351
|
Wang D, Wei C. Bacterial communities in digestive and excretory organs of cicadas. Arch Microbiol 2019; 202:539-553. [PMID: 31720723 DOI: 10.1007/s00203-019-01763-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/13/2019] [Accepted: 10/31/2019] [Indexed: 01/29/2023]
Abstract
Bacteriocyte-associated symbionts are essential for the health of many sap-sucking insects, such as cicadas, leafhoppers and treehoppers, etc., but little is known about the bacterial community in the gut and other related organs in these insects. We characterized the bacterial communities in the salivary glands, alimentary canal and the Malpighian tubules of two populations of the cicada Subpsaltria yangi occurring in different habitats and feeding on different hosts. A high degree of similarity of core microbiota was revealed between the two populations, both with the top three bacteria belonging to Meiothermus, Candidatus Sulcia and Halomonas. The bacterial communities in various organs clustered moderately by populations possibly reflect adaptive changes in the microbiota of related S. yangi populations, which provide a better understanding of the speciation and adaptive mechanism of this species to different diets and habitats. When compared with two phylogenetically distant cicada species, Hyalessa maculaticollis and Meimuna mongolica, the core microbiota in S. yangi was significantly different to that of these species. In addition, our results confirm that Ca. Sulcia distributes in the digestive and excretory organs besides the bacteriomes and gonads, which provide potential important information onto the trophic functions of this obligate endosymbiont to the host insects.
Collapse
Affiliation(s)
- Dandan Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
352
|
Weishaar R, Wellmann R, Camarinha-Silva A, Rodehutscord M, Bennewitz J. Selecting the hologenome to breed for an improved feed efficiency in pigs-A novel selection index. J Anim Breed Genet 2019; 137:14-22. [PMID: 31701578 DOI: 10.1111/jbg.12447] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/28/2019] [Accepted: 09/20/2019] [Indexed: 01/14/2023]
Abstract
Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect m i of the microbiota composition on the breeding value g i of an animal i is the conditional expectation of its breeding value, given the vector φ i with microbiota frequencies, that is m i = E g i | φ i . The breeding value g i of an animal can therefore be decomposed into a heritable contribution m i that arises from an altered microbiota composition and a heritable contribution p i that arises from altered metabolic pathways within the animal, so g i = m i + p i . Instead of selecting for breeding value g ^ i , an index comprising the two components m ^ i and p ^ i with appropriate weights, that is I i = λ 1 m ^ i + λ 2 p ^ i , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.
Collapse
Affiliation(s)
- Ramona Weishaar
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Robin Wellmann
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | | | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
353
|
Dmitrieva AS, Ivnitsky SB, Maksimova IA, Panchenko PL, Kachalkin AV, Markov AV. Yeasts affect tolerance of Drosophila melanogaster to food substrate with high NaCl concentration. PLoS One 2019; 14:e0224811. [PMID: 31693706 PMCID: PMC6834263 DOI: 10.1371/journal.pone.0224811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/22/2019] [Indexed: 11/21/2022] Open
Abstract
The ability of model animal species, such as Drosophila melanogaster, to adapt quickly to various adverse conditions has been shown in many experimental evolution studies. It is usually assumed by default that such adaptation is due to changes in the gene pool of the studied population of macroorganisms. At the same time, it is known that microbiome can influence biological processes in macroorganisms. In order to assess the possible impact of microbiome on adaptation, we performed an evolutionary experiment in which some D. melanogaster lines were reared on a food substrate with high NaCl concentration while the others were reared on the standard (favourable) substrate. We evaluated the reproductive efficiency of experimental lines on the high salt substrate three years after the experiment started. Our tests confirmed that the lines reared on the salty substrate became more tolerant to high NaCl concentration. Moreover, we found that pre-inoculation of the high salt medium with homogenized salt-tolerant flies tended to improve reproductive efficiency of naïve flies on this medium (compared to pre-inoculation with homogenized control flies). The analysis of yeast microbiome in fly homogenates revealed significant differences in number and species richness of yeasts between salt-tolerant and control lines. We also found that some individual yeast lines extracted from the salt-tolerant flies improved reproductive efficiency of naïve flies on salty substrate (compared to baker's yeast and no yeast controls), whereas the effect of the yeast lines extracted from the control flies tended to be smaller. The yeast Starmerella bacillaris extracted from the salt-tolerant flies showed the strongest positive effect. This yeast is abundant in all salt-tolerant lines, and very rare or absent in all control lines. The results are consistent with the hypothesis that some components of the yeast microbiome of D. melanogaster contribute to to flies' tolerance to food substrate with high NaCl concentration.
Collapse
Affiliation(s)
- A. S. Dmitrieva
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - S. B. Ivnitsky
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I. A. Maksimova
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia
| | - P. L. Panchenko
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A. V. Kachalkin
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - A. V. Markov
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
354
|
Jørgensen PS, Folke C, Carroll SP. Evolution in the Anthropocene: Informing Governance and Policy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024621] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.
