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Gopalakrishnan V, Dozier EA, Glover MS, Novick S, Ford M, Morehouse C, Warrener P, Caceres C, Hess S, Sellman BR, Cohen TS. Engraftment of Bacteria after Fecal Microbiota Transplantation Is Dependent on Both Frequency of Dosing and Duration of Preparative Antibiotic Regimen. Microorganisms 2021; 9:1399. [PMID: 34209573 PMCID: PMC8306289 DOI: 10.3390/microorganisms9071399] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
The gut microbiota has emerged as a key mediator of human physiology, and germ-free mice have been essential in demonstrating a role for the microbiome in disease. Preclinical models using conventional mice offer the advantage of working with a mature immune system. However, optimal protocols for fecal microbiota transplant (FMT) engraftment in conventional mice are yet to be established. Conventional BALB/c mice were randomized to receive 3-day (3d) or 3-week (3w) antibiotic (ABX) regimen in their drinking water followed by 1 or 5-daily FMTs from a human donor. Fecal samples were collected longitudinally and characterized using 16S ribosomal RNA (rRNA) sequencing. Semi-targeted metabolomic profiling of fecal samples was also done with liquid chromatography-mass spectrometry (LC-MS). Lastly, we sought to confirm our findings in BKS mice. Recovery of baseline diversity scores were greatest in the 3d groups, driven by re-emergence of mouse commensal microbiota, whereas the most resemblance to donor microbiota was seen in the 3w + 5-FMT group. Amplicon sequence variants (ASVs) that were linked to the input material (human ASVs) engrafted to a significantly greater extent when compared to mouse ASVs in the 3-week groups but not the 3-day groups. Lastly, comparison of metabolomic profiles revealed distinct functional profiles by ABX regimen. These results indicate successful model optimization and emphasize the importance of ABX duration and frequency of FMT dosing; the most stable and reliable colonization by donor ASVs was seen in the 3wk + 5-FMT group.
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Affiliation(s)
- Vancheswaran Gopalakrishnan
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Elizabeth Ashley Dozier
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Matthew S. Glover
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Steven Novick
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Michael Ford
- Animal Sciences and Technologies, R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Christopher Morehouse
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Paul Warrener
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Carolina Caceres
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Sonja Hess
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Bret R. Sellman
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Taylor S. Cohen
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
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Lundberg R, Toft MF, Metzdorff SB, Hansen CHF, Licht TR, Bahl MI, Hansen AK. Human microbiota-transplanted C57BL/6 mice and offspring display reduced establishment of key bacteria and reduced immune stimulation compared to mouse microbiota-transplantation. Sci Rep 2020; 10:7805. [PMID: 32385373 PMCID: PMC7211022 DOI: 10.1038/s41598-020-64703-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Transplantation of germ-free (GF) mice with microbiota from mice or humans stimulates the intestinal immune system in disparate ways. We transplanted a human microbiota into GF C57BL/6 mice and a murine C57BL/6 microbiota into GF C57BL/6 mice and Swiss-Webster (SW) mice. Mice were bred to produce an offspring generation. 56% of the Operational Taxonomic Units (OTUs) present in the human donor microbiota established in the recipient mice, whereas 81% of the C57BL/6 OTUs established in the recipient C57BL/6 and SW mice. Anti-inflammatory bacteria such as Faecalibacterium and Bifidobacterium from humans were not transferred to mice. Expression of immune-related intestinal genes was lower in human microbiota-mice and not different between parent and offspring generation. Expression of intestinal barrier-related genes was slightly higher in human microbiota-mice. Cytokines and chemokines measured in plasma were differentially present in human and mouse microbiota-mice. Minor differences in microbiota and gene expression were found between transplanted mice of different genetics. It is concluded that important immune-regulating bacteria are lost when transplanting microbiota from humans to C57BL/6 mice, and that the established human microbiota is a weak stimulator of the murine immune system. The results are important for study design considerations in microbiota transplantation studies involving immunological parameters.
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Affiliation(s)
- Randi Lundberg
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark.
- Internal Research and Development, Taconic Biosciences, 4623, Lille Skensved, Denmark.
