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Abstract
PURPOSE OF REVIEW Probiotics are promising remedial treatments for symptoms of small intestine (SI) diseases and promoters of overall good health. Probiotics play an important role in supporting a healthy SI microbiome (eubiosis), and in preventing establishment of unhealthy microbiota. SI eubiosis promotes optimal nutrient uptake, and optimal nutritional status maintains a healthy SI, reducing the likelihood of SI diseases. It is important to understand the advantages and limitations of probiotic therapies. RECENT FINDINGS Microbial dysbiosis decreases the capacity of the small bowel to utilize and absorb dietary compounds. In some studies, probiotic supplements containing lactic acid bacteria and Bifidobacterium have been demonstrated effective in supporting beneficial microbes in the SI while improving barrier integrity and reducing nutrient malabsorption and SI disease-related pathology. Strain-specific probiotic therapy may be a natural and effective approach to restoring SI barrier integrity and eubiosis, resulting in improved nutrient absorption and better health, including reducing the incidence of and severity of SI diseases.
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Affiliation(s)
- Taylor C Judkins
- Food Science and Human Nutrition Department, University of Florida, 572 Newell Dr., Gainesville, FL, 32611, USA
| | - Douglas L Archer
- Food Science and Human Nutrition Department, University of Florida, 572 Newell Dr., Gainesville, FL, 32611, USA
| | | | - Rebecca J Solch
- Food Science and Human Nutrition Department, University of Florida, 572 Newell Dr., Gainesville, FL, 32611, USA.
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Das B, Okamoto K, Rabalais J, Kozan PA, Marchelletta RR, McGeough MD, Durali N, Go M, Barrett KE, Das S, Sivagnanam M. Enteroids expressing a disease-associated mutant of EpCAM are a model for congenital tufting enteropathy. Am J Physiol Gastrointest Liver Physiol 2019; 317:G580-G591. [PMID: 31433211 PMCID: PMC6879886 DOI: 10.1152/ajpgi.00098.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Congenital tufting enteropathy (CTE) is an autosomal recessive disease characterized by severe intestinal failure in infancy and mutations in the epithelial cell adhesion molecule (EPCAM) gene. Previous studies of CTE in mice expressing mutant EpCAM show neonatal lethality. Hence, to study the cellular, molecular, and physiological alterations that result from EpCAM mutation, a tamoxifen-inducible mutant EpCAM enteroid model has been generated. The presence of mutant EpCAM in the model was confirmed at both mRNA and protein levels. Immunofluorescence microscopy demonstrated the reduced expression of mutant EpCAM. Mutant enteroids had reduced budding potential as well as significantly decreased mRNA expression for epithelial lineage markers (Mucin 2, lysozyme, sucrase-isomaltase), proliferation marker Ki67, and secretory pathway transcription factors (Atoh1, Hnf1b). Significantly decreased numbers of Paneth and goblet cells were confirmed by staining. These findings were correlated with intestinal tissue from CTE patients and the mutant mice model that had significantly fewer Paneth and goblet cells than in healthy counterparts. FITC-dextran studies demonstrated significantly impaired barrier function in monolayers derived from mutant enteroids compared with control monolayers. In conclusion, we have established an ex vivo CTE model. The role of EpCAM in the budding potential, differentiation, and barrier function of enteroids is noted. Our study establishes new facets of EpCAM biology that will aid in understanding the pathophysiology of CTE and role of EpCAM in health and disease.NEW & NOTEWORTHY Here, we develop a novel ex vivo enteroid model for congenital tufting enteropathy (CTE) based on epithelial cell adhesion molecule (EPCAM) gene mutations found in patients. With this model we demonstrate the role of EpCAM in maintaining the functional homeostasis of the intestinal epithelium, including differentiation, proliferation, and barrier integrity. This study further establishes a new direction in EpCAM biology that will help in understanding the detailed pathophysiology of CTE and role of EpCAM.