Collapse
Affiliation(s)
- Peter Søgaard Jørgensen
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
| | - Carl Folke
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
- Beijer Institute of Ecological Economics, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden
| | - Scott P. Carroll
- Institute for Contemporary Evolution, Davis, California 95616, USA
- Department of Entomology and Nematology, University of California, Davis, California 95616, USA
| |
Collapse
|
355
|
Sbihi H, Boutin RCT, Cutler C, Suen M, Finlay BB, Turvey SE. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 2019; 74:2103-2115. [PMID: 30964945 DOI: 10.1111/all.13812] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/27/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
Abstract
Imbalance, or dysbiosis, of the gut microbiome of infants has been linked to an increased risk of asthma and allergic diseases. Most studies to date have provided a wealth of data showing correlations between early-life risk factors for disease and changes in the structure of the gut microbiome that disrupt normal immunoregulation. These studies have typically focused on one specific risk factor, such as mode of delivery or early-life antibiotic use. Such "micro-level" exposures have a considerable impact on affected individuals but not necessarily the whole population. In this review, we place these mechanisms under a larger lens that takes into account the influence of upstream "macro-level" environmental factors such as air pollution and the built environment. While these exposures likely have a smaller impact on the microbiome at an individual level, their ubiquitous nature confers them with a large influence at the population level. We focus on features of the indoor and outdoor human-made environment, their microbiomes and the research challenges inherent in integrating the built environment microbiomes with the early-life gut microbiome. We argue that an exposome perspective integrating internal and external microbiomes with macro-level environmental factors can provide a more comprehensive framework to define how environmental exposures can shape the gut microbiome and influence the development of allergic disease.
Collapse
Affiliation(s)
- Hind Sbihi
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Rozlyn CT. Boutin
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Chelsea Cutler
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Mandy Suen
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - B. Brett Finlay
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Stuart E. Turvey
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| |
Collapse
|
356
|
Sherwin E, Bordenstein SR, Quinn JL, Dinan TG, Cryan JF. Microbiota and the social brain. Science 2019; 366:366/6465/eaar2016. [DOI: 10.1126/science.aar2016] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sociability can facilitate mutually beneficial outcomes such as division of labor, cooperative care, and increased immunity, but sociability can also promote negative outcomes, including aggression and coercion. Accumulating evidence suggests that symbiotic microorganisms, specifically the microbiota that reside within the gastrointestinal system, may influence neurodevelopment and programming of social behaviors across diverse animal species. This relationship between host and microbes hints that host-microbiota interactions may have influenced the evolution of social behaviors. Indeed, the gastrointestinal microbiota is used by certain species as a means to facilitate communication among conspecifics. Further understanding of how microbiota influence the brain in nature may be helpful for elucidating the causal mechanisms underlying sociability and for generating new therapeutic strategies for social disorders in humans, such as autism spectrum disorders (ASDs).
Collapse
Affiliation(s)
- Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN, USA
| | - John L. Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioral Sciences, University College Cork, Cork, Ireland
| | - John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| |
Collapse
|
357
|
Quigley KM, Alvarez Roa C, Torda G, Bourne DG, Willis BL. Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. Microbiologyopen 2019; 9:e959. [PMID: 31670480 PMCID: PMC7002099 DOI: 10.1002/mbo3.959] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 02/04/2023] Open
Abstract
Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.
Collapse
Affiliation(s)
- Kate M Quigley
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Greg Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| |
Collapse
|
358
|
Dheilly NM, Martínez Martínez J, Rosario K, Brindley PJ, Fichorova RN, Kaye JZ, Kohl KD, Knoll LJ, Lukeš J, Perkins SL, Poulin R, Schriml L, Thompson LR. Parasite microbiome project: Grand challenges. PLoS Pathog 2019; 15:e1008028. [PMID: 31600339 PMCID: PMC6786532 DOI: 10.1371/journal.ppat.1008028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail: (NMD); (JMM)
| | - Joaquín Martínez Martínez
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
- * E-mail: (NMD); (JMM)
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, Florida, United States of America
| | - Paul J. Brindley
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States of America
| | - Raina N. Fichorova
- Genital Tract Biology Division, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan Z. Kaye
- Gordon and Betty Moore Foundation, Palo Alto, California, United States of America
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Laura J. Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Susan L. Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Lynn Schriml
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Luke R. Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, California, United States of America
| |
Collapse
|
359
|
van Vliet S, Doebeli M. The role of multilevel selection in host microbiome evolution. Proc Natl Acad Sci U S A 2019; 116:20591-20597. [PMID: 31548380 PMCID: PMC6789794 DOI: 10.1073/pnas.1909790116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.
Collapse
Affiliation(s)
- Simon van Vliet
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| |
Collapse
|
360
|
Amato KR, Mallott EK, McDonald D, Dominy NJ, Goldberg T, Lambert JE, Swedell L, Metcalf JL, Gomez A, Britton GAO, Stumpf RM, Leigh SR, Knight R. Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome Biol 2019; 20:201. [PMID: 31590679 PMCID: PMC6781418 DOI: 10.1186/s13059-019-1807-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/29/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates. RESULTS Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. CONCLUSIONS Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.
Collapse
Affiliation(s)
- Katherine R. Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208 USA
| | - Elizabeth K. Mallott
- Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL 60208 USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, 92093 USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 USA
| | | | - Tony Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 USA
| | - Joanna E. Lambert
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, 80302 USA
| | - Larissa Swedell
- Department of Anthropology, City University of New York - Queens College, New York, 11367 USA
| | - Jessica L. Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, 80521 USA
| | - Andres Gomez
- Department of Animal Sciences, University of Minnesota, Minneapolis, 55108 USA
| | | | - Rebecca M. Stumpf
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, 61801 USA
| | - Steven R. Leigh
- Department of Anthropology, University of Colorado Boulder, Boulder, 80302 USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, 92093 USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, 92093 USA
- Department of Bioengineering, University of California San Diego, San Diego, 92093 USA
| |
Collapse
|
361
|
Inda ME, Broset E, Lu TK, de la Fuente-Nunez C. Emerging Frontiers in Microbiome Engineering. Trends Immunol 2019; 40:952-973. [PMID: 31601521 DOI: 10.1016/j.it.2019.08.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/15/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023]
Abstract
The gut microbiome has a significant impact on health and disease and can actively contribute to obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disorders. We do not yet have the necessary tools to fine-tune the microbial communities that constitute the microbiome, though such tools could unlock extensive benefits to human health. Here, we provide an overview of the current state of technological tools that may be used for microbiome engineering. These tools can enable investigators to define the parameters of a healthy microbiome and to determine how gut bacteria may contribute to the etiology of a variety of diseases. These tools may also allow us to explore the exciting prospect of developing targeted therapies and personalized treatments for microbiome-linked diseases.
