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Krueger Q, Phippen B, Reitzel A. Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis. PeerJ 2024; 12:e17349. [PMID: 38784394 PMCID: PMC11114123 DOI: 10.7717/peerj.17349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Background Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis. Methods Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL-1, and in combination at 50 µg mL-1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones. Results Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments. Discussion Antibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.
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Affiliation(s)
- Quinton Krueger
- Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Center, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Britney Phippen
- Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Adam Reitzel
- Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Center, University of North Carolina at Charlotte, Charlotte, NC, United States of America
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2
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Zimmermann J, Piecyk A, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H. Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life. mBio 2024; 15:e0001224. [PMID: 38634692 PMCID: PMC11077962 DOI: 10.1128/mbio.00012-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function. IMPORTANCE The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Agnes Piecyk
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Michael Sieber
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Julia Johnke
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lucas Moitinho-Silva
- />Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Lena Bluhm
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Arne Traulsen
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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3
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Singh A, Luallen RJ. Understanding the factors regulating host-microbiome interactions using Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230059. [PMID: 38497260 PMCID: PMC10945399 DOI: 10.1098/rstb.2023.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Anupama Singh
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Robert J. Luallen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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4
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Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
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5
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Pees B, Peters L, Treitz C, Hamerich IK, Kissoyan KAB, Tholey A, Dierking K. The Caenorhabditis elegans proteome response to two protective Pseudomonas symbionts. mBio 2024; 15:e0346323. [PMID: 38411078 PMCID: PMC11005407 DOI: 10.1128/mbio.03463-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The Caenorhabditis elegans natural microbiota isolates Pseudomonas lurida MYb11 and Pseudomonas fluorescens MYb115 protect the host against pathogens through distinct mechanisms. While P. lurida produces an antimicrobial compound and directly inhibits pathogen growth, P. fluorescens MYb115 protects the host without affecting pathogen growth. It is unknown how these two protective microbes affect host biological processes. We used a proteomics approach to elucidate the C. elegans response to MYb11 and MYb115. We found that both Pseudomonas isolates increase vitellogenin protein production in young adults, which confirms previous findings on the effect of microbiota on C. elegans reproductive timing. Moreover, the C. elegans responses to MYb11 and MYb115 exhibit common signatures with the response to other vitamin B12-producing bacteria, emphasizing the importance of vitamin B12 in C. elegans-microbe metabolic interactions. We further analyzed signatures in the C. elegans response specific to MYb11 or MYb115. We provide evidence for distinct modifications in lipid metabolism by both symbiotic microbes. We could identify the activation of host-pathogen defense responses as an MYb11-specific proteome signature and provide evidence that the intermediate filament protein IFB-2 is required for MYb115-mediated protection. These results indicate that MYb11 not only produces an antimicrobial compound but also activates host antimicrobial defenses, which together might increase resistance to infection. In contrast, MYb115 affects host processes such as lipid metabolism and cytoskeleton dynamics, which might increase host tolerance to infection. Overall, this study pinpoints proteins of interest that form the basis for additional exploration into the mechanisms underlying C. elegans microbiota-mediated protection from pathogen infection and other microbiota-mediated traits.IMPORTANCESymbiotic bacteria can defend their host against pathogen infection. While some protective symbionts directly interact with pathogenic bacteria, other protective symbionts elicit a response in the host that improves its own pathogen defenses. To better understand how a host responds to protective symbionts, we examined which host proteins are affected by two protective Pseudomonas bacteria in the model nematode Caenorhabditis elegans. We found that the C. elegans response to its protective symbionts is manifold, which was reflected in changes in proteins that are involved in metabolism, the immune system, and cell structure. This study provides a foundation for exploring the contribution of the host response to symbiont-mediated protection from pathogen infection.
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Affiliation(s)
- Barbara Pees
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Lena Peters
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Inga K. Hamerich
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Kohar A. B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
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6
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Choi R, Bodkhe R, Pees B, Kim D, Berg M, Monnin D, Cho J, Narayan V, Deller E, Savage-Dunn C, Shapira M. An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome. AGING BIOLOGY 2024; 2:20240024. [PMID: 38736850 PMCID: PMC11085993 DOI: 10.59368/agingbio.20240024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
The gut microbiome plays important roles in host function and health. Core microbiomes have been described for different species, and imbalances in their composition, known as dysbiosis, are associated with pathology. Changes in the gut microbiome and dysbiosis are common in aging, possibly due to multi-tissue deterioration, which includes metabolic shifts, dysregulated immunity, and disrupted epithelial barriers. However, the characteristics of these changes, as reported in different studies, are varied and sometimes conflicting. Using clonal populations of Caenorhabditis elegans to highlight trends shared among individuals, we employed 16s rRNA gene sequencing, CFU counts and fluorescent imaging, identifying an Enterobacteriaceae bloom as a common denominator in aging animals. Experiments using Enterobacter hormaechei, a representative commensal, suggested that the Enterobacteriaceae bloom was facilitated by a decline in Sma/BMP immune signaling in aging animals and demonstrated its potential for exacerbating infection susceptibility. However, such detrimental effects were context-dependent, mitigated by competition with commensal communities, highlighting the latter as determinants of healthy versus unhealthy aging, depending on their ability to restrain opportunistic pathobionts.
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Affiliation(s)
- Rebecca Choi
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rahul Bodkhe
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Barbara Pees
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dan Kim
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maureen Berg
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David Monnin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Juhyun Cho
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vivek Narayan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ethan Deller
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing NY, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
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7
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Miller BC, Mathai M, Yadav H, Jain S. Geroprotective potential of microbiome modulators in the Caenorhabditis elegans model. GeroScience 2024; 46:129-151. [PMID: 37561384 PMCID: PMC10828408 DOI: 10.1007/s11357-023-00901-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aging is associated with cellular and physiological changes, which significantly reduce the quality of life and increase the risk for disease. Geroprotectors improve lifespan and slow the progression of detrimental aging-related changes such as immune system senescence, mitochondrial dysfunction, and dysregulated nutrient sensing and metabolism. Emerging evidence suggests that gut microbiota dysbiosis is a hallmark of aging-related diseases and microbiome modulators, such as probiotics (live bacteria) or postbiotics (non-viable bacteria/bacterial byproducts) may be promising geroprotectors. However, because they are strain-specific, the geroprotective effects of probiotics and postbiotics remain poorly understood and understudied. Drosophila melanogaster, Caenorhabditis elegans, and rodents are well-validated preclinical models for studying lifespan and the role of probiotics and/or postbiotics, but each have their limitations, including cost and their translation to human aging biology. C. elegans is an excellent model for large-scale screening to determine the geroprotective potential of drugs or probiotics/postbiotics due to its short lifecycle, easy maintenance, low cost, and homology to humans. The purpose of this article is to review the geroprotective effects of microbiome modulators and their future scope, using C. elegans as a model. The proposed geroprotective mechanisms of these probiotics and postbiotics include delaying immune system senescence, preventing or reducing mitochondrial dysfunction, and regulating food intake (dietary restriction) and metabolism. More studies are warranted to understand the geroprotective potential of probiotics and postbiotics, as well as other microbiome modulators, like prebiotics and fermented foods, and use them to develop effective therapeutics to extend lifespan and reduce the risk of debilitating aging-related diseases.
