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Bruno P, Schüler T, Rosshart SP. Born to be wild: utilizing natural microbiota for reliable biomedical research. Trends Immunol 2024:S1471-4906(24)00298-9. [PMID: 39690004 DOI: 10.1016/j.it.2024.11.013] [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: 10/11/2024] [Revised: 11/11/2024] [Accepted: 11/19/2024] [Indexed: 12/19/2024]
Abstract
Laboratory mice housed under specific pathogen-free (SPF) conditions are the standard model in biomedical research. However, experiments with a particular inbred mouse strain performed in different laboratories often yield inconsistent or conflicting data due to housing-specific variations in the composition and diversity of SPF microbiota. These variations affect immune and nonimmune cell functions, leading to systemic physiological changes. Consequently, microbiota-dependent inconsistencies have raised general doubts regarding the suitability of mice as model organisms. Since stability positively correlates with biological diversity, we postulate that increasing species diversity can improve microbiota stability and mouse physiology, enhancing robustness, reproducibility, and experimental validity. Similar to the generation of inbred mouse strains in the last century, we suggest a worldwide initiative to define a transplantable 'wild' microbiota that stably colonizes mice irrespective of housing conditions.
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Affiliation(s)
- Philipp Bruno
- Department of Microbiome Research, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany.
| | - Stephan P Rosshart
- Department of Microbiome Research, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Medicine II, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany.
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2
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Mi K, Xu R, Liu X. RFW captures species-level metagenomic functions by integrating genome annotation information. CELL REPORTS METHODS 2024; 4:100932. [PMID: 39662474 DOI: 10.1016/j.crmeth.2024.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/01/2024] [Accepted: 11/14/2024] [Indexed: 12/13/2024]
Abstract
Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.
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Affiliation(s)
- Kai Mi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Rui Xu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; The Second Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China.
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3
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Lippincott RA, O’Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS 2024; 19:228-233. [PMID: 38884255 PMCID: PMC11305906 DOI: 10.1097/coh.0000000000000866] [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] [Indexed: 06/18/2024]
Abstract
PURPOSE OF REVIEW To review novel experimental approaches for studying host:microbe interactions and their role in intestinal and systemic inflammation in people living with HIV (PLWH). RECENT FINDINGS Inflammation in PLWH is impacted by interactions between the microbiome, the intestinal epithelium, and immune cells. This complex interplay is not fully understood and requires a variety of analytical techniques to study. Using a multiomic systems biology approach provides hypothesis generating data on host:microbe interactions that can be used to guide further investigation. The direct interactions between host cells and microbes can be elucidated using peripheral blood mononuclear cells (PBMCs), lamina propria mononuclear cells (LPMC's) or human intestinal organoids (HIO). Additionally, the broader relationship between the host and the microbiome can be explored using animal models such as nonhuman primates and germ-free and double humanized mice. SUMMARY To explore complex host:microbe relationships, hypotheses are generated and investigations are guided by multiomic data, while causal components are identified using in-vitro and in-vivo assays.
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Affiliation(s)
| | - John O’Connor
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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4
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Cohen DG, Wingert RA. Forever young by Alpha(diversity)ville: restricting intestinal microbiome maturation stunts immune system development and increases susceptibility to infection. Tissue Barriers 2024; 12:2281209. [PMID: 37978888 PMCID: PMC11262204 DOI: 10.1080/21688370.2023.2281209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
The microbiome is a keystone of adult gastrointestinal (GI) tract health, where it facilitates digestion, wards off pathogen colonization, and exerts a powerful influence on the physiological health of organs ranging from the brain to the kidneys. From its establishment at birth and through the initial years of childhood, the human microbiome is particularly dynamic, shifting in its composition and alpha (species) diversity to an adult profile as dietary sustenance transitions from milk-based sources to others such as solid food. An innovative study has now demonstrated how microbiome maturation is requisite both for the progression of immune system development and for long-term gut barrier function. These insights have significant ramifications for designing pediatric approaches to cultivate immune cell ontogeny in the formative stages of human infancy.