Collapse
Affiliation(s)
- María Eugenia Inda
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Esther Broset
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, 50009, Spain
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
362
|
Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
Collapse
Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
| |
Collapse
|
363
|
Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O'Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsimons SE, Hyland N, Clarke G, Dinan TG. The Microbiota-Gut-Brain Axis. Physiol Rev 2019; 99:1877-2013. [DOI: 10.1152/physrev.00018.2018] [Citation(s) in RCA: 1243] [Impact Index Per Article: 248.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-related, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been paramount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.
Collapse
Affiliation(s)
- John F. Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kenneth J. O'Riordan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitlin S. M. Cowan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kiran V. Sandhu
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Thomaz F. S. Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcus Boehme
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Martin G. Codagnone
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Sofia Cussotto
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Christine Fulling
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Anna V. Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Katherine E. Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Minal Jaggar
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Caitriona M. Long-Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joshua M. Lyte
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Jason A. Martin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Alicia Molinero-Perez
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emanuela Morelli
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Enrique Morillas
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Rory O'Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Joana S. Cruz-Pereira
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Veronica L. Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Kieran Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Eoin Sherwin
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Emily M. Teichman
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Ana Paula Ventura-Silva
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Shauna E. Wallace-Fitzsimons
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Niall Hyland
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland
| |
Collapse
|
364
|
Abstract
Microbial communities associated with animals exert powerful influences on host physiology, regulating metabolism and immune function, as well as complex host behaviors. The importance of host–microbiome interactions for maintaining homeostasis and promoting health raises evolutionarily complicated questions about how animals and their microbiomes have coevolved, and how these relationships affect the ways that animals interact with their environment. Here, we review the literature on the contributions of host factors to microbial community structure and corresponding influences of microbiomes on emergent host phenotypes. We focus in particular on animal behaviors as a basis for understanding potential roles for the microbiome in shaping host neurobiology.
Collapse
|
365
|
Reen FJ, McGlacken GP, O'Gara F. The expanding horizon of alkyl quinolone signalling and communication in polycellular interactomes. FEMS Microbiol Lett 2019; 365:4953739. [PMID: 29718276 DOI: 10.1093/femsle/fny076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/25/2018] [Indexed: 02/07/2023] Open
Abstract
Population dynamics within natural ecosystems is underpinned by microbial diversity and the heterogeneity of host-microbe and microbe-microbe interactions. Small molecule signals that intersperse between species have been shown to govern many virulence-related processes in established and emerging pathogens. Understanding the capacity of microbes to decode diverse languages and adapt to the presence of 'non-self' cells will provide an important new direction to the understanding of the 'polycellular' interactome. Alkyl quinolones (AQs) have been described in the ESKAPE pathogen Pseudomonas aeruginosa, the primary agent associated with mortality in patients with cystic fibrosis and the third most prevalent nosocomial pathogen worldwide. The role of these molecules in governing the physiology and virulence of P. aeruginosa and other pathogens has received considerable attention, while a role in interspecies and interkingdom communication has recently emerged. Herein we discuss recent advances in our understanding of AQ signalling and communication in the context of microbe-microbe and microbe-host interactions. The integrated knowledge from these systems-based investigations will facilitate the development of new therapeutics based on the AQ framework that serves to disarm the pathogenesis of P. aeruginosa and competing pathogens.
Collapse
Affiliation(s)
- F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gerard P McGlacken
- School of Chemistry and Analytical & Biological Chemistry Research Facility (ABCRF), University College Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, USA
| |
Collapse
|
366
|
González-Pech RA, Bhattacharya D, Ragan MA, Chan CX. Genome Evolution of Coral Reef Symbionts as Intracellular Residents. Trends Ecol Evol 2019; 34:799-806. [DOI: 10.1016/j.tree.2019.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023]
|
367
|
Weisskopf L, Newton ILG, Berry D, Webster NS. Spotlight on how microbes influence their host's behavior. Environ Microbiol 2019; 21:3185-3187. [PMID: 31342631 DOI: 10.1111/1462-2920.14757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - David Berry
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
| |
Collapse
|
368
|
Paix B, Othmani A, Debroas D, Culioli G, Briand JF. Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria. Environ Microbiol 2019; 21:3346-3363. [PMID: 30945796 DOI: 10.1111/1462-2920.14617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/31/2019] [Indexed: 11/30/2022]
Abstract
An integrative multi-omics approach allowed monthly variations for a year of the surface metabolome and the epibacterial community of the Mediterranean Phaeophyceae Taonia atomaria to be investigated. The LC-MS-based metabolomics and 16S rDNA metabarcoding data sets were integrated in a multivariate meta-omics analysis (multi-block PLS-DA from the MixOmic DIABLO analysis) showing a strong seasonal covariation (Mantel test: p < 0.01). A network based on positive and negative correlations between the two data sets revealed two clusters of variables, one relative to the 'spring period' and a second to the 'summer period'. The 'spring period' cluster was mainly characterized by dipeptides positively correlated with a single bacterial taxon of the Alteromonadaceae family (BD1-7 clade). Moreover, 'summer' dominant epibacterial taxa from the second cluster (including Erythrobacteraceae, Rhodospirillaceae, Oceanospirillaceae and Flammeovirgaceae) showed positive correlations with few metabolites known as macroalgal antifouling defences [e.g. dimethylsulphoniopropionate (DMSP) and proline] which exhibited a key role within the correlation network. Despite a core community that represents a significant part of the total epibacteria, changes in the microbiota structure associated with surface metabolome variations suggested that both environment and algal host shape the bacterial surface microbiota.