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Affiliation(s)
- Brandi C Miller
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, 12901 Bruce B Downs Blvd, MDC 78, Tampa, FL, 33612, USA
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Megha Mathai
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, 12901 Bruce B Downs Blvd, MDC 78, Tampa, FL, 33612, USA
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Hariom Yadav
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, 12901 Bruce B Downs Blvd, MDC 78, Tampa, FL, 33612, USA
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Shalini Jain
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, 12901 Bruce B Downs Blvd, MDC 78, Tampa, FL, 33612, USA.
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA.
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8
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Chai VZ, Farajzadeh T, Meng Y, Lo SB, Asaed TA, Taylor CJ, Glater EE. Chemical basis of microbiome preference in the nematode C. elegans. Sci Rep 2024; 14:1350. [PMID: 38228683 PMCID: PMC10791660 DOI: 10.1038/s41598-024-51533-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Animals are exposed to many microbes in their environment, some of which have been shown to colonize various tissues including the intestine. The composition of the intestinal microbiota affects many aspects of the host's physiology and health. Despite this, very little is known about whether host behavior contributes to the colonization. We approach this question in the nematode C. elegans, which feeds on bacteria and also harbors an intestinal microbiome. We examined the behavior of C. elegans towards CeMbio, a simplified microbiome consisting of twelve strains that represent the bacteria found in the animal's natural environment. We observed that C. elegans raised on E. coli shows a strong preference for three members of CeMbio (Lelliottia amnigena JUb66, Enterobacter hormaechei CEent1, and Pantoea nemavictus BIGb0393) compared to E. coli. Previously, these three bacterial strains have been shown to support faster C. elegans development time than E. coli OP50 and are low colonizers compared to eight other members of CeMbio. We then used gas chromatography coupled to mass spectrometry to identify that these three bacteria release isoamyl alcohol, a previously described C. elegans chemoattractant. We suggest that C. elegans seeks bacteria that release isoamyl alcohol and support faster growth.
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Affiliation(s)
- Victor Z Chai
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | | | - Yufei Meng
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | - Sokhna B Lo
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | - Tymmaa A Asaed
- Department of Neuroscience, Pomona College, Claremont, CA, USA
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9
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Choi R, Bodkhe R, Pees B, Kim D, Berg M, Monnin D, Cho J, Narayan V, Deller E, Shapira M. An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544815. [PMID: 37398063 PMCID: PMC10312681 DOI: 10.1101/2023.06.13.544815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The gut microbiome plays important roles in host function and health. Core microbiomes have been described for different species, and imbalances in their composition, known as dysbiosis, are associated with pathology. Changes in the gut microbiome and dysbiosis are common in aging, possibly due to multi-tissue deterioration, which includes metabolic shifts, dysregulated immunity, and disrupted epithelial barriers. However, the characteristics of these changes, as reported in different studies, are varied and sometimes conflicting. Using clonal populations of C. elegans to highlight trends shared among individuals, and employing NextGen sequencing, CFU counts and fluorescent imaging to characterize age-dependent changes in worms raised in different microbial environments, we identified an Enterobacteriaceae bloom as a common denominator in aging animals. Experiments using Enterobacter hormachei, a representative commensal, suggested that the Enterobacteriaceae bloom was facilitated by a decline in Sma/BMP immune signaling in aging animals and demonstrated its detrimental potential for increasing susceptibility to infection. However, such detrimental effects were context-dependent, mitigated by competition with commensal communities, highlighting the latter as determinants of healthy versus unhealthy aging, depending on their ability to restrain opportunistic pathobionts.
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Affiliation(s)
- Rebecca Choi
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rahul Bodkhe
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Barbara Pees
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dan Kim
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maureen Berg
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David Monnin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Juhyun Cho
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vivek Narayan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ethan Deller
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
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10
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Staab TA, McIntyre G, Wang L, Radeny J, Bettcher L, Guillen M, Peck MP, Kalil AP, Bromley SP, Raftery D, Chan JP. The lipidomes of C. elegans with mutations in asm-3/acid sphingomyelinase and hyl-2/ceramide synthase show distinct lipid profiles during aging. Aging (Albany NY) 2023; 15:650-674. [PMID: 36787434 PMCID: PMC9970312 DOI: 10.18632/aging.204515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023]
Abstract
Lipid metabolism affects cell and physiological functions that mediate animal healthspan and lifespan. Lipidomics approaches in model organisms have allowed us to better understand changes in lipid composition related to age and lifespan. Here, using the model C. elegans, we examine the lipidomes of mutants lacking enzymes critical for sphingolipid metabolism; specifically, we examine acid sphingomyelinase (asm-3), which breaks down sphingomyelin to ceramide, and ceramide synthase (hyl-2), which synthesizes ceramide from sphingosine. Worm asm-3 and hyl-2 mutants have been previously found to be long- and short-lived, respectively. We analyzed longitudinal lipid changes in wild type animals compared to mutants at 1-, 5-, and 10-days of age. We detected over 700 different lipids in several lipid classes. Results indicate that wildtype animals exhibit increased triacylglycerols (TAG) at 10-days compared to 1-day, and decreased lysophoshatidylcholines (LPC). We find that 10-day hyl-2 mutants have elevated total polyunsaturated fatty acids (PUFA) and increased LPCs compared to 10-day wildtype animals. These changes mirror another short-lived model, the daf-16/FOXO transcription factor that is downstream of the insulin-like signaling pathway. In addition, we find that hyl-2 mutants have poor oxidative stress response, supporting a model where mutants with elevated PUFAs may accumulate more oxidative damage. On the other hand, 10-day asm-3 mutants have fewer TAGs. Intriguingly, asm-3 mutants have a similar lipid composition as the long-lived, caloric restriction model eat-2/mAChR mutant. Together, these analyses highlight the utility of lipidomic analyses to characterize metabolic changes during aging in C. elegans.
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Affiliation(s)
- Trisha A. Staab
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Grace McIntyre
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joycelyn Radeny
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | - Lisa Bettcher
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98195, USA
| | - Melissa Guillen
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Margaret P. Peck
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | - Azia P. Kalil
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | | | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98195, USA
| | - Jason P. Chan
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
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Parr McQueen J, Gattoni K, Gendron E, Schmidt S, Sommers P, Porazinska DL. External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment. J Nematol 2023; 55:20230004. [PMID: 36969543 PMCID: PMC10035304 DOI: 10.2478/jofnem-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 03/11/2023] Open
Abstract
Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.
