1
|
Muñoz-Juan A, Assié A, Esteve-Codina A, Gut M, Benseny-Cases N, Samuel BS, Dalfó E, Laromaine A. Caenorhabditis elegans endorse bacterial nanocellulose fibers as functional dietary Fiber reducing lipid markers. Carbohydr Polym 2024; 331:121815. [PMID: 38388067 DOI: 10.1016/j.carbpol.2024.121815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/24/2024]
Abstract
Bacterial nanocellulose (BNC) is a promising dietary fiber with potential as a functional food additive. We evaluated BNC fibers (BNCf) in the Caenorhabditis elegans model to obtain insight into the BNCf's biointeraction with its gastrointestinal tract while reducing the variables of higher complex animals. BNCf were uptaken and excreted by worms without crossing the intestinal barrier, confirming its biosafety regarding survival rate, reproduction, and aging for concentrations up to 34 μg/ml BNCf. However, a slight decrease in the worms' length was detected. A possible nutrient shortage or stress produced by BNCf was discarded by measuring stress and chemotactic response pathways. Besides, we detected a lipid-lowering effect of BNCf in N2 C. elegans in normal and high-caloric diets. Oxidative damage was computed in N2 worms and Rac1/ced-10 mutants. The GTPase Rac1 is involved in neurological diseases, where its dysregulation enhances ROS production and neuronal damage. BNCf reduced the lipid oxidative markers produced by ROS species in this worm strain. Finally, we detected that BNCf activated the genetic expression of the immunological response and lipid catabolic process. These results strengthen the use of BNCf as a functional dietary fiber and encourage the potential treatment of neurological disease by modulating diet.
Collapse
Affiliation(s)
- Amanda Muñoz-Juan
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Núria Benseny-Cases
- Universitat Autònoma de Barcelona, Biophysics Unit, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Avinguda de Can Domènech, 08193 Cerdanyola del Vallès, Spain
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Esther Dalfó
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain; Institute for Research and Innovation in Life Sciences and Health in Central Catalonia (IRIS-CC), Can Baumann, 08500, Vic, Spain; Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Laromaine
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain.
| |
Collapse
|
2
|
Zhang F, Blackburn D, Hosea CN, Assié A, Samuel BS. Application of Flow Vermimetry for Quantification and Analysis of the <em>Caenorhabditis elegans</em> Gut Microbiome. J Vis Exp 2023. [PMID: 37067276 DOI: 10.3791/64605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The composition of the gut microbiome can have a dramatic impact on host physiology throughout the development and the life of the animal. Measuring compositional changes in the microbiome is crucial in identifying the functional relationships between these physiological changes. Caenorhabditis elegans has emerged as a powerful host system to examine the molecular drivers of host-microbiome interactions. With its transparent body plan and fluorescent-tagged natural microbes, the relative levels of microbes within the gut microbiome of an individual C. elegans animal can be easily quantified using a large particle sorter. Here we describe the procedures for the experimental setup of a microbiome, collection, and analysis of C. elegans populations in the desired life stage, operation, and maintenance of the sorter, and statistical analyses of the resulting datasets. We also discuss considerations for optimizing sorter settings based on the microbes of interest, the development of effective gating strategies for C. elegans life stages, and how to utilize sorter capabilities to enrich animal populations based on gut microbiome composition. Examples of potential applications will be presented as part of the protocol, including the potential for scalability to high-throughput applications.