Collapse
Affiliation(s)
- Benoît Paix
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Ahlem Othmani
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, UMR 6023, Clermont-Ferrand, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | | |
Collapse
|
369
|
Arias-Sánchez FI, Vessman B, Mitri S. Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? PLoS Biol 2019; 17:e3000356. [PMID: 31469824 PMCID: PMC6716632 DOI: 10.1371/journal.pbio.3000356] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment.
Collapse
Affiliation(s)
- Flor I Arias-Sánchez
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Björn Vessman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
370
|
Koch EJ, McFall-Ngai M. Model systems for the study of how symbiotic associations between animals and extracellular bacterial partners are established and maintained. DRUG DISCOVERY TODAY. DISEASE MODELS 2019; 28:3-12. [PMID: 32855643 PMCID: PMC7449258 DOI: 10.1016/j.ddmod.2019.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This contribution describes the current state of experimental model development and use as a strategy for gaining insight into the form and function of certain types of host-microbe associations. Development of quality models for the study of symbiotic systems will be critical not only to facilitate an understanding of mechanisms underlying symbiosis, but also for providing insights into how drug development can promote healthy animal-microbe interactions as well as the treatment of pathogenic infections. Because of the growing awareness over the last decade of the importance of symbiosis in biology, a number of model systems has emerged to examine how these partnerships are maintained within and across generations of the host. The focus here will be upon host-bacterial symbiotic systems that, as in humans, (i) are acquired from the environment each generation, or horizontally transmitted, and (ii) are defined by interactions at the interface of their cellular boundaries, i.e., extracellular symbiotic associations. As with the use of models in other fields of biology where complexity is daunting (e.g., developmental biology or brain circuitry), each model has its strengths and weaknesses, i.e., no one model system will provide easy access to all the questions defining what is conserved in cell-cell interactions in symbiosis and what creates diversity within such partnerships. Rather, as discussed here, the more models explored, the richer our understanding of these associations is likely to be.
Collapse
Affiliation(s)
- Eric J. Koch
- Kewalo Marine Laboratory, University of Hawaiʻi at Mānoa, 41 Ahui Street, Honolulu, Hawaii 96813 USA
| | - Margaret McFall-Ngai
- Kewalo Marine Laboratory, University of Hawaiʻi at Mānoa, 41 Ahui Street, Honolulu, Hawaii 96813 USA
| |
Collapse
|
371
|
Perez‐Lamarque B, Morlon H. Characterizing symbiont inheritance during host–microbiota evolution: Application to the great apes gut microbiota. Mol Ecol Resour 2019; 19:1659-1671. [DOI: 10.1111/1755-0998.13063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Benoît Perez‐Lamarque
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM PSL University Paris France
- Muséum national d'Histoire naturelleUMR 7205 CNRS‐MNHN‐UPMC‐EPHE “Institut de Systématique, Evolution, Biodiversité – ISYEB” Herbier National 16 rue Buffon Paris France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM PSL University Paris France
| |
Collapse
|
372
|
Boem F, Amedei A. Healthy axis: Towards an integrated view of the gut-brain health. World J Gastroenterol 2019; 25:3838-3841. [PMID: 31413521 PMCID: PMC6689813 DOI: 10.3748/wjg.v25.i29.3838] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/14/2019] [Accepted: 06/23/2019] [Indexed: 02/06/2023] Open
Abstract
Despite the lack of precise mechanisms of action, a growing number of studies suggests that gut microbiota is involved in a great number of physiological functions of the human organism. In fact, the composition and the relations of intestinal microbial populations play a role, either directly or indirectly, to both the onset and development of various pathologies. In particular, the gastrointestinal tract and nervous system are closely connected by the so-called gut–brain axis, a complex bidirectional system in which the central and enteric nervous system interact with each other, also engaging endocrine, immune and neuronal circuits. This allows us to put forward new working hypotheses on the origin of some multifactorial diseases: from eating to neuropsychiatric disorders (such as autism spectrum disorders and depression) up to diabetes and tumors (such as colorectal cancer). This scenario reinforces the idea that the microbiota and its composition represent a factor, which is no longer negligible, not only in preserving what we call “health” but also in defining and thus determining it. Therefore, we propose to consider the gut-brain axis as the focus of new scientific and clinical investigation as long as the locus of possible systemic therapeutic interventions.
Collapse
Affiliation(s)
- Federico Boem
- Department of Oncology and Hemato-Oncology, University of Milan, Milano 20122, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50134, Italy
- Department of Biomedicine, Azienda Ospedaliera Universitaria Careggi, Firenze 50134, Italy
| |
Collapse
|
373
|
Ye S, Badhiwala KN, Robinson JT, Cho WH, Siemann E. Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts. THE ISME JOURNAL 2019; 13:2058-2067. [PMID: 31015561 PMCID: PMC6775974 DOI: 10.1038/s41396-019-0413-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/16/2019] [Accepted: 03/15/2019] [Indexed: 11/08/2022]
Abstract
Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.