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Affiliation(s)
- J. Parr McQueen
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - K. Gattoni
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - E.M.S. Gendron
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - S.K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - P. Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - D. L. Porazinska
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
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12
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McQueen JP, Gattoni K, Gendron EMS, Schmidt SK, Sommers P, Porazinska DL. Host identity is the dominant factor in the assembly of nematode and tardigrade gut microbiomes in Antarctic Dry Valley streams. Sci Rep 2022; 12:20118. [PMID: 36446870 PMCID: PMC9709161 DOI: 10.1038/s41598-022-24206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Recent work examining nematode and tardigrade gut microbiomes has identified species-specific relationships between host and gut community composition. However, only a handful of species from either phylum have been examined. How microbiomes differ among species and what factors contribute to their assembly remains unexplored. Cyanobacterial mats within Antarctic Dry Valley streams host a simple and tractable natural ecosystem of identifiable microinvertebrates to address these questions. We sampled 2 types of coexisting mats (i.e., black and orange) across four spatially isolated streams, hand-picked single individuals of two nematode species (i.e., Eudorylaimus antarcticus and Plectus murrayi) and tardigrades, to examine their gut microbiomes using 16S and 18S rRNA metabarcoding. All gut microbiomes (bacterial and eukaryotic) were significantly less diverse than the mats they were isolated from. In contrast to mats, microinvertebrates' guts were depleted of Cyanobacteria and differentially enriched in taxa of Bacteroidetes, Proteobacteria, and Fungi. Among factors investigated, gut microbiome composition was most influenced by host identity while environmental factors (e.g., mats and streams) were less important. The importance of host identity in predicting gut microbiome composition suggests functional value to the host, similar to other organisms with strong host selected microbiomes.
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Affiliation(s)
- J. Parr McQueen
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Kaitlin Gattoni
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Eli M. S. Gendron
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Steven K. Schmidt
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Pacifica Sommers
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Dorota L. Porazinska
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
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13
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Zhu X, Teng J, Xu EG, Zhao J, Shan E, Sun C, Wang Q. Toxicokinetics and toxicodynamics of plastic and metallic nanoparticles: A comparative study in shrimp. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120069. [PMID: 36064064 DOI: 10.1016/j.envpol.2022.120069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/13/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Nanoplastic is recognized as an emerging environmental pollutant due to the anticipated ubiquitous distribution, increasing concentration in the ocean, and potential adverse health effects. While our understanding of the ecological impacts of nanoplastics is still limited, we benefit from relatively rich toxicological studies on other nanoparticles such as nano metal oxides. However, the similarity and difference in the toxicokinetic and toxicodynamic aspects of plastic and metallic nanoparticles remain largely unknown. In this study, juvenile Pacific white shrimp Litopenaeus vannamei was exposed to two types of nanoparticles at environmentally relative low and high concentrations, i.e., 100 nm polystyrene nanoplastics (nano-PS) and titanium dioxide nanoparticles (nano-TiO2) via dietary exposure for 28 days. The systematic toxicological evaluation aimed to quantitatively compare the accumulation, excretion, and toxic effects of nano-PS and nano-TiO2. Our results demonstrated that both nanoparticles were ingested by L. vannamei with lower egestion of nano-TiO2 than nano-PS. Both nanoparticles inhibited the growth of shrimps, damaged tissue structures of the intestine and hepatopancreas, disrupted expression of immune-related genes, and induced intestinal microbiota dysbiosis. Nano-PS exposure caused proliferative cells in the intestinal tissue, and the disturbance to the intestinal microbes was also more serious than that of nano-TiO2. The results indicated that the effect of nano-PS on the intestinal tissue of L. vannamei was more severe than that of nano-TiO2 with the same particle size. The study provides new theoretical basis of the similarity and differences of their toxicity, and highlights the current lack of knowledge on various aspects of absorption, distribution, metabolism, and excretion (ADME) pathways of nanoplastics.
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Affiliation(s)
- Xiaopeng Zhu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jia Teng
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Elvis Genbo Xu
- Department of Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Jianmin Zhao
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Encui Shan
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chaofan Sun
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Qing Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
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14
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Krueger QA, Shore MH, Reitzel AM. Comparative transmission of bacteria from Artemia salina and Brachionus plicatilis to the cnidarian Nematostella vectensis. FEMS Microbiol Ecol 2022; 98:fiac096. [PMID: 36036952 PMCID: PMC9521339 DOI: 10.1093/femsec/fiac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 12/14/2022] Open
Abstract
The microbial community associated with animals (microbiome) is essential for development, physiology, and health of host organisms. A critical step to understand the assembly of microbiomes is to determine how effectively bacteria colonize and establish within the host. Bacteria commonly colonize hosts through vertical transmission, passively from the environment, or through food consumption. Using the prey feeding method (PFM), we test transmittance of Bacillus velezensis, Pseudoalteromonas spiralis, and Vibrio alginolyticus to Nematostella vectensis using two prey, Artemia salina and Brachionus plicatilis. We compare PFM to a solution uptake method (SUM) to quantify the concentration of bacteria in these host organisms, with plate counts. Larvae had a similar uptake with SUM at 6 h but had greater concentrations at 48 h versus PFM. Juveniles acquired similar concentrations at 6 h for SUM and PFM using B. plicatilis and A. salina. At 2 days, the quantity of bacteria vectored from PFM increased. After 7 days the CFUs decreased 2-fold with B. plicatilis and A. salina relative to the 2-day concentrations, and further decreased after 14 days. Therefore, prey-mediated methods provide greater microbe transplantation than SUM after 24 h, supporting this approach as a more successful inoculation method of individual bacterial species.
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Affiliation(s)
- Quinton A Krueger
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
| | - Madisun H Shore
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
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15
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Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A, Salome Correa JA, Stevens L, Kiontke K, Blaxter M, Rockman MV. Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. Ecol Evol 2022; 12:e9124. [PMID: 35898425 PMCID: PMC9309040 DOI: 10.1002/ece3.9124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best-studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low.