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Affiliation(s)
- Dorrian G. Cohen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Rebecca A. Wingert
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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5
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Eddoubaji Y, Aldeia C, Campos-Madueno EI, Moser AI, Kundlacz C, Perreten V, Hilty M, Endimiani A. A new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones. Front Microbiol 2024; 15:1381051. [PMID: 38659985 PMCID: PMC11039899 DOI: 10.3389/fmicb.2024.1381051] [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: 02/02/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Finding strategies for decolonizing gut carriers of multidrug-resistant Escherichia coli (MDR-Ec) is a public-health priority. In this context, novel approaches should be validated in preclinical in vivo gut colonization models before being translated to humans. However, the use of mice presents limitations. Here, we used for the first time Zophobas morio larvae to design a new model of intestinal colonization (28-days duration, T28). Three hyperepidemic MDR-Ec producing extended-spectrum β-lactamases (ESBLs) or carbapenemases were administered via contaminated food to larvae for the first 7 days (T7): Ec-4901.28 (ST131, CTX-M-15), Ec-042 (ST410, OXA-181) and Ec-050 (ST167, NDM-5). Growth curve analyses showed that larvae became rapidly colonized with all strains (T7, ~106-7 CFU/mL), but bacterial load remained high after the removal of contaminated food only in Ec-4901.28 and Ec-042 (T28, ~103-4 CFU/mL). Moreover, larvae receiving a force-feeding treatment with INTESTI bacteriophage cocktail (on T7 and T10 via gauge needle) were decolonized by Ec-4901.28 (INTESTI-susceptible); however, Ec-042 and Ec-050 (INTESTI-resistant) did not. Initial microbiota (before administering contaminated food) was very rich of bacterial genera (e.g., Lactococcus, Enterococcus, Spiroplasma), but patterns were heterogeneous (Shannon diversity index: range 1.1-2.7) and diverse to each other (Bray-Curtis dissimilarity index ≥30%). However, when larvae were challenged with the MDR-Ec with or without administering bacteriophages the microbiota showed a non-significant reduction of the diversity during the 28-day experiments. In conclusion, the Z. morio larvae model promises to be a feasible and high-throughput approach to study novel gut decolonization strategies for MDR-Ec reducing the number of subsequent confirmatory mammalian experiments.
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Affiliation(s)
- Yasmine Eddoubaji
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Cindy Kundlacz
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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6
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Jans M, Vereecke L. A guide to germ-free and gnotobiotic mouse technology to study health and disease. FEBS J 2024. [PMID: 38523409 DOI: 10.1111/febs.17124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/17/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.
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Affiliation(s)
- Maude Jans
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Lars Vereecke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Belgium
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Jimonet P, Druart C, Blanquet-Diot S, Boucinha L, Kourula S, Le Vacon F, Maubant S, Rabot S, Van de Wiele T, Schuren F, Thomas V, Walther B, Zimmermann M. Gut Microbiome Integration in Drug Discovery and Development of Small Molecules. Drug Metab Dispos 2024; 52:274-287. [PMID: 38307852 DOI: 10.1124/dmd.123.001605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024] Open
Abstract
Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.
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Affiliation(s)
- Patrick Jimonet
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Céline Druart
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stéphanie Blanquet-Diot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Lilia Boucinha
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Stephanie Kourula
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Françoise Le Vacon
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Maubant
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Sylvie Rabot
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Tom Van de Wiele
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Frank Schuren
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Vincent Thomas
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Bernard Walther
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
| | - Michael Zimmermann
- Medicen Paris Région, Paris, France (P.J.); Pharmabiotic Research Institute, Narbonne, France (C.D.); UMR 454 MEDIS, Université Clermont Auvergne, Clermont-Ferrand, France (S.B.D.); Global Bioinformatics, Evotec ID, Lyon, France (L.B.); Preclinical Sciences & Translational Safety, JNJ Innovative Medicine, Beerse, Belgium (S.K.); Biofortis, Saint-Herblain, France (F.L.V.); Translational Pharmacology Department, Oncodesign Services, Dijon, France (S.M.); Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France (S.R.); Center of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium (T.V.W.); TNO, Leiden, The Netherlands (F.S.); Lallemand Health Solutions, Blagnac, France (V.T.); Servier, Saclay, France (B.W.); and Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany (M.Z.)