Collapse
Affiliation(s)
- Siao Ye
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
| | | | - Jacob T Robinson
- Bioengineering Department, Rice University, Houston, TX, 77005, USA
- Electrical and Computer Engineering Department, Rice University, Houston, TX, 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Won Hee Cho
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - Evan Siemann
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| |
Collapse
|
374
|
Carrier TJ, Dupont S, Reitzel AM. Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins. FEMS Microbiol Ecol 2019; 95:5526217. [PMID: 31260050 DOI: 10.1093/femsec/fiz103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/27/2019] [Indexed: 12/17/2022] Open
Abstract
Determining the factors underlying the assembly, structure, and diversity of symbiont communities remains a focal point of animal-microbiome research. Much of these efforts focus on taxonomic variation of microbiota within or between animal populations, but rarely test the proportional impacts of ecological components that may affect animal-associated microbiota. Using larvae from the sea urchin Strongylocentrotus droebachiensis from the Atlantic and Pacific Oceans, we test the hypothesis that, under natural conditions, inter-population differences in the composition of larval-associated bacterial communities are larger than intra-population variation due to a heterogeneous feeding environment. Despite significant differences in bacterial community structure within each S. droebachiensis larval population based on food availability, development, phenotype, and time, variation in OTU membership and community composition correlated more strongly with geographic location. Moreover, 20-30% of OTUs associated with larvae were specific to a single location while less than 10% were shared. Taken together, these results suggest that inter-populational variation in symbiont communities may be more pronounced than intra-populational variation, and that this difference may suggest that broad-scale ecological variables (e.g., across ocean basins) may mask smaller scale ecological variables (e.g., food availability).
Collapse
Affiliation(s)
- Tyler J Carrier
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, The Sven Lovén Centre for Marine Infrastructure, Kristineberg, 45178 Sweden
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| |
Collapse
|
375
|
Leeks A, Dos Santos M, West SA. Transmission, relatedness, and the evolution of cooperative symbionts. J Evol Biol 2019; 32:1036-1045. [PMID: 31271473 PMCID: PMC6852075 DOI: 10.1111/jeb.13505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/15/2019] [Accepted: 06/24/2019] [Indexed: 11/29/2022]
Abstract
Cooperative interactions between species, termed mutualisms, play a key role in shaping natural ecosystems, economically important agricultural systems, and in influencing human health. Across different mutualisms, there is significant variation in the benefit that hosts receive from their symbionts. Empirical data suggest that transmission mode can help explain this variation: vertical transmission, where symbionts infect their host's offspring, leads to symbionts that provide greater benefits to their hosts than horizontal transmission, where symbionts leave their host and infect other hosts in the population. However, two different theoretical explanations have been given for this pattern: firstly, vertical transmission aligns the fitness interests of hosts and their symbionts; secondly, vertical transmission leads to increased relatedness between symbionts sharing a host, favouring cooperation between symbionts. We used a combination of analytical models and dynamic simulations to tease these factors apart, in order to compare their separate influences and see how they interact. We found that relatedness between symbionts sharing a host, rather than transmission mode per se, was the most important factor driving symbiont cooperation. Transmission mode mattered mainly because it determined relatedness. We also found evolutionary branching throughout much of our simulation, suggesting that a combination of transmission mode and multiplicity of infections could lead to the stable coexistence of different symbiont strategies.
Collapse
Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, UK
| | - Miguel Dos Santos
- Department of Social Psychology and Social Neuroscience, University of Bern, Bern, UK
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, UK
| |
Collapse
|
376
|
Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
Collapse
Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
| | | |
Collapse
|
377
|
Sinnesael A, Leroux O, Janssens SB, Smets E, Panis B, Verstraete B. Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant. PLoS One 2019; 14:e0219863. [PMID: 31310638 PMCID: PMC6634412 DOI: 10.1371/journal.pone.0219863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND & AIMS The bacterial leaf nodule symbiosis is an interaction where bacteria are housed in specialised structures in the leaves of their plant host. In the Rubiaceae plant family, host plants interact with Burkholderia bacteria. This interaction might play a role in the host plant defence system. It is unique due to its high specificity; the vertical transmission of the endophyte to the next generation of the host plant; and its supposedly obligatory character. Although previous attempts have been made to investigate this obligatory character by developing Burkholderia-free plants, none have succeeded and nodulating plants were still produced. In order to investigate the obligatory character of this endosymbiosis, our aims were to develop Burkholderia-free Psychotria umbellata plants and to investigate the effect of the absence of the endophytes on the host in a controlled environment. METHODS The Burkholderia-free plants were obtained via embryo culture, a plant cultivation technique. In order to analyse the endophyte-free status, we screened the plants morphologically, microscopically and molecularly over a period of three years. To characterise the phenotype and growth of the in vitro aposymbiotic plants, we compared the growth of the Burkholderia-free plants to the nodulating plants under the same in vitro conditions. KEY RESULTS All the developed plants were Burkholderia-free and survived in a sterile in vitro environment. The growth analysis showed that plants without endophytes had a slower development. CONCLUSIONS Embryo culture is a cultivation technique with a high success rate for the development of Burkholderia-free plants of P. umbellata. The increased growth rate in vitro when the specific endophyte is present cannot be explained by possible benefits put forward in previous studies. This might indicate that the benefits of the endosymbiosis are not yet completely understood.