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Affiliation(s)
- Solomon A. Sloat
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Luke M. Noble
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Annalise B. Paaby
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Max Bernstein
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Audrey Chang
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Taniya Kaur
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Yuen
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Sophia C. Tintori
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jacqueline L. Jackson
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Arielle Martel
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jose A. Salome Correa
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | | | - Karin Kiontke
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger InstituteHinxtonUK
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
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16
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Pérez-Carrascal OM, Choi R, Massot M, Pees B, Narayan V, Shapira M. Host Preference of Beneficial Commensals in a Microbially-Diverse Environment. Front Cell Infect Microbiol 2022; 12:795343. [PMID: 35782135 PMCID: PMC9240469 DOI: 10.3389/fcimb.2022.795343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Gut bacteria are often described by the neutral term commensals. However, the more we learn about their interactions with hosts, the more apparent it becomes that gut commensals often contribute positively to host physiology and fitness. Whether hosts can prefer beneficial bacteria, and how they do so, is not clear. This is of particular interest in the case of the bacterivore C. elegans, which depends on bacteria as food source, but also as gut colonizers that contribute to its physiology, from development to immunity. It is further unclear to what extent worms living in their microbially-diverse habitats can sense and distinguish between beneficial bacteria, food, and pathogens. Focusing on Enterobacteriaceae and members of closely related families, we isolated gut bacteria from worms raised in compost microcosms, as well as bacteria from the respective environments and evaluated their contributions to host development. Most isolates, from worms or from the surrounding environment, promoted faster development compared to the non-colonizing E. coli food strain. Pantoea strains further showed differential contributions of gut isolates versus an environmental isolate. Characterizing bacterial ability to hinder pathogenic colonization with Pseudomonas aeruginosa, supported the trend of Pantoea gut commensals being beneficial, in contrast to the environmental strain. Interestingly, worms were attracted to the beneficial Pantoea strains, preferring them over non-beneficial bacteria, including the environmental Pantoea strain. While our understanding of the mechanisms underlying these host-microbe interactions are still rudimentary, the results suggest that hosts can sense and prefer beneficial commensals.
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17
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Identification of nosZ-expressing microorganisms consuming trace N 2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales. THE ISME JOURNAL 2022; 16:2087-2098. [PMID: 35676322 PMCID: PMC9381517 DOI: 10.1038/s41396-022-01260-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022]
Abstract
Microorganisms possessing N2O reductases (NosZ) are the only known environmental sink of N2O. While oxygen inhibition of NosZ activity is widely known, environments where N2O reduction occurs are often not devoid of O2. However, little is known regarding N2O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h−1) of N2O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O2 sustained dissolved oxygen concentration above 4 µM; however, complete N2O reduction of influent N2O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N2O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N2O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N2O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.
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18
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Romeralo C, Martín-García J, Martínez-Álvarez P, Muñoz-Adalia EJ, Gonçalves DR, Torres E, Witzell J, Diez JJ. Pine species determine fungal microbiome composition in a common garden experiment. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2021.101137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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19
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Manohar P, Loh B, Elangovan N, Loganathan A, Nachimuthu R, Leptihn S. A Multiwell-Plate Caenorhabditis elegans Assay for Assessing the Therapeutic Potential of Bacteriophages against Clinical Pathogens. Microbiol Spectr 2022; 10:e0139321. [PMID: 35171008 PMCID: PMC8849058 DOI: 10.1128/spectrum.01393-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
In order to establish phage therapy as a standard clinical treatment for bacterial infections, testing of every phage to ensure the suitability and safety of the biological compound is required. While some issues have been addressed over recent years, standard and easy-to-use animal models to test phages are still rare. Testing of phages in highly suitable mammalian models such as mice is subjected to strict ethical regulations, while insect larvae such as the Galleria mellonella model suffer from batch-to-batch variations and require manual operator skills to inject bacteria, resulting in unreliable experimental outcomes. A much simpler model is the nematode Caenorhabditis elegans, which feeds on bacteria, a fast growing and easy to handle organism that can be used in high-throughput screening. In this study, two clinical bacterial strains of Escherichia coli, one Klebsiella pneumoniae, and one Enterobacter cloacae strain were tested on the model system together with lytic bacteriophages that we isolated previously. We developed a liquid-based assay, in which the efficiency of phage treatment was evaluated using a scoring system based on microscopy and counting of the nematodes, allowing increasing statistical significance compared to other assays such as larvae or mice. Our work demonstrates the potential to use Caenorhabditis elegans to test the virulence of strains of Klebsiella pneumoniae, Enterobacter cloacae, and EHEC/EPEC as well as the efficacy of bacteriophages to treat or prevent infections, allowing a more reliable evaluation for the clinical therapeutic potential of lytic phages. IMPORTANCE Validating the efficacy and safety of phages prior to clinical application is crucial to see phage therapy in practice. Current animal models include mice and insect larvae, which pose ethical or technical challenges. This study examined the use of the nematode model organism C. elegans as a quick, reliable, and simple alternative for testing phages. The data show that all the four tested bacteriophages can eliminate bacterial pathogens and protect the nematode from infections. Survival rates of the nematodes increased from <20% in the infection group to >90% in the phage treatment group. Even the nematodes with poly-microbial infections recovered during phage cocktail treatment. The use of C. elegans as a simple whole-animal infection model is a rapid and robust way to study the efficacy of phages before testing them on more complex model animals such as mice.
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Affiliation(s)
- Prasanth Manohar
- Zhejiang University-University of Edinburgh (ZJE) Institute, Zhejiang University, School of Medicine, Haining, Zhejiang, People’s Republic of China
- The Second Affiliated Hospital Zhejiang University (SAHZU), School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Belinda Loh
- Zhejiang University-University of Edinburgh (ZJE) Institute, Zhejiang University, School of Medicine, Haining, Zhejiang, People’s Republic of China
| | - Namasivayam Elangovan
- Department of Biotechnology, School of Bioscience, Periyar University, Salem, Tamil Nadu, India
| | - Archana Loganathan
- Antibiotic Resistance and Phage Therapy Lab, Department of Biomedical Science, School of Biosciences and Technology, Vellore, Tamil Nadu, India
| | - Ramesh Nachimuthu
- Antibiotic Resistance and Phage Therapy Lab, Department of Biomedical Science, School of Biosciences and Technology, Vellore, Tamil Nadu, India
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh (ZJE) Institute, Zhejiang University, School of Medicine, Haining, Zhejiang, People’s Republic of China
- Department of Infectious Diseases, Sir Run Department Shaw Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
- University of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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20
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The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution. Life (Basel) 2022; 12:life12020287. [PMID: 35207574 PMCID: PMC8879143 DOI: 10.3390/life12020287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran–Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.
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21
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Ryu EP, Davenport ER. Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle. Annu Rev Anim Biosci 2022; 10:203-226. [PMID: 35167316 PMCID: PMC11000414 DOI: 10.1146/annurev-animal-020420-032054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.
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Affiliation(s)
- Erica P Ryu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
| | - Emily R Davenport
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
- Huck Institutes of the Life Sciences and Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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22
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Kissoyan KAB, Peters L, Giez C, Michels J, Pees B, Hamerich IK, Schulenburg H, Dierking K. Exploring Effects of C. elegans Protective Natural Microbiota on Host Physiology. Front Cell Infect Microbiol 2022; 12:775728. [PMID: 35237530 PMCID: PMC8884406 DOI: 10.3389/fcimb.2022.775728] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
The Caenorhabditis elegans natural microbiota was described only recently. Thus, our understanding of its effects on nematode physiology is still in its infancy. We previously showed that the C. elegans natural microbiota isolates Pseudomonas lurida MYb11 and P. fluorescens MYb115 protect the worm against pathogens such as Bacillus thuringiensis (Bt). However, the overall effects of the protective microbiota on worm physiology are incompletely understood. Here, we investigated how MYb11 and MYb115 affect C. elegans lifespan, fertility, and intestinal colonization. We further studied the capacity of MYb11 and MYb115 to protect the worm against purified Bt toxins. We show that while MYb115 and MYb11 affect reproductive timing and increase early reproduction only MYb11 reduces worm lifespan. Moreover, MYb11 aggravates killing upon toxin exposure. We conclude that MYb11 has a pathogenic potential in some contexts. This work thus highlights that certain C. elegans microbiota members can be beneficial and costly to the host in a context-dependent manner, blurring the line between good and bad.