Collapse
Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine
| | - Ciara N Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine; Development, Disease Models and Therapeutics Program, Graduate School of Biomedical Sciences, Baylor College of Medicine
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine; Development, Disease Models and Therapeutics Program, Graduate School of Biomedical Sciences, Baylor College of Medicine;
| |
Collapse
|
3
|
Hill AA, Kim M, Zegarra-Ruiz DF, Chang LC, Norwood K, Assié A, Wu WJH, Renfroe MC, Song HW, Major AM, Samuel BS, Hyser JM, Longman RS, Diehl GE. Acute high-fat diet impairs macrophage-supported intestinal damage resolution. JCI Insight 2023; 8:164489. [PMID: 36538527 PMCID: PMC9977439 DOI: 10.1172/jci.insight.164489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term HFD feeding in a model of intestinal injury and found sustained damage with increased cecal dead neutrophil accumulation, along with dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD-treated mice showed reduced capacity to engulf dead neutrophils. Macrophage clearance of dead neutrophils activates critical barrier repair and antiinflammatory pathways, including IL-10, which was lost after acute HFD feeding and intestinal injury. IL-10 overexpression restored intestinal repair after HFD feeding and intestinal injury. Macrophage exposure to lipids from the HFD prevented tethering and uptake of apoptotic cells and Il10 induction. Milk fat globule-EGF factor 8 (MFGE8) is a bridging molecule that facilitates macrophage uptake of dead cells. MFGE8 also facilitates lipid uptake, and we demonstrate that dietary lipids interfere with MFGE8-mediated macrophage apoptotic neutrophil uptake and subsequent Il10 production. Our findings demonstrate that HFD promotes intestinal pathology by interfering with macrophage clearance of dead neutrophils, leading to unresolved tissue damage.
Collapse
Affiliation(s)
| | - Myunghoo Kim
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel F. Zegarra-Ruiz
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lin-Chun Chang
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kendra Norwood
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wan-Jung H. Wu
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael C. Renfroe
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hyo Wong Song
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph M. Hyser
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Randy S. Longman
- Jill Roberts Institute for Research in IBD and Jill Roberts Center for IBD, Weill Cornell Medicine, New York, New York, USA
| | - Gretchen E. Diehl
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.,Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
4
|
Schiffer JA, Stumbur SV, Seyedolmohadesin M, Xu Y, Serkin WT, McGowan NG, Banjo O, Torkashvand M, Lin A, Hosea CN, Assié A, Samuel BS, O’Donnell MP, Venkatachalam V, Apfeld J. Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide. PLoS Pathog 2021; 17:e1010112. [PMID: 34941962 PMCID: PMC8699984 DOI: 10.1371/journal.ppat.1010112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/14/2021] [Indexed: 02/07/2023] Open
Abstract
Hydrogen peroxide (H2O2) is the most common chemical threat that organisms face. Here, we show that H2O2 alters the bacterial food preference of Caenorhabditis elegans, enabling the nematodes to find a safe environment with food. H2O2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial communities have insufficient H2O2-degrading capacity. The nematode's behavior is directed by H2O2-sensing neurons that promote escape from H2O2 and by bacteria-sensing neurons that promote attraction to bacteria. However, the input for H2O2-sensing neurons is removed by bacterial H2O2-degrading enzymes and the bacteria-sensing neurons' perception of bacteria is prevented by H2O2. The resulting cross-attenuation provides a general mechanism that ensures the nematode's behavior is faithful to the lethal threat of hydrogen peroxide, increasing the nematode's chances of finding a niche that provides both food and protection from hydrogen peroxide.