Collapse
Affiliation(s)
- Arne Sinnesael
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | | | - Steven B. Janssens
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Bart Panis
- Bioversity International, Leuven, Belgium
| | | |
Collapse
|
378
|
Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nat Ecol Evol 2019; 3:1172-1183. [PMID: 31285574 DOI: 10.1038/s41559-019-0935-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/29/2019] [Indexed: 01/18/2023]
Abstract
Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model was a better fit to larval (R2 = 0.66) than to the adult microbiota (R2 = 0.27), suggesting that the importance of non-neutral processes increases as the sponge host matures. Microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent shared only 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.
Collapse
|
379
|
Metabolism, bioenergetics and thermal physiology: influences of the human intestinal microbiota. Nutr Res Rev 2019; 32:205-217. [PMID: 31258100 DOI: 10.1017/s0954422419000076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, 'Are intestinal microbiota effects measurable and meaningful?' and 'What research methods and variables are influenced by intestinal microbiota effects?'. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.
Collapse
|
380
|
The Macroalgal Holobiont in a Changing Sea. Trends Microbiol 2019; 27:635-650. [DOI: 10.1016/j.tim.2019.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
|
381
|
Morar N, Bohannan BJM. The Conceptual Ecology of the Human Microbiome. QUARTERLY REVIEW OF BIOLOGY 2019. [DOI: 10.1086/703582] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
382
|
Wong JWH, Plett JM. Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:597-612. [PMID: 31029179 DOI: 10.1071/fp18200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
A major goal in agricultural research is to develop 'elite' crops with stronger, resilient root systems. Within this context, breeding practices have focussed on developing plant varieties that are, primarily, able to withstand pathogen attack and, secondarily, able to maximise plant productivity. Although great strides towards breeding disease-tolerant or -resistant root stocks have been made, this has come at a cost. Emerging studies in certain crop species suggest that domestication of crops, together with soil management practices aimed at improving plant yield, may hinder beneficial soil microbial association or reduce microbial diversity in soil. To achieve more sustainable management of agricultural lands, we must not only shift our soil management practices but also our breeding strategy to include contributions from beneficial microbes. For this latter point, we need to advance our understanding of how plants communicate with, and are able to differentiate between, microbes of different lifestyles. Here, we present a review of the key findings on belowground plant-microbial interactions that have been made over the past decade, with a specific focus on how plants and microbes communicate. We also discuss the currently unresolved questions in this area, and propose plausible ways to use currently available research and integrate fast-emerging '-omics' technologies to tackle these questions. Combining past and developing research will enable the development of new crop varieties that will have new, value-added phenotypes belowground.
Collapse
Affiliation(s)
- Johanna W-H Wong
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; and Corresponding author.
| |
Collapse
|
383
|
Microbiota: Overview and Implication in Immunotherapy-Based Cancer Treatments. Int J Mol Sci 2019; 20:ijms20112699. [PMID: 31159348 PMCID: PMC6600175 DOI: 10.3390/ijms20112699] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/17/2019] [Accepted: 05/26/2019] [Indexed: 12/12/2022] Open
Abstract
During the last few years, the gut microbiota has gained increasing attention as a consequence of its emerging role as a modulator of the immune system. With the advent of the era of checkpoint inhibitors immunotherapy and adoptive cell transfer (ACT) in oncology, these findings became of primary relevance in light of experimental data that suggested the microbiota involvement as a plausible predictor of a good or poor response. These remarks justify the efforts to pinpoint the specific actions of the microbiota and to identify new strategies to favorably edit its composition.
Collapse
|
384
|
Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle. Genet Sel Evol 2019; 51:23. [PMID: 31142263 PMCID: PMC6542034 DOI: 10.1186/s12711-019-0464-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/14/2019] [Indexed: 12/15/2022] Open
Abstract
Background Fatty acids (FA) in bovine milk derive through body mobilization, de novo synthesis or from the feed via the blood stream. To be able to digest feedstuff, the cow depends on its rumen microbiome. The relative abundance of the microbes has been shown to differ between cows. To date, there is little information on the impact of the microbiome on the formation of specific milk FA. Therefore, in this study, our aim was to investigate the impact of the rumen bacterial microbiome on milk FA composition. Furthermore, we evaluated the predictive value of the rumen microbiome and the host genetics on the composition of individual FA in milk. Results Our results show that the proportion of variance explained by the rumen bacteria composition (termed microbiability or \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{B}^{2}$$\end{document}hB2) was generally smaller than that of the genetic component (heritability), and that rumen bacteria influenced most C15:0, C17:0, C18:2 n-6, C18:3 n-3 and CLA cis-9, trans-11 with estimated \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{B}^{2}$$\end{document}hB2 ranging from 0.26 to 0.42. For C6:0, C8:0, C10:0, C12:0, C16:0, C16:1 cis-9 and C18:1 cis-9, the variance explained by the rumen bacteria component was close to 0. In general, both the rumen microbiome and the host genetics had little value for predicting FA phenotype. Compared to genetic information only, adding rumen bacteria information resulted in a significant improvement of the predictive value for C15:0 from 0.22 to 0.38 (P = 9.50e−07) and C18:3 n-3 from 0 to 0.29 (P = 8.81e−18). Conclusions The rumen microbiome has a pronounced influence on the content of odd chain FA and polyunsaturated C18 FA, and to a lesser extent, on the content of the short- and medium-chain FA in the milk of Holstein cattle. The accuracy of prediction of FA phenotypes in milk based on information from either the animal’s genotypes or rumen bacteria composition was very low. Electronic supplementary material The online version of this article (10.1186/s12711-019-0464-8) contains supplementary material, which is available to authorized users.