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8
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Jennings SAV, Clavel T. Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition. Annu Rev Anim Biosci 2024; 12:283-300. [PMID: 37963399 DOI: 10.1146/annurev-animal-021022-025552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.
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Affiliation(s)
- Susan A V Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
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9
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Jansma J, Chatziioannou AC, Castricum K, van Hemert S, El Aidy S. Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community. mSystems 2023; 8:e0033223. [PMID: 37668401 PMCID: PMC10654062 DOI: 10.1128/msystems.00332-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/13/2023] [Indexed: 09/06/2023] Open
Abstract
IMPORTANCE The development of probiotic therapies targeted at the small intestinal microbiota represents a significant advancement in the field of probiotic interventions. This region poses unique opportunities due to its low number of gut microbiota, along with the presence of heightened immune and metabolic host responses. However, progress in this area has been hindered by a lack of detailed understanding regarding the molecular mechanisms through which probiotics exert their effects in the small intestine. Our study, utilizing a synthetic community of three small intestinal bacterial strains and the addition of two different probiotic species, and kynurenine as a representative dietary or endogenously produced compound, highlights the importance of selecting probiotic species with diverse genetic capabilities that complement the functional capacity of the resident microbiota, or alternatively, constructing a multispecies formula. This approach holds great promise for the development of effective probiotic therapies and underscores the need to consider the functional capacity of probiotic species when designing interventions.
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Affiliation(s)
- Jack Jansma
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | | | | | | | - Sahar El Aidy
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
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10
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Marcolla CS, Ju T, Willing BP. Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources. Appl Environ Microbiol 2023; 89:e0027123. [PMID: 37098952 PMCID: PMC10231219 DOI: 10.1128/aem.00271-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/28/2023] [Indexed: 04/27/2023] Open
Abstract
Broilers in intensive systems may lack commensal microbes that have coevolved with chickens in nature. This study evaluated the effects of microbial inocula and delivery methods applied to day-old chicks on the development of the cecal microbiota. Specifically, chicks were inoculated with cecal contents or microbial cultures, and the efficacies of three delivery methods (oral gavage, spraying inoculum into the bedding, and cohousing) were evaluated. Also, a competitive study evaluated the colonization ability of bacteria sourced from extensive or intensive poultry production systems. The microbiota of inoculated birds presented higher phylogenetic diversity values (PD) and higher relative abundance values of Bacteroidetes, compared with a control. Additionally, a reduction in the ileal villus height/crypt depth ratio and increased cecal IL-6, IL-10, propionate, and valerate concentrations were observed in birds that were inoculated with cecal contents. Across the experiments, the chicks in the control groups presented higher relative abundance values of Escherichia/Shigella than did the inoculated birds. Specific microbes from intensively or extensively raised chickens were able to colonize the ceca, and inocula from intensive production systems promoted higher relative abundance values of Escherichia/Shigella. We concluded that Alistipes, Bacteroides, Barnesiella, Mediterranea, Parabacteroides, Megamonas, and Phascolarctobacterium are effective colonizers of the broiler ceca. In addition, oral gavage, spray, and cohousing can be used as delivery methods for microbial transplantation, as indicated by their effects on the cecal microbiota, intestinal morphology, short-chain fatty acids concentration, and cytokine/chemokine levels. These findings will guide future research on the development of next-generation probiotics that are able to colonize and persist in the chicken intestinal tract after a single exposure. IMPORTANCE The strict biosecurity procedures employed in the poultry industry may inadvertently hinder the transmission of beneficial commensal bacteria that chickens would encounter in natural environments. This research aims at identifying bacteria that can colonize and persist in the chicken gut after a single exposure. We evaluated different microbial inocula that were obtained from healthy adult chicken donors as well as three delivery methods for their effects on microbiota composition and bird physiology. In addition, we conducted a competitive assay to test the colonization abilities of bacteria sourced from intensively versus extensively raised chickens. Our results indicated that some bacteria are consistently increased in birds that are exposed to microbial inoculations. These bacteria can be isolated and employed in future research on the development of next-generation probiotics that contain species that are highly adapted to the chicken gut.