- Chr. Hansen, 2970, Hoersholm, Denmark.
| | - Martin F Toft
- Internal Research and Development, Taconic Biosciences, 4623, Lille Skensved, Denmark
- QM Diagnostics, 6534, AT Nijmegen, The Netherlands
| | - Stine B Metzdorff
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Camilla H F Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Tine R Licht
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Martin I Bahl
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Axel K Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
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Flemer B, Gaci N, Borrel G, Sanderson IR, Chaudhary PP, Tottey W, O'Toole PW, Brugère JF. Fecal microbiota variation across the lifespan of the healthy laboratory rat. Gut Microbes 2017; 8:428-439. [PMID: 28586297 PMCID: PMC5628645 DOI: 10.1080/19490976.2017.1334033] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Laboratory rats are commonly used in life science research as a model for human biology and disease, but the composition and development of their gut microbiota during life is poorly understood. We determined the fecal microbiota composition of healthy Sprague Dawley laboratory rats from 3 weeks to 2 y of age, kept under controlled environmental and dietary conditions. Additionally, we determined fecal short-chain fatty acid profiles, and we compared the rat fecal microbiota with that of mice and humans. Gut microbiota and to a lesser extent SCFAs profiles separated rats into 3 different clusters according to age: before weaning, first year of life (12- to 26-week-old animals) and second year of life (52- to 104-week-old). A core of 46 bacterial species was present in all rats but its members' relative abundance progressively decreased with age. This was accompanied by an increase of microbiota α-diversity, likely due to the acquisition of environmental microorganisms during the lifespan. Contrastingly, the functional profile of the microbiota across animal species became more similar upon aging. Lastly, the microbiota of rats and mice were most similar to each other but at the same time the microbiota profile of rats was more similar to that of humans than was the microbiota profile of mice. These data offer an explanation as to why germ-free rats are more efficient recipients and retainers of human microbiota than mice. Furthermore, experimental design should take into account dynamic changes in the microbiota of model animals considering that their changing gut microbiota interacts with their physiology.
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Affiliation(s)
- Burkhardt Flemer
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland
| | - Nadia Gaci
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Guillaume Borrel
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Ian R. Sanderson
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Prem P. Chaudhary
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - William Tottey
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Paul W. O'Toole
- School of Microbiology and APC Microbiome Institute, University College Cork, Ireland,Paul W. O'Toole School of Microbiology and APC Microbiome Institute, University College Cork, College Road, Cork, Ireland
| | - Jean-François Brugère
- EA-4678 CIDAM, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France,CONTACT Jean-François Brugère 5e CBRV, Facultés de Médecine et de Pharmacie de Clermont-Ferrand, 28 place Henri Dunant, F-63000 Clermont-Ferrand France
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Zeng B, Li G, Yuan J, Li W, Tang H, Wei H. Effects of age and strain on the microbiota colonization in an infant human flora-associated mouse model. Curr Microbiol 2013; 67:313-21. [PMID: 23604540 DOI: 10.1007/s00284-013-0360-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Accepted: 03/04/2013] [Indexed: 01/15/2023]
Abstract
The establishment of human flora-associated animal models allows the in vivo manipulation of host, microbial, and environmental parameters to influence the gut microbial community. However, it is difficult to simulate infant gut microbiota in germ-free animals because of the variation and dynamic state of infant microbial communities. In this study, the effects of age and strain on intestinal microbiota were observed in an infant human flora-associated (IHFA) mouse model. To establish an IHFA model, postnatal day (PND) 1 germ-free mice (Kunming, n = 10; BALB/c, n = 10) were infected with feces from a breast-fed infant. Microbiota in the feces of BALB/c mice (at PND 7, 14, and 21), and Kunming mice (at PND 14) were analyzed by PCR-denaturing gradient gel electrophoresis. Bifidobacteria and lactobacilli levels in the feces of BALB/c and Kunming mice (PND 7/14/21) were detected by quantitative real-time PCR. The Dice similarity coefficient (Cs) for the fecal microbiota of IHFA mice in comparison with the HD donor sample was higher for BALB/c mice than for Kunming mice (P < 0.05). In addition, the DCs at PND 7 were lower than those at PND 14 and PND 21 in both mouse strains (P < 0.05). The Bifidobacteria and Lactobacillus species colonizing the BALB/c mice were similar to those in the Kunming mice (at PND 7/14/21). The bifidobacteria counts increased with age in both mouse strains, whereas the lactobacilli counts decreased with age in both strains. These results suggest that both age and strain influence microbiota patterns in the IHFA mouse model.