Collapse
|
385
|
Qian X, Li H, Wang Y, Wu B, Wu M, Chen L, Li X, Zhang Y, Wang X, Shi M, Zheng Y, Guo L, Zhang D. Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere. Front Microbiol 2019; 10:1015. [PMID: 31143169 PMCID: PMC6521803 DOI: 10.3389/fmicb.2019.01015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/24/2019] [Indexed: 12/21/2022] Open
Abstract
Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.
Collapse
Affiliation(s)
- Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hanzhou Li
- Biomarker Technologies Corporation, Beijing, China
| | - Yonglong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Binwei Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingsong Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingchun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangping Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Zheng
- Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
386
|
|
387
|
The Costs of Living Together: Immune Responses to the Microbiota and Chronic Gut Inflammation. Appl Environ Microbiol 2019; 85:AEM.02147-18. [PMID: 30530709 DOI: 10.1128/aem.02147-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While the vertebrate microbiota is critical to the normal function of many host traits, hosts may expend a large amount of energy to constrain and interface with their microbiota via their immune system to avoid the high fitness costs associated with gut dysbiosis, pathobionts, and opportunistic pathogens. All jawed vertebrates share mucosal immunity dedicated to isolating the microbiota, and a breakdown of this system can result in chronic gut inflammation. In humans, chronic gut inflammation negatively affects growth and development. There is little information available on the prevalence of chronic gut inflammation in wild animals, but given that animals with different life histories emphasize different immune responses, it follows that wild animals may vary in their susceptibility to chronic gut inflammation, and most animals will experience signaling that can lead to this state. These can be top-down signals originating from sources like the central nervous system or bottom-up signals originating from changes in the gut microbiota. The sources of these signals might include stress, developmental transitions, food restriction, and dietary shifts. Here, we briefly discuss host-microbiota interactions from the perspective of life history theory and ecoimmunology, focusing on the mucosal immune system and chronic gut inflammation. We also include future directions for research and the tools necessary to investigate them.
Collapse
|
388
|
Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
Collapse
|
389
|
Greene LK, Bornbusch SL, McKenney EA, Harris RL, Gorvetzian SR, Yoder AD, Drea CM. The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs. Am J Primatol 2019; 81:e22974. [PMID: 30932230 DOI: 10.1002/ajp.22974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022]
Abstract
Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host-microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage-specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent-gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host-microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis-driven research.
Collapse
Affiliation(s)
- Lydia K Greene
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Sally L Bornbusch
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Rachel L Harris
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Sarah R Gorvetzian
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, North Carolina
| | - Christine M Drea
- Duke University Program in Ecology, Duke University, Durham, North Carolina.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.,Department of Biology, Duke University, Durham, North Carolina
| |
Collapse
|
390
|
Stock SP. Partners in crime: symbiont-assisted resource acquisition in Steinernema entomopathogenic nematodes. CURRENT OPINION IN INSECT SCIENCE 2019; 32:22-27. [PMID: 31113627 DOI: 10.1016/j.cois.2018.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 06/09/2023]
Abstract
Entomopathogenic nematodes in the genus Steinernema (Nematoda: Steinernematidae) have a mutualistic relationship with Xenorhabdus bacteria (Gram-negative Enterobacteriaceae). This partnership however, is pathogenic to a wide range of insect species. Because of their potent insecticidal ability, they have successfully been implemented in biological control and integrated pest management programs worldwide. Steinernema-Xenorhabdus-insect partnerships are extremely diverse and represent a model system in ecology and evolution to investigate symbioses between invertebrates and microbes. The reproductive fitness of the nematode-bacterium partnership is tightly associated, and maintenance of their virulence is critical to the conversion of the insect host as a suitable environment where this partnership can be perpetuated.
Collapse
|
391
|
Ding J, Zhu D, Li H, Ding K, Chen QL, Lassen SB, Ke X, O'Connor P, Zhu YG. The gut microbiota of soil organisms show species-specific responses to liming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:715-723. [PMID: 31096401 DOI: 10.1016/j.scitotenv.2018.12.445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Liming is a common agronomic practice used for alleviating soil acidification to improve plant growth. However, it is still unclear how liming can affect the gut microbiota composition of soil fauna, and subsequently the nutrient cycling and litter decomposition mediated by soil fauna. In the present study the effect of liming on the gut microbiota of two types of soil fauna, Folsomia candida, and Enchytraeus crypticus was investigated by using 16S rRNA gene high-throughput sequencing. The results revealed that there are differences between the gut microbial communities of the two types of soil fauna as well as between the gut microbiome of the soil fauna and the surrounding soil. Enterobacteriaceae and Bacillaceae were the predominant families in the gut microbiota of E. crypticus, while Rickettsiaceae and Moraxellaceae were the predominant families in the gut microbiota of F. candida. Liming affected the gut microbiota of E. crypticus at both the taxonomical and core microbiota level. The gut microbiota of F. candida was not affected by liming. Structural equation models suggest that 97% of the variation in the E. crypticus gut microbiota could be explained by liming-induced changes in soil properties and the soil microbial community. The indirect effects of liming, caused by a shift in the soil microbial community, contributed more in reshaping the gut microbiota of E. crypticus than the direct effects of the changed soil properties did. These findings suggest that the effects of liming on the gut microbiota composition in soil fauna are species-specific and are likely dependent on the response of the host to changes in soil properties and the soil microbial community.