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Affiliation(s)
- Camila S. Marcolla
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
| | - Benjamin P. Willing
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
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11
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Even G, Mouray A, Vandenabeele N, Martel S, Merlin S, Lebrun-Ruer S, Chabé M, Audebert C. Bact-to-Batch: A Microbiota-Based Tool to Determine Optimal Animal Allocation in Experimental Designs. Int J Mol Sci 2023; 24:ijms24097912. [PMID: 37175619 PMCID: PMC10178137 DOI: 10.3390/ijms24097912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested approach was challenged with previously published data from a third-party study. This new method allows to embrace the unavoidable microbiota variability between animals in order to limit artefacts and to provide an additional assurance for the reproducibility of animal experiments.
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Affiliation(s)
- Gaël Even
- GD Biotech-Gènes Diffusion, F-59000 Lille, France
- PEGASE-Biosciences, Institut Pasteur de Lille, F-59019 Lille, France
| | - Anthony Mouray
- Plateforme d'Expérimentations et de Hautes Technologies Animales, Institut Pasteur de Lille, F-59019 Lille, France
- Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Université Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France
| | - Nicolas Vandenabeele
- Plateforme d'Expérimentations et de Hautes Technologies Animales, Institut Pasteur de Lille, F-59019 Lille, France
- Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Université Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France
| | - Sophie Martel
- GD Biotech-Gènes Diffusion, F-59000 Lille, France
- PEGASE-Biosciences, Institut Pasteur de Lille, F-59019 Lille, France
| | - Sophie Merlin
- GD Biotech-Gènes Diffusion, F-59000 Lille, France
- PEGASE-Biosciences, Institut Pasteur de Lille, F-59019 Lille, France
| | - Ségolène Lebrun-Ruer
- GD Biotech-Gènes Diffusion, F-59000 Lille, France
- PEGASE-Biosciences, Institut Pasteur de Lille, F-59019 Lille, France
| | - Magali Chabé
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Université de Lille, F-59000 Lille, France
| | - Christophe Audebert
- GD Biotech-Gènes Diffusion, F-59000 Lille, France
- PEGASE-Biosciences, Institut Pasteur de Lille, F-59019 Lille, France
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12
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Lubin JB, Green J, Maddux S, Denu L, Duranova T, Lanza M, Wynosky-Dolfi M, Flores JN, Grimes LP, Brodsky IE, Planet PJ, Silverman MA. Arresting microbiome development limits immune system maturation and resistance to infection in mice. Cell Host Microbe 2023; 31:554-570.e7. [PMID: 36996818 PMCID: PMC10935632 DOI: 10.1016/j.chom.2023.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/09/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023]
Abstract
Disruptions to the intestinal microbiome during weaning lead to negative effects on host immune function. However, the critical host-microbe interactions during weaning that are required for immune system development remain poorly understood. We find that restricting microbiome maturation during weaning stunts immune system development and increases susceptibility to enteric infection. We developed a gnotobiotic mouse model of the early-life microbiome Pediatric Community (PedsCom). These mice develop fewer peripheral regulatory T cells and less IgA, hallmarks of microbiota-driven immune system development. Furthermore, adult PedsCom mice retain high susceptibility to Salmonella infection, which is characteristic of young mice and children. Altogether, our work illustrates how the post-weaning transition in microbiome composition contributes to normal immune maturation and protection from infection. Accurate modeling of the pre-weaning microbiome provides a window into the microbial requirements for healthy development and suggests an opportunity to design microbial interventions at weaning to improve immune development in human infants.