Collapse
Affiliation(s)
- Jodie A. Schiffer
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Stephanie V. Stumbur
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Maedeh Seyedolmohadesin
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Yuyan Xu
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - William T. Serkin
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Natalie G. McGowan
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Oluwatosin Banjo
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Mahdi Torkashvand
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ciara N. Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. O’Donnell
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Vivek Venkatachalam
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Javier Apfeld
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
- Bioengineering Department, Northeastern University, Boston, Massachusetts, United States of America
| |
Collapse
|
5
|
Chavez IN, Brown TM, Assié A, Bryant AS, Samuel BS, Hallem EA. Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria. BMC Biol 2021; 19:221. [PMID: 34620172 PMCID: PMC8499433 DOI: 10.1186/s12915-021-01153-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasitic generation, infective third-stage larvae (iL3s) actively engage in host seeking. During the free-living generation, the nematodes develop and reproduce on host feces. At different points during their life cycle, Strongyloides species encounter a wide variety of host-associated and environmental bacteria. However, the microbiome associated with Strongyloides species, and the behavioral and physiological interactions between Strongyloides species and bacteria, remain unclear. Results We first investigated the microbiome of the human parasite Strongyloides stercoralis using 16S-based amplicon sequencing. We found that S. stercoralis free-living adults have an associated microbiome consisting of specific fecal bacteria. We then investigated the behavioral responses of S. stercoralis and the closely related rat parasite Strongyloides ratti to an ecologically diverse panel of bacteria. We found that S. stercoralis and S. ratti showed similar responses to bacteria. The responses of both nematodes to bacteria varied dramatically across life stages: free-living adults were strongly attracted to most of the bacteria tested, while iL3s were attracted specifically to a narrow range of environmental bacteria. The behavioral responses to bacteria were dynamic, consisting of distinct short- and long-term behaviors. Finally, a comparison of the growth and reproduction of S. stercoralis free-living adults on different bacteria revealed that the bacterium Proteus mirabilis inhibits S. stercoralis egg hatching, and thereby greatly decreases parasite viability. Conclusions Skin-penetrating nematodes encounter bacteria from various ecological niches throughout their life cycle. Our results demonstrate that bacteria function as key chemosensory cues for directing parasite movement in a life-stage-specific manner. Some bacterial genera may form essential associations with the nematodes, while others are detrimental and serve as a potential source of novel nematicides. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01153-7.
Collapse
Affiliation(s)
- Ivan N Chavez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Taylor M Brown
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Astra S Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
6
|
Zhang F, Weckhorst JL, Assié A, Hosea C, Ayoub CA, Khodakova AS, Cabrera ML, Vidal Vilchis D, Félix MA, Samuel BS. Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut. Curr Biol 2021; 31:2603-2618.e9. [PMID: 34048707 DOI: 10.1016/j.cub.2021.04.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the strain-level phylogenetic diversity naturally encountered by C. elegans in the wild. Using this community, we show that C. elegans utilizes immune, xenobiotic, and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of DAF-2/IGFR and modulated by the competitive action of insulin signaling transcription factors DAF-16/FOXO and PQM-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum as adults is correlated with faster animal growth rates and larger body size at the end of development. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of gut microbiome composition in C. elegans.
Collapse
Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jessica L Weckhorst
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Ciara Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christopher A Ayoub
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anastasia S Khodakova
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Mario Loeza Cabrera
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniela Vidal Vilchis
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Marie-Anne Félix
- Ecole Normale Supérieure, IBENS, CNRS UMR8197, INSERM U1024, Paris, France
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| |
Collapse
|
7
|
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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
8
|
Assié A, Samuel BS. The Devil Is in the Microbial Genetic Details. Mol Cell 2019; 74:1108-1109. [PMID: 31226275 DOI: 10.1016/j.molcel.2019.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The work of Zeevi et al. (2019) in a recent issue of Nature shows that variations in gene content and organization between different strains of the same microbial species are widespread in the human gut microbiota and could be linked to many measures of health.
Collapse
Affiliation(s)
- Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
9
|
Assié A, Borowski C, van der Heijden K, Raggi L, Geier B, Leisch N, Schimak MP, Dubilier N, Petersen JM. A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria. Environ Microbiol Rep 2016; 8:805-813. [PMID: 27428292 DOI: 10.1111/1758-2229.12442] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.
Collapse
Affiliation(s)
- Adrien Assié
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | | | - Luciana Raggi
- CIGoM, Instituto de Biotecnologia, UNAM, Av. Universidad 2001, C.P.62210, Cuernavaca, Morelos, Mexico
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Mario P Schimak
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
- MARUM, University of Bremen, Germany
| | - Jillian M Petersen
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
| |
Collapse
|