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Petersen C, Pees B, Martínez Christophersen C, Leippe M. Preconditioning With Natural Microbiota Strain Ochrobactrum vermis MYb71 Influences Caenorhabditis elegans Behavior. Front Cell Infect Microbiol 2021; 11:775634. [PMID: 34976859 PMCID: PMC8718863 DOI: 10.3389/fcimb.2021.775634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
In comparison with the standard monoxenic maintenance in the laboratory, rearing the nematode Caenorhabditis elegans on its natural microbiota improves its fitness and immunity against pathogens. Although C. elegans is known to exhibit choice behavior and pathogen avoidance behavior, little is known about whether C. elegans actively chooses its (beneficial) microbiota and whether the microbiota influences worm behavior. We examined eleven natural C. elegans isolates in a multiple-choice experiment for their choice behavior toward four natural microbiota bacteria and found that microbiota choice varied among C. elegans isolates. The natural C. elegans isolate MY2079 changed its choice behavior toward microbiota isolate Ochrobactrum vermis MYb71 in both multiple-choice and binary-choice experiments, in particular on proliferating bacteria: O. vermis MYb71 was chosen less than other microbiota bacteria or OP50, but only after preconditioning with MYb71. Examining escape behavior and worm fitness on MYb71, we ruled out pathogenicity of MYb71 and consequently learned pathogen avoidance behavior as the main driver of the behavioral change toward MYb71. The change in behavior of C. elegans MY2079 toward microbiota bacterium MYb71 demonstrates how the microbiota influences the worm's choice. These results might give a baseline for future research on host-microbiota interaction in the C. elegans model.
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Affiliation(s)
- Carola Petersen
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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24
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Topalović O, Vestergård M. Can microorganisms assist the survival and parasitism of plant-parasitic nematodes? Trends Parasitol 2021; 37:947-958. [PMID: 34162521 DOI: 10.1016/j.pt.2021.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022]
Abstract
Plant-parasitic nematodes (PPNs) remain a hardly treatable problem in many crops worldwide. Low efficacy of many biocontrol agents may be due to negligence of the native microbiota that is naturally associated with nematodes in soil, and which may protect nematodes against microbial antagonists. This phenomenon is more extensively studied for other nematode parasites, so we compiled these studies and drew parallels to the existing knowledge on PPN. We describe how microbial-mediated modulation of host immune responses facilitate nematode parasitism and discuss the role of Caenorhabditis elegans-protective microbiota to get an insight into the microbial protection of PPNs in soil. Molecular mechanisms of PPN-microbial interactions are also discussed. An understanding of microbial-aided PPN performance is thus pivotal for efficient management of PPNs.
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Affiliation(s)
- Olivera Topalović
- Aarhus University, Institute for Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark.
| | - Mette Vestergård
- Aarhus University, Institute for Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark.
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25
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Backes C, Martinez-Martinez D, Cabreiro F. C. elegans: A biosensor for host-microbe interactions. Lab Anim (NY) 2021; 50:127-135. [PMID: 33649581 DOI: 10.1038/s41684-021-00724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Microbes are an integral part of life on this planet. Microbes and their hosts influence each other in an endless dance that shapes how the meta-organism interacts with its environment. Although great advances have been made in microbiome research over the past 20 years, the mechanisms by which both hosts and their microbes interact with each other and the environment are still not well understood. The nematode Caenorhabditis elegans has been widely used as a model organism to study a remarkable number of human-like processes. Recent evidence shows that the worm is a powerful tool to investigate in fine detail the complexity that exists in microbe-host interactions. By combining the large array of genetic tools available for both organisms together with deep phenotyping approaches, it has been possible to uncover key effectors in the complex relationship between microbes and their hosts. In this perspective, we survey the literature for insightful discoveries in the microbiome field using the worm as a model. We discuss the latest conceptual and technological advances in the field and highlight the strengths that make C. elegans a valuable biosensor tool for the study of microbe-host interactions.
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Affiliation(s)
- Cassandra Backes
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | | | - Filipe Cabreiro
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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26
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Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model. mSystems 2021; 6:6/2/e00608-20. [PMID: 33879498 PMCID: PMC8561663 DOI: 10.1128/msystems.00608-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation—and the consequences for the ecology of these communities—remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans. Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology. IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.
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27
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Hoang KL, Gerardo NM, Morran LT. Association with a novel protective microbe facilitates host adaptation to a stressful environment. Evol Lett 2021; 5:118-129. [PMID: 33868708 PMCID: PMC8045907 DOI: 10.1002/evl3.223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 01/19/2023] Open
Abstract
Protective symbionts can allow hosts to occupy otherwise uninhabitable niches. Despite the importance of symbionts in host evolution, we know little about how these associations arise. Encountering a microbe that can improve host fitness in a stressful environment may favor persistent interactions with that microbe, potentially facilitating a long-term association. The bacterium Bacillus subtilis protects Caenorhabditis elegans nematodes from heat shock by increasing host fecundity compared to the nonprotective Escherichia coli. In this study, we ask how the protection provided by the bacterium affects the host's evolutionary trajectory. Because of the stark fitness contrast between hosts heat shocked on B. subtilis versus E. coli, we tested whether the protection conferred by the bacteria could increase the rate of host adaptation to a stressful environment. We passaged nematodes on B. subtilis or E. coli, under heat stress or standard conditions for 20 host generations of selection. When assayed under heat stress, we found that hosts exhibited the greatest fitness increase when evolved with B. subtilis under stress compared to when evolved with E. coli or under standard (nonstressful) conditions. Furthermore, despite not directly selecting for increased B. subtilis fitness, we found that hosts evolved to harbor more B. subtilis as they adapted to heat stress. Our findings demonstrate that the context under which hosts evolve is important for the evolution of beneficial associations and that protective microbes can facilitate host adaptation to stress. In turn, such host adaptation can benefit the microbe.
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Affiliation(s)
- Kim L. Hoang
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
- Department of ZoologyUniversity of OxfordOxfordOX1 3SZUnited Kingdom
| | | | - Levi T. Morran
- Department of BiologyEmory UniversityAtlantaGeorgia30322USA
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28
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Bo TB, Kohl KD. Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry. Anim Microbiome 2021; 3:26. [PMID: 33785073 PMCID: PMC8011129 DOI: 10.1186/s42523-021-00087-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.