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Affiliation(s)
- Jean-Bernard Lubin
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jamal Green
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Maddux
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lidiya Denu
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Tereza Duranova
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew Lanza
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | | | - Julia N Flores
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Logan P Grimes
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, IFI, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael A Silverman
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Research Unit, GlaxoSmithKline, Collegeville, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Horvathova K, Modrackova N, Splichal I, Splichalova A, Amin A, Ingribelli E, Killer J, Doskocil I, Pechar R, Kodesova T, Vlkova E. Defined Pig Microbiota with a Potential Protective Effect against Infection with Salmonella Typhimurium. Microorganisms 2023; 11:microorganisms11041007. [PMID: 37110429 PMCID: PMC10146858 DOI: 10.3390/microorganisms11041007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
A balanced microbiota is a main prerequisite for the host's health. The aim of the present work was to develop defined pig microbiota (DPM) with the potential ability to protect piglets against infection with Salmonella Typhimurium, which causes enterocolitis. A total of 284 bacterial strains were isolated from the colon and fecal samples of wild and domestic pigs or piglets using selective and nonselective cultivation media. Isolates belonging to 47 species from 11 different genera were identified by MALDI-TOF mass spectrometry (MALDI-TOF MS). The bacterial strains for the DPM were selected for anti-Salmonella activity, ability to aggregate, adherence to epithelial cells, and to be bile and acid tolerant. The selected combination of 9 strains was identified by sequencing of the 16S rRNA gene as Bacillus sp., Bifidobacterium animalis subsp. lactis, B. porcinum, Clostridium sporogenes, Lactobacillus amylovorus, L. paracasei subsp. tolerans, Limosilactobacillus reuteri subsp. suis, and Limosilactobacillus reuteri (two strains) did not show mutual inhibition, and the mixture was stable under freezing for at least 6 months. Moreover, strains were classified as safe without pathogenic phenotype and resistance to antibiotics. Future experiments with Salmonella-infected piglets are needed to test the protective effect of the developed DPM.
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Affiliation(s)
- Kristyna Horvathova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Ahmad Amin
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Eugenio Ingribelli
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Ivo Doskocil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Tereza Kodesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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14
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 173] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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15
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Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Commun Biol 2023; 6:289. [PMID: 36934156 PMCID: PMC10024726 DOI: 10.1038/s42003-023-04671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.
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Affiliation(s)
- Yuanyuan Ma
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Jinru He
- Kiel University, Zoological Institute, Cell and Developmental Biology, Kiel, Germany
| | - Michael Sieber
- Max-Planck Institute for Evolutionary Biology, Dept. Evolutionary Theory, Plön, Germany
| | - Jakob von Frieling
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Iris Bruchhaus
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John F Baines
- Kiel University, Medical Faculty, Institute for Experimental Medicine, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Group Evolutionary Medicine, Plön, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institute, Biosciences, Ecological Chemistry, Bremerhaven, Germany
| | - Thomas Roeder
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North, Kiel, Germany.
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16
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Zhao R, Symonds JE, Walker SP, Steiner K, Carter CG, Bowman JP, Nowak BF. Relationship between gut microbiota and Chinook salmon ( Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems. Front Microbiol 2023; 14:1065823. [PMID: 36825086 PMCID: PMC9941681 DOI: 10.3389/fmicb.2023.1065823] [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: 10/10/2022] [Accepted: 01/06/2023] [Indexed: 02/10/2023] Open
Abstract
Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.
