotic stress. The substrates provided by PHs, such as amino acids, could provide an ideal food source for these plant-associated microbes. Indeed, recent studies have provided evidence that plant microbiomes are modified by the application of PHs, supporting the hypothesis that PHs might be acting, at least in part, via changes in the composition and activity of these microbial communities. Application of PHs has great potential to meet the twin challenges of a feeding a growing population while minimizing agriculture's impact on human health and the environment. However, to fully realize the potential of PHs, further studies are required to shed light on the mechanisms conferring the beneficial effects of these products, as well as identify product formulations and application methods that optimize benefits under a range of agro-ecological conditions.
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Affiliation(s)
- Giuseppe Colla
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Mariateresa Cardarelli
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca Orticoltura e Florovivaismo, Pontecagnano, Italy
| | | | | | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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