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Affiliation(s)
- Ting-Bei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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29
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Take a Walk to the Wild Side of Caenorhabditis elegans-Pathogen Interactions. Microbiol Mol Biol Rev 2021; 85:85/2/e00146-20. [PMID: 33731489 DOI: 10.1128/mmbr.00146-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Microbiomes form intimate functional associations with their hosts. Much has been learned from correlating changes in microbiome composition to host organismal functions. However, in-depth functional studies require the manipulation of microbiome composition coupled with the precise interrogation of organismal physiology-features available in few host study systems. Caenorhabditis elegans has proven to be an excellent genetic model organism to study innate immunity and, more recently, microbiome interactions. The study of C. elegans-pathogen interactions has provided in depth understanding of innate immune pathways, many of which are conserved in other animals. However, many bacteria were chosen for these studies because of their convenience in the lab setting or their implication in human health rather than their native interactions with C. elegans In their natural environment, C. elegans feed on a variety of bacteria found in rotting organic matter, such as rotting fruits, flowers, and stems. Recent work has begun to characterize the native microbiome and has identified a common set of bacteria found in the microbiome of C. elegans While some of these bacteria are beneficial to C. elegans health, others are detrimental, leading to a complex, multifaceted understanding of bacterium-nematode interactions. Current research on nematode-bacterium interactions is focused on these native microbiome components, both their interactions with each other and with C. elegans We will summarize our knowledge of bacterial pathogen-host interactions in C. elegans, as well as recent work on the native microbiome, and explore the incorporation of these bacterium-nematode interactions into studies of innate immunity and pathogenesis.
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30
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Goodrich-Blair H. Interactions of host-associated multispecies bacterial communities. Periodontol 2000 2021; 86:14-31. [PMID: 33690897 DOI: 10.1111/prd.12360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.
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Affiliation(s)
- Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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31
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Zheng F, Zhu D, Chen QL, Bi QF, Yang XR, O'Connor P, Zhu YG. The driving factors of nematode gut microbiota under long-term fertilization. FEMS Microbiol Ecol 2020; 96:5804725. [PMID: 32166316 DOI: 10.1093/femsec/fiaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/11/2020] [Indexed: 12/19/2022] Open
Abstract
Animal bodies are colonized by many microorganisms which can provide indispensable services to their hosts. Although nematode gut microbiota has been extensively studied in recent years, the driving factors of gut microbiome of soil nematodes from a long-term fertilization field are unclear. Here, using 16S rRNA gene amplicon sequencing, we explored the nematode gut microbiota under different fertilization patterns (control, inorganic fertilizers and mixed fertilizers) and fertilization durations (5 y, 8 y and 10 y). Our results revealed that nematode gut microbiota was dominated by core bacterial taxa AF502208 (anaerobic bacteria), Enterobacter (plant litter decomposition) and Ancylobacter (organic matter decomposition and nitrogen cycling), significantly distinct from soil microbiome, and the assembly of that was a non-random process, which suggested host conditions contributed to maintaining the gut microbiota. Moreover, fertilization pattern had a greater influence on nematode gut microbiome than fertilization duration. Inorganic fertilization (5.19) significantly reduced the diversity of the nematode gut microbiota (6.68) shown by Shannon index (P < 0.05). Canonical correspondence analysis demonstrates that soil properties such as pH, organic matter, total phosphorus, available phosphorus, ammonium nitrogen, moisture content, nitrate nitrogen and total nitrogen have significant effects on the nematode microbiome. Structured equation models further revealed that fertilization could obviously affect the nematode gut microbiota, and the effects were maintained even when accounting simultaneously for the drivers of soil bacteria and soil properties. This study provides a solid evidence that the shifting of nematode gut microbiota under long-term fertilization was resulted from environmental factors and host conditions, and advance the insights into host-microbiome in the agricultural ecosystems.
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Affiliation(s)
- Fei Zheng
- 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
| | - 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
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Qing-Fang Bi
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,Collage of Environment & Resource Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide, 5005, Australia
| | - Yong-Guan 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.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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32
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Slowinski S, Ramirez I, Narayan V, Somayaji M, Para M, Pi S, Jadeja N, Karimzadegan S, Pees B, Shapira M. Interactions with a Complex Microbiota Mediate a Trade-Off between the Host Development Rate and Heat Stress Resistance. Microorganisms 2020; 8:microorganisms8111781. [PMID: 33202910 PMCID: PMC7697855 DOI: 10.3390/microorganisms8111781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022] Open
Abstract
Animals and plants host diverse communities of microorganisms, and these microbiotas have been shown to influence host life history traits. Much has been said about the benefits that host-associated microbiotas bestow on the host. However, life history traits often demonstrate tradeoffs among one another. Raising Caenorhabditis elegans nematodes in compost microcosms emulating their natural environment, we examined how complex microbiotas affect host life history traits. We show that soil microbes usually increase the host development rate but decrease host resistance to heat stress, suggesting that interactions with complex microbiotas may mediate a tradeoff between host development and stress resistance. What element in these interactions is responsible for these effects is yet unknown, but experiments with live versus dead bacteria suggest that such effects may depend on bacterially provided signals.
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Affiliation(s)
- Samuel Slowinski
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
- Department of Biology, 4223 Biology-Psychology Bldg., University of Maryland, College Park, MD 20742, USA
- Correspondence: (S.S.); (M.S.)
| | - Isabella Ramirez
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Vivek Narayan
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Medha Somayaji
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Maya Para
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Sarah Pi
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Niharika Jadeja
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Siavash Karimzadegan
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Barbara Pees
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
| | - Michael Shapira
- Department of Integrative Biology, 3040 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3140, USA; (I.R.); (V.N.); (M.S.); (M.P.); (S.P.); (N.J.); (S.K.); (B.P.)
- Correspondence: (S.S.); (M.S.)
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33
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Díez‐Vives C, Taboada S, Leiva C, Busch K, Hentschel U, Riesgo A. On the way to specificity - Microbiome reflects sponge genetic cluster primarily in highly structured populations. Mol Ecol 2020; 29:4412-4427. [PMID: 32931063 PMCID: PMC7756592 DOI: 10.1111/mec.15635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Most animals, including sponges (Porifera), have species-specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host-specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica - both with weak population structure (high gene flow) - seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location.
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Affiliation(s)
| | - Sergi Taboada
- Departamento de Ciencias de la VidaEU‐US Marine Biodiversity GroupUniversidad de AlcaláAlcalá de HenaresSpain
- Departamento de Biología (Zoología)Universidad Autónoma de MadridFacultad de CienciasMadridSpain
| | - Carlos Leiva
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Genetics, Microbiology and StatisticsFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ana Riesgo
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de Madrid (CSIC)MadridSpain
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34
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Dirksen P, Assié A, Zimmermann J, Zhang F, Tietje AM, Marsh SA, Félix MA, Shapira M, Kaleta C, Schulenburg H, Samuel BS. CeMbio - The Caenorhabditis elegans Microbiome Resource. G3 (BETHESDA, MD.) 2020; 10:3025-3039. [PMID: 32669368 PMCID: PMC7466993 DOI: 10.1534/g3.120.401309] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022]
Abstract
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.