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Affiliation(s)
- Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia
| | - Jane E. Symonds
- Cawthron Institute, Nelson, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | | | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - John P. Bowman
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, Hobart, TAS, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia
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17
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Adade EE, Stevick RJ, Pérez-Pascual D, Ghigo JM, Valm AM. Gnotobiotic zebrafish microbiota display inter-individual variability affecting host physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526612. [PMID: 36778358 PMCID: PMC9915576 DOI: 10.1101/2023.02.01.526612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Gnotobiotic animal models reconventionalized under controlled laboratory conditions with multi-species bacterial communities are commonly used to study host-microbiota interactions under presumably more reproducible conditions than conventional animals. The usefulness of these models is however limited by inter-animal variability in bacterial colonization and our general lack of understanding of the inter-individual fluctuation and spatio-temporal dynamics of microbiota assemblies at the micron to millimeter scale. Here, we show underreported variability in gnotobiotic models by analyzing differences in gut colonization efficiency, bacterial composition, and host intestinal mucus production between conventional and gnotobiotic zebrafish larvae re-conventionalized with a mix of 9 bacteria isolated from conventional microbiota. Despite similar bacterial community composition, we observed high variability in the spatial distribution of bacteria along the intestinal tract in the reconventionalized model. We also observed that, whereas bacteria abundance and intestinal mucus per fish were not correlated, reconventionalized fish had lower intestinal mucus compared to conventional animals, indicating that the stimulation of mucus production depends on the microbiota composition. Our findings, therefore, suggest that variable colonization phenotypes affect host physiology and impact the reproducibility of experimental outcomes in studies that use gnotobiotic animals. This work provides insights into the heterogeneity of gnotobiotic models and the need to accurately assess re-conventionalization for reproducibility in host-microbiota studies.
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Affiliation(s)
- Emmanuel E. Adade
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222, USA
- The RNA Institute, State University of New York at Albany, Albany, NY 12222, USA
| | - Rebecca J. Stevick
- Institut Pasteur, Université de Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris F-75015, France
| | - David Pérez-Pascual
- Institut Pasteur, Université de Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris F-75015, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris F-75015, France
| | - Alex M. Valm
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222, USA
- The RNA Institute, State University of New York at Albany, Albany, NY 12222, USA
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18
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Interrogation of the mammalian gut-brain axis using LC-MS/MS-based targeted metabolomics with in vitro bacterial and organoid cultures and in vivo gnotobiotic mouse models. Nat Protoc 2023; 18:490-529. [PMID: 36352124 DOI: 10.1038/s41596-022-00767-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/26/2022] [Indexed: 11/11/2022]
Abstract
Interest in the communication between the gastrointestinal tract and central nervous system, known as the gut-brain axis, has prompted the development of quantitative analytical platforms to analyze microbe- and host-derived signals. This protocol enables investigations into connections between microbial colonization and intestinal and brain neurotransmitters and contains strategies for the comprehensive evaluation of metabolites in in vitro (organoids) and in vivo mouse model systems. Here we present an optimized workflow that includes procedures for preparing these gut-brain axis model systems: (stage 1) growth of microbes in defined media; (stage 2) microinjection of intestinal organoids; and (stage 3) generation of animal models including germ-free (no microbes), specific-pathogen-free (complete gut microbiota) and specific-pathogen-free re-conventionalized (germ-free mice associated with a complete gut microbiota from a specific-pathogen-free mouse), and Bifidobacterium dentium and Bacteroides ovatus mono-associated mice (germ-free mice colonized with a single gut microbe). We describe targeted liquid chromatography-tandem mass spectrometry-based metabolomics methods for analyzing microbially derived short-chain fatty acids and neurotransmitters from these samples. Unlike other protocols that commonly examine only stool samples, this protocol includes bacterial cultures, organoid cultures and in vivo samples, in addition to monitoring the metabolite content of stool samples. The incorporation of three experimental models (microbes, organoids and animals) enhances the impact of this protocol. The protocol requires 3 weeks of murine colonization with microbes and ~1-2 weeks for liquid chromatography-tandem mass spectrometry-based instrumental and quantitative analysis, and sample post-processing and normalization.