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Affiliation(s)
- Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Gaotanyan Street, Chongqing, China.
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Bibiloni R. Rodent models to study the relationships between mammals and their bacterial inhabitants. Gut Microbes 2012; 3:536-43. [PMID: 22918304 PMCID: PMC3495791 DOI: 10.4161/gmic.21905] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Laboratory rodents have been instrumental in helping researchers to unravel the complex interactions that mammals have with their microbial commensals. Progress in defining these interactions has also been possible thanks to the development of culture-independent methods for describing the microbiota associated to body surfaces. Understanding the mechanisms that govern this relationship at the molecular, cellular, and ecological levels is central to both health and disease. The present review of rodent models commonly used to investigate microbial-host "conversations" is focused on those complex bacterial communities residing in the lower gut. Although many types of pathology have been studied using gnotobiotic animals, only the models relevant to commensal bacteria will be described.
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Wos-Oxley ML, Bleich A, Oxley AP, Kahl S, Janus LM, Smoczek A, Nahrstedt H, Pils MC, Taudien S, Platzer M, Hedrich HJ, Medina E, Pieper DH. Comparative evaluation of establishing a human gut microbial community within rodent models. Gut Microbes 2012; 3:234-49. [PMID: 22572831 PMCID: PMC3427216 DOI: 10.4161/gmic.19934] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The structure of the human gut microbial community is determined by host genetics and environmental factors, where alterations in its structure have been associated with the onset of different diseases. Establishing a defined human gut microbial community within inbred rodent models provides a means to study microbial-related pathologies, however, an in-depth comparison of the established human gut microbiota in the different models is lacking. We compared the efficiency of establishing the bacterial component of a defined human microbial community within germ-free (GF) rats, GF mice, and antibiotic-treated specific pathogen-free mice. Remarkable differences were observed between the different rodent models. While the majority of abundant human-donor bacterial phylotypes were established in the GF rats, only a subset was present in the GF mice. Despite the fact that members of the phylum Bacteriodetes were well established in all rodent models, mice enriched for phylotypes related to species of Bacteroides. In contrary to the efficiency of Clostridiales to populate the GF rat in relative proportions to that of the human-donor, members of Clostridia cluster IV only poorly colonize the mouse gut. Thus, the genetic background of the different recipient rodent systems (that is, rats and mice) strongly influences the nature of the populating human gut microbiota, determining each model's biological suitability.
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Affiliation(s)
- Melissa L. Wos-Oxley
- Microbial Interactions and Processes Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany,Correspondence to: Melissa L. Wos-Oxley,
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility; Hannover Medical School; Hannover, Germany
| | - Andrew P.A. Oxley
- Infection Immunology Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany
| | - Silke Kahl
- Microbial Interactions and Processes Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany
| | - Lydia M. Janus
- Institute for Laboratory Animal Science and Central Animal Facility; Hannover Medical School; Hannover, Germany
| | - Anna Smoczek
- Institute for Laboratory Animal Science and Central Animal Facility; Hannover Medical School; Hannover, Germany
| | - Hannes Nahrstedt
- Microbial Interactions and Processes Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany
| | - Marina C. Pils
- Central Animal Facility; Helmholtz Centre for Infection Research; Braunschweig, Germany
| | - Stefan Taudien
- Genome Analysis; Leibniz Institute for Age Research; Fritz Lipmann Institute; Jena, Germany
| | - Matthias Platzer
- Genome Analysis; Leibniz Institute for Age Research; Fritz Lipmann Institute; Jena, Germany
| | - Hans-Jürgen Hedrich
- Institute for Laboratory Animal Science and Central Animal Facility; Hannover Medical School; Hannover, Germany
| | - Eva Medina
- Infection Immunology Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group; Department of Medical Microbiology; Helmholtz Centre for Infection Research; Braunschweig, Germany
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Crost E, Pujol A, Ladiré M, Dabard J, Raibaud P, Carlier J, Fons M. Production of an antibacterial substance in the digestive tract involved in colonization-resistance against Clostridium perfringens. Anaerobe 2010; 16:597-603. [DOI: 10.1016/j.anaerobe.2010.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 05/18/2010] [Accepted: 06/25/2010] [Indexed: 11/17/2022]
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