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Affiliation(s)
- Philipp Dirksen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Johannes Zimmermann
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Adina-Malin Tietje
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, Paris, France
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley CA
| | - Christoph Kaleta
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
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35
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Carlson HK, Lui LM, Price MN, Kazakov AE, Carr AV, Kuehl JV, Owens TK, Nielsen T, Arkin AP, Deutschbauer AM. Selective carbon sources influence the end products of microbial nitrate respiration. THE ISME JOURNAL 2020; 14:2034-2045. [PMID: 32372050 PMCID: PMC7368043 DOI: 10.1038/s41396-020-0666-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 11/09/2022]
Abstract
Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.
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Affiliation(s)
- Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex V Carr
- Institute for Systems Biology, University of Washington, Seattle, WA, 98109, USA
- Molecular Engineering Program, University of Washington, Seattle, WA, 98105, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Torben Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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36
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Kohl KD. Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190251. [PMID: 32200746 PMCID: PMC7133527 DOI: 10.1098/rstb.2019.0251] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play. This paper discusses the roles that each of these processes and their interactions may play in yielding phylosymbiotic signals across hosts. Finally, this paper will identify open questions and methods that are required to better understand the relative contributions of these basic processes to phylosymbiosis. Given that phylosymbiosis has been shown to relate to functional components of host fitness, understanding the processes that contribute to these patterns will be important for our understanding of the ecology and evolution of host-microbe interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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37
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Kumar A, Baruah A, Tomioka M, Iino Y, Kalita MC, Khan M. Caenorhabditis elegans: a model to understand host-microbe interactions. Cell Mol Life Sci 2020; 77:1229-1249. [PMID: 31584128 PMCID: PMC11104810 DOI: 10.1007/s00018-019-03319-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
Host-microbe interactions within the gut are fundamental to all higher organisms. Caenorhabditis elegans has been in use as a surrogate model to understand the conserved mechanisms in host-microbe interactions. Morphological and functional similarities of C. elegans gut with the human have allowed the mechanistic investigation of gut microbes and their effects on metabolism, development, reproduction, behavior, pathogenesis, immune responses and lifespan. Recent reports suggest their suitability for functional investigations of human gut bacteria, such as gut microbiota of healthy and diseased individuals. Our knowledge on the gut microbial diversity of C. elegans in their natural environment and the effect of host genetics on their core gut microbiota is important. Caenorhabditis elegans, as a model, is continuously bridging the gap in our understanding the role of genetics, environment, and dietary factors on physiology of the host.
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Affiliation(s)
- Arun Kumar
- Molecular Biology and Microbial Biotechnology Laboratory, Division of Life Sciences, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, 781035, India
| | - Aiswarya Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Masahiro Tomioka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuichi Iino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Mohan C Kalita
- Department of Biotechnology, Gauhati University, Guwahati, Assam, 781014, India
| | - Mojibur Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Division of Life Sciences, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, 781035, India.
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38
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Johnke J, Dirksen P, Schulenburg H. Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa. Environ Microbiol 2020; 22:1265-1279. [PMID: 32003074 DOI: 10.1111/1462-2920.14932] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/18/2022]
Abstract
Microbiome communities are complex assemblages of bacteria. The dissection of their assembly dynamics is challenging because it requires repeated sampling of both host and source communities. We used the nematode Caenorhabditis elegans as a model to study these dynamics. We characterized microbiome variation from natural worm populations and their substrates for two consecutive years using 16S rDNA amplicon sequencing. We found conservation in microbiome composition across time at the genus, but not amplicon sequencing variant (ASV) level. Only three ASVs were consistently present across worm samples (Comamonas ASV10859, Pseudomonas ASV7162 and Cellvibrio ASV9073). ASVs were more diverse in worms from different rather than the same substrates, indicating an influence of the source community on microbiome assembly. Surprisingly, almost 50% of worm-associated ASVs were absent in corresponding substrates, potentially due to environmental filtering. Ecological network analysis revealed strong effects of bacteria-bacteria interactions on community composition: While a dominant Erwinia strain correlated with decreased alpha-diversity, predatory bacteria of the Bdellovibrio and like organisms associated with increased alpha-diversity. High alpha-diversity was further linked to high worm population growth, especially on species-poor substrates. Our results highlight that microbiomes are individually shaped and sensitive to dramatic community shifts in response to particular competitive species.
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Affiliation(s)
- Julia Johnke
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany
| | - Philipp Dirksen
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany.,Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, Kiel, Germany.,Max-Planck Institute for Evolutionary Biology, Plön, Germany
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39
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Affiliation(s)
- J. Gijs Kuenen
- Environmental Biotechnology Section, Department of BiotechnologyDelft University of Technology The Netherlands
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40
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Abstract
The timing of life history events has important fitness consequences. Since the 1950s, researchers have combined first principles and data to predict the optimal timing of life history transitions. Recently, a striking mystery has emerged. Such transitions can be shaped by a completely different branch of the tree of life: species in the microbiome. The timing of life history events has important fitness consequences. Since the 1950s, researchers have combined first principles and data to predict the optimal timing of life history transitions. Recently, a striking mystery has emerged. Such transitions can be shaped by a completely different branch of the tree of life: species in the microbiome. Probing these interactions using testable predictions from evolutionary theory could illuminate whether and how host-microbiome integrated life histories can evolve and be maintained. Beyond advancing fundamental science, this research program could yield important applications. In an age of microbiome engineering, understanding the contexts that lead to microbiota signaling shaping ontogeny could offer novel mechanisms for manipulations to increase yield in agriculture by manipulating plant responses to stressful environments, or to reduce pathogen transmission by affecting vector efficiency. We combine theory and evidence to illuminate the essential questions underlying the existence of microbiome-dependent ontogenetic timing (MiDOT) to fuel research on this emerging topic.
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41
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Ávila MP, Oliveira-Junior ES, Reis MP, Hester ER, Diamantino C, Veraart AJ, Lamers LPM, Kosten S, Nascimento AMA. The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling. MICROBIAL ECOLOGY 2019; 78:575-588. [PMID: 30706113 DOI: 10.1007/s00248-019-01331-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Ernandes S Oliveira-Junior
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Eric R Hester
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cristiane Diamantino
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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43
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Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H. The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. Front Microbiol 2019; 10:1793. [PMID: 31440221 PMCID: PMC6693516 DOI: 10.3389/fmicb.2019.01793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.
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Affiliation(s)
- Wentao Yang
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Barbara Pees
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Dirksen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Research Group Proteomics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Matthias Leippe
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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44
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Bosch TCG, Guillemin K, McFall-Ngai M. Evolutionary "Experiments" in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host-Microbe Interactions. Bioessays 2019; 41:e1800256. [PMID: 31099411 DOI: 10.1002/bies.201800256] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/11/2019] [Indexed: 12/13/2022]
Abstract
Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host-microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host-microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.