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19
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Wang R, Cui L, Li J, Li W. Factors driving the halophyte rhizosphere bacterial communities in coastal salt marshes. Front Microbiol 2023; 14:1127958. [PMID: 36910212 PMCID: PMC9992437 DOI: 10.3389/fmicb.2023.1127958] [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: 12/20/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Root-associated microorganisms promote plant growth and provide protection from stresses. Halophytes are the fundamental components maintaining ecosystem functions of coastal salt marshes; however, it is not clear how their microbiome are structured across large spatial scales. Here, we investigated the rhizosphere bacterial communities of typical coastal halophyte species (Phragmites australis and Suaeda salsa) in temperate and subtropical salt marshes across 1,100 km in eastern China. Methods The sampling sites were located from 30.33 to 40.90°N and 119.24 to 121.79°E across east China. A total of 36 plots were investigated in the Liaohe River Estuary, the Yellow River Estuary, Yancheng, and Hangzhou Bay in August 2020. We collected shoot, root, and rhizosphere soil samples. the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. The soil properties, plant functional traits, the genome sequencing, and metabolomics assay were detected. Results The results showed that soil nutrients (total organic carbon, dissolved organic carbon, total nitrogen, soluble sugars, and organic acids) are high in the temperate marsh, while root exudates (measured by metabolite expressions) are significantly higher in the subtropical marsh. We observed higher bacterial alpha diversity, more complex network structure, and more negative connections in the temperate salt marsh, which suggested intense competition among bacterial groups. Variation partitioning analysis showed that climatic, edaphic, and root exudates had the greatest effects on the bacteria in the salt marsh, especially for abundant and moderate subcommunities. Random forest modeling further confirmed this but showed that plant species had a limited effect. Conclutions Taken together, the results of this study revealed soil properties (chemical properties) and root exudates (metabolites) had the greatest influence on the bacterial community of salt marsh, especially for abundant and moderate taxa. Our results provided novel insights into the biogeography of halophyte microbiome in coastal wetlands and can be beneficial for policymakers in decision-making on the management of coastal wetlands.
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Affiliation(s)
- Rumiao Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Lijuan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
| | - Wei Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, China
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20
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Kurt F, Leventhal GE, Spalinger MR, Anthamatten L, Rogalla von Bieberstein P, Menzi C, Reichlin M, Meola M, Rosenthal F, Rogler G, Lacroix C, de Wouters T. Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP). Gut Microbes 2023; 15:2177486. [PMID: 36794804 PMCID: PMC9980632 DOI: 10.1080/19490976.2023.2177486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
The success of fecal microbiota transplants (FMT) has provided the necessary proof-of-concept for microbiome therapeutics. Yet, feces-based therapies have many associated risks and uncertainties, and hence defined microbial consortia that modify the microbiome in a targeted manner have emerged as a promising safer alternative to FMT. The development of such live biotherapeutic products has important challenges, including the selection of appropriate strains and the controlled production of the consortia at scale. Here, we report on an ecology- and biotechnology-based approach to microbial consortium construction that overcomes these issues. We selected nine strains that form a consortium to emulate the central metabolic pathways of carbohydrate fermentation in the healthy human gut microbiota. Continuous co-culturing of the bacteria produces a stable and reproducible consortium whose growth and metabolic activity are distinct from an equivalent mix of individually cultured strains. Further, we showed that our function-based consortium is as effective as FMT in counteracting dysbiosis in a dextran sodium sulfate mouse model of acute colitis, while an equivalent mix of strains failed to match FMT. Finally, we showed robustness and general applicability of our approach by designing and producing additional stable consortia of controlled composition. We propose that combining a bottom-up functional design with continuous co-cultivation is a powerful strategy to produce robust functionally designed synthetic consortia for therapeutic use.