Collapse
Affiliation(s)
- Jing Ding
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Simon Bo Lassen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Xin Ke
- Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| |
Collapse
|
392
|
Smith LK, Wissel EF. Microbes and the Mind: How Bacteria Shape Affect, Neurological Processes, Cognition, Social Relationships, Development, and Pathology. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2019; 14:397-418. [DOI: 10.1177/1745691618809379] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent data suggest that the human body is not so exclusively human after all. Specifically, humans share their bodies with approximately 10 trillion microorganisms, collectively known as the microbiome. Chief among these microbes are bacteria, and there is a growing consensus that they are critical to virtually all facets of normative functioning. This article reviews the ways in which bacteria shape affect, neurological processes, cognition, social relationships, development, and psychological pathology. To date, the vast majority of research on interactions between microbes and humans has been conducted by scientists outside the field of psychology, despite the fact that psychological scientists are experts in many of the topics being explored. This review aims to orient psychological scientists to the most relevant research and perspectives regarding the microbiome so that we might contribute to the now widespread, interdisciplinary effort to understand the relationship between microbes and the mind.
Collapse
Affiliation(s)
- Leigh K. Smith
- Department of Psychology, University of California, Davis
| | | |
Collapse
|
393
|
Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci 2019; 1447:21-52. [DOI: 10.1111/nyas.14044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular BiologyUniversity of Chicago Chicago Illinois
| |
Collapse
|
394
|
Clarke G, Sandhu KV, Griffin BT, Dinan TG, Cryan JF, Hyland NP. Gut Reactions: Breaking Down Xenobiotic–Microbiome Interactions. Pharmacol Rev 2019; 71:198-224. [DOI: 10.1124/pr.118.015768] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
395
|
Abstract
The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all plants). The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all plants). Because of this heritability, and potentially reciprocal exchange of microbes between generations of ramets, we propose to extend the existing holobiont framework to the concept of meta-holobiont. A meta-holobiont is a network of holobionts that can exchange biomolecules and microbiota across generations, thus impacting the fitness of both biological scales: holobionts and meta-holobionts. Specifically, meta-holobiont dynamics can result in sharing, specialization, and division of labor across plant clonal generations. This paper, which coins the meta-holobiont concept, is expected to stimulate discussion and to be applied beyond the context of networked clonal plants (e.g., to social insects).
Collapse
|
396
|
O'Connor KM, Lucking EF, Golubeva AV, Strain CR, Fouhy F, Cenit MC, Dhaliwal P, Bastiaanssen TFS, Burns DP, Stanton C, Clarke G, Cryan JF, O'Halloran KD. Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats. EBioMedicine 2019; 44:618-638. [PMID: 30898652 PMCID: PMC6606895 DOI: 10.1016/j.ebiom.2019.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease. METHODS In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats. FINDINGS Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbiota transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbiota transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla. INTERPRETATION Chronic antibiotic administration and faecal microbiota transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress. FUND: Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland.
Collapse
Affiliation(s)
- Karen M O'Connor
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eric F Lucking
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Anna V Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Conall R Strain
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Fiona Fouhy
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - María C Cenit
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; Institute of Agrochemistry and Food Technology (IATA), National Council for Scientific Research (CSIC), Valencia, Spain
| | - Pardeep Dhaliwal
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David P Burns
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - John F Cryan
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken D O'Halloran
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
| |
Collapse
|
397
|
Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. ZOOLOGY 2019; 133:81-87. [PMID: 30979392 DOI: 10.1016/j.zool.2019.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023]
Abstract
Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.
Collapse
Affiliation(s)
- Cornelia Jaspers
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany; National Institute of Aquatic Resources, Technical University of Denmark, DTU Aqua, Kemitorvet, Building 202, 2800 Kgs. Lyngby, Denmark
| | - Sebastian Fraune
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - A Elizabeth Arnold
- School of Plant Sciences and the Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85719, USA
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Thomas C G Bosch
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
398
|
Nakatsuji T, Gallo RL. The role of the skin microbiome in atopic dermatitis. Ann Allergy Asthma Immunol 2019; 122:263-269. [PMID: 30550810 PMCID: PMC7147826 DOI: 10.1016/j.anai.2018.12.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, California
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, California.
| |
Collapse
|
399
|
Dominguez Bello MG. Effects of C-section on the human microbiota. Am J Hum Biol 2019; 31:e23196. [PMID: 30585360 DOI: 10.1002/ajhb.23196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/29/2018] [Accepted: 10/02/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- M G Dominguez Bello
- Department of Biochemistry and Miocrobiology, Rutgers University, New Brunswick, New Jersey.,Department of Anthropology, Rutgers University, New Brunswick, New Jersey
| |
Collapse
|
400
|
Gibson JD. The Voices Missing from the Autonomy Discourse (Are Also the Most Indispensable). INTERNATIONAL JOURNAL OF FEMINIST APPROACHES TO BIOETHICS 2019. [DOI: 10.3138/ijfab.12.1.05] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Jonathan Beever and Nicolae Morar’s (2016) article “The Porosity of Autonomy: Social and Biological Constitution of the Patient in Biomedicine” and its accompanying commentaries in the American Journal of Bioethics—though insightful, innovative, and provocative—overlook key interlocutors necessary for any discussion of whether the mid-twentieth-century biomedical principle of autonomy should be revised or revoked. The conversation sparked by “The Porosity of Autonomy” will remain both incomplete and politically untenable so long as there is no meaningful engagement with persons/communities who appeal to the principle of patient autonomy in order to articulate and challenge the conditions of their oppression.
Collapse
|