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Affiliation(s)
- Thomas C G Bosch
- Canadian Institute for Advanced Research, Toronto, ON, M5G 1M1, Canada.,Zoological Institute, University of Kiel, 24118, Kiel, Germany
| | - Karen Guillemin
- Canadian Institute for Advanced Research, Toronto, ON, M5G 1M1, Canada.,Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Margaret McFall-Ngai
- Canadian Institute for Advanced Research, Toronto, ON, M5G 1M1, Canada.,Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
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45
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Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model. Sci Rep 2019; 9:4399. [PMID: 30867481 PMCID: PMC6416287 DOI: 10.1038/s41598-019-40762-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/20/2019] [Indexed: 12/31/2022] Open
Abstract
The genetic model organism, Caenorhabditis elegans (C. elegans), shares many genes with humans and is the best-annotated of the eukaryotic genome. Therefore, the identification of new genes and pathways is unlikely. Nevertheless, host-pathogen interaction studies from viruses, recently discovered in the environment, has created new opportunity to discover these pathways. For example, the exogenous RNAi response in C. elegans by the Orsay virus as seen in plants and other eukaryotes is not systemic and transgenerational, suggesting different RNAi pathways between these organisms. Using a bioinformatics meta-analysis approach, we show that the top 17 genes differentially-expressed during C. elegans infection by Orsay virus are functionally uncharacterized genes. Furthermore, functional annotation using similarity search and comparative modeling, was able to predict folds correctly, but could not assign easily function to the majority. However, we could identify gene expression studies that showed a similar pattern of gene expression related to toxicity, stress and immune response. Those results were strengthened using protein-protein interaction network analysis. This study shows that novel molecular pathway components, of viral innate immune response, can be identified and provides models that can be further used as a framework for experimental studies. Whether these features are reminiscent of an ancient mechanism evolutionarily conserved, or part of a novel pathway, remain to be established. These results reaffirm the tremendous value of this approach to broaden our understanding of viral immunity in C. elegans.
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46
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Berg M, Monnin D, Cho J, Nelson L, Crits-Christoph A, Shapira M. TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals. Nat Commun 2019; 10:604. [PMID: 30723205 PMCID: PMC6363772 DOI: 10.1038/s41467-019-08379-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
The gut microbiota contributes to host health and fitness, and imbalances in its composition are associated with pathology. However, what shapes microbiota composition is not clear, in particular the role of genetic factors. Previous work in Caenorhabditis elegans defined a characteristic worm gut microbiota significantly influenced by host genetics. The current work explores the role of central regulators of host immunity and stress resistance, employing qPCR and CFU counts to measure abundance of core microbiota taxa in mutants raised on synthetic communities of previously-isolated worm gut commensals. This revealed a bloom, specifically of Enterobacter species, in immune-compromised TGFβ/BMP mutants. Imaging of fluorescently labeled Enterobacter showed that TGFβ/BMP-exerted control operated primarily in the anterior gut and depended on multi-tissue contributions. Enterobacter commensals are common in the worm gut, contributing to infection resistance. However, disruption of TGFβ/BMP signaling turned a normally beneficial Enterobacter commensal to pathogenic. These results demonstrate specificity in gene-microbe interactions underlying gut microbial homeostasis and highlight the pathogenic potential of their disruption.
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Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - David Monnin
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Juhyun Cho
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lydia Nelson
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alex Crits-Christoph
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA.
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47
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Sirová D, Bárta J, Šimek K, Posch T, Pech J, Stone J, Borovec J, Adamec L, Vrba J. Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant. MICROBIOME 2018; 6:225. [PMID: 30558682 PMCID: PMC6297986 DOI: 10.1186/s40168-018-0600-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/18/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces. RESULTS Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts. CONCLUSIONS We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.
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Affiliation(s)
- Dagmara Sirová
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic.
| | - Jiří Bárta
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802, Kilchberg, Switzerland
| | - Jiří Pech
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - James Stone
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK-99775, USA
- Institute of Experimental Botany CAS, Rozvojová 263, CZ-16502, Praha 6-Lysolaje, Czech Republic
| | - Jakub Borovec
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
| | - Lubomír Adamec
- Institute of Botany CAS, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jaroslav Vrba
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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48
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Han B, Lin CCJ, Hu G, Wang MC. 'Inside Out'- a dialogue between mitochondria and bacteria. FEBS J 2018; 286:630-641. [PMID: 30390412 DOI: 10.1111/febs.14692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/05/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
Abstract
Mitochondria play crucial roles in regulating metabolism and longevity. A body of recent evidences reveals that the gut microbiome can also exert significant effects on these activities in the host. Here, by summarizing the currently known mechanisms underlying these regulations, and by comparing mitochondrial fission-fusion dynamics with bacterial interactions such as quorum sensing, we hypothesize that the microbiome impacts the host by communicating with their intracellular relatives, mitochondria. We highlight recent discoveries supporting this model, and these new findings reveal that metabolite molecules derived from bacteria can fine-tune mitochondrial dynamics in intestinal cells and hence influence host metabolic fitness and longevity. This perspective mode of chemical communication between bacteria and mitochondria may help us understand complex and dynamic environment-microbiome-host interactions regarding their vital impacts on health and diseases.
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Affiliation(s)
- Bing Han
- Children's Hospital, Fudan University, Minhang, Shanghai, China.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Chun Janet Lin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Guo Hu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
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Khan F, Jain S, Oloketuyi SF. Bacteria and bacterial products: Foe and friends to Caenorhabditis elegans. Microbiol Res 2018; 215:102-113. [DOI: 10.1016/j.micres.2018.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/11/2018] [Accepted: 06/24/2018] [Indexed: 02/07/2023]
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Ezcurra M. Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system. Biogerontology 2018; 19:567-578. [PMID: 29557050 PMCID: PMC6223720 DOI: 10.1007/s10522-018-9752-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/07/2018] [Indexed: 12/12/2022]
Abstract
High-throughput molecular studies are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links between microbial community disequilibria (dysbiosis) and human diseases. However, due to the inherent complexity and heterogeneity of the human microbiome we need robust experimental models that allow the systematic manipulation of variables to test the multitude of hypotheses arisen from large-scale ‘meta-omic’ projects. The nematode C. elegans combined with bacterial models offers an avenue to dissect cause and effect in host-microbiome interactions. This combined model allows the genetic manipulation of both host and microbial genetics and the use of a variety of tools, to identify pathways affecting host health. A number of recent high impact studies have used C. elegans to identify microbial pathways affecting ageing and longevity, demonstrating the power of the combined C. elegans-bacterial model. Here I will review the current state of the field, what we have learned from using C. elegans to study gut microbiome and host interactions, and the potential of using this model system in the future.
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Affiliation(s)
- Marina Ezcurra
- Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK. .,School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
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