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Affiliation(s)
- Fabienne Kurt
- PharmaBiome AG, Schlieren, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Marianne Rebecca Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Laura Anthamatten
- PharmaBiome AG, Schlieren, Switzerland
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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21
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Proctor A, Parvinroo S, Richie T, Jia X, Lee STM, Karp PD, Paley S, Kostic AD, Pierre JF, Wannemuehler MJ, Phillips GJ. Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function. mSystems 2022; 7:e0029322. [PMID: 35968975 PMCID: PMC9600240 DOI: 10.1128/msystems.00293-22] [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: 03/25/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Animals colonized with a defined microbiota represent useful experimental systems to investigate microbiome function. The altered Schaedler flora (ASF) represents a consortium of eight murine bacterial species that have been used for more than 4 decades where the study of mice with a reduced microbiota is desired. In contrast to germ-free mice, or mice colonized with only one or two species, ASF mice show the normal gut structure and immune system development. To further expand the utility of the ASF, we have developed technical and bioinformatic resources to enable a systems-based analysis of microbiome function using this model. Here, we highlighted four distinct applications of these resources that enable and improve (i) measurements of the abundance of each ASF member by quantitative PCR; (ii) exploration and comparative analysis of ASF genomes and the metabolic pathways they encode that comprise the entire gut microbiome; (iii) global transcriptional profiling to identify genes whose expression responds to environmental changes within the gut; and (iv) discovery of genetic changes resulting from the evolutionary adaptation of the microbiota. These resources were designed to be accessible to a broad community of researchers that, in combination with conventionally-reared mice (i.e., with complex microbiome), should contribute to our understanding of microbiome structure and function. IMPORTANCE Improved experimental systems are needed to advance our understanding of how the gut microbiome influences processes of the mammalian host as well as microbial community structure and function. An approach that is receiving considerable attention is the use of animal models that harbor a stable microbiota of known composition, i.e., defined microbiota, which enables control over an otherwise highly complex and variable feature of mammalian biology. The altered Schaedler flora (ASF) consortium is a well-established defined microbiota model, where mice are stably colonized with 8 distinct murine bacterial species. To take better advantage of the ASF, we established new experimental and bioinformatics resources for researchers to make better use of this model as an experimental system to study microbiome function.
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Affiliation(s)
- Alexandra Proctor
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Shadi Parvinroo
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Tanner Richie
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Xinglin Jia
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Aleksandar D. Kostic
- Department of Microbiology and Immunology, Joslin Diabetes Center, Harvard University, Cambridge Massachusetts, USA
| | - Joseph F. Pierre
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison Wisconsin, USA
| | | | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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22
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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities. Cell Host Microbe 2022; 30:1630-1645.e25. [DOI: 10.1016/j.chom.2022.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/30/2022] [Accepted: 09/13/2022] [Indexed: 12/26/2022]
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23
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From germ-free to wild: modulating microbiome complexity to understand mucosal immunology. Mucosal Immunol 2022; 15:1085-1094. [PMID: 36065057 DOI: 10.1038/s41385-022-00562-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 02/04/2023]
Abstract
The gut microbiota influences host responses at practically every level, and as research into host-microbe interactions expands, it is not surprising that we are uncovering similar roles for the microbiota at other barrier sites, such as the lung and skin. Using standard laboratory mice to assess host-microbe interactions, or even host intrinsic responses, can be challenging, as slight variations in the microbiota can affect experimental outcomes. When it comes to designing and selecting an appropriate level of microbial diversity and community structure for colonization of our laboratory rodents, we have more choices available to us than ever before. Here we will discuss the different approaches used to modulate microbial complexity that are available to study host-microbe interactions. We will describe how different models have been used to answer distinct biological questions, covering the entire microbial spectrum, from germ-free to wild.
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