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Affiliation(s)
- Barun Das
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Kevin Okamoto
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - John Rabalais
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Philip A. Kozan
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | | | - Matthew D. McGeough
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Nassim Durali
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Maria Go
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Kim E. Barrett
- 2Department of Medicine, University of California, San Diego, La Jolla, California
| | - Soumita Das
- 3Department of Pathology, University of California, San Diego, La Jolla, California
| | - Mamata Sivagnanam
- 1Department of Pediatrics, University of California, San Diego, La Jolla, California,4Rady Children’s Hospital, San Diego, California
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Kolawole AO, Mirabelli C, Hill DR, Svoboda SA, Janowski AB, Passalacqua KD, Rodriguez BN, Dame MK, Freiden P, Berger RP, Vu DL, Hosmillo M, O'Riordan MXD, Schultz-Cherry S, Guix S, Spence JR, Wang D, Wobus CE. Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. PLoS Pathog 2019; 15:e1008057. [PMID: 31671153 PMCID: PMC6957189 DOI: 10.1371/journal.ppat.1008057] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 01/13/2020] [Accepted: 08/30/2019] [Indexed: 12/26/2022] Open
Abstract
Human astroviruses (HAstV) are understudied positive-strand RNA viruses that cause gastroenteritis mostly in children and the elderly. Three clades of astroviruses, classic, MLB-type and VA-type have been reported in humans. One limitation towards a better understanding of these viruses has been the lack of a physiologically relevant cell culture model that supports growth of all clades of HAstV. Herein, we demonstrate infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts. A detailed investigation of infection of VA1, a member of the non-canonical HAstV-VA/HMO clade, showed robust replication in HIE derived from different patients and from different intestinal regions independent of the cellular differentiation status. Flow cytometry and immunofluorescence analysis revealed that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes, in HIE cultures. RNA profiling of VA1-infected HIE uncovered that the host response to infection is dominated by interferon (IFN)-mediated innate immune responses. A comparison of the antiviral host response in non-transformed HIE and transformed human colon carcinoma Caco-2 cells highlighted significant differences between these cells, including an increased magnitude of the response in HIE. Additional studies confirmed the sensitivity of VA1 to exogenous IFNs, and indicated that the endogenous IFN response of HIE to curtail the growth of strains from all three clades. Genotypic variation in the permissiveness of different HIE lines to HAstV could be overcome by pharmacologic inhibition of JAK/STAT signaling. Collectively, our data identify HIE as a universal infection model for HAstV and an improved model of the intestinal epithelium to investigate enteric virus-host interactions. Human astroviruses (HAstV) are understudied positive-strand RNA viruses that typically cause gastroenteritis mostly in children and the elderly, but more recent studies also implicate them in neurological disease in immunocompromised patients. To better understand these viruses, a physiologically relevant cell culture model that supports growth of all clades of HAstV would be highly beneficial. Herein, we demonstrated robust infection of HAstV strains belonging to all three clades in epithelium-only human intestinal enteroids (HIE) isolated from biopsy-derived intestinal crypts from different patients and intestinal regions, making HIE a valuable model to study HAstV biology. Using this system, we identify for the first time that VA1 infects several cell types, including intestinal progenitor cells and mature enterocytes. Analysis of the antiviral host response to infection demonstrated that HIE respond to infection with a type I and III interferon response. This response reduced HAstV replication and when blocked resulted in increased infection. Establishment of the HIE system for HAstV research lays the foundation for future basic and translational discoveries.
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Affiliation(s)
- Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R Hill
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sophia A Svoboda
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew B Janowski
- Department of Pediatrics, Washington University, St. Louis, Missouri, United States of America
| | - Karla D Passalacqua
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Benancio N Rodriguez
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Pamela Freiden
- St. Jude Children's Hospital, Memphis, Tennessee, United States of America
| | - Ryan P Berger
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Mary X D O'Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Biomedical Engineering, University of Michigan, Ann arbor, Michigan, United States of America
| | - David Wang
- Departments of Molecular Microbiology, and Pathology and Immunology, Washington University, St. Louis, Missouri, United States of America
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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54
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Engevik MA, Morra CN, Röth D, Engevik K, Spinler JK, Devaraj S, Crawford SE, Estes MK, Kalkum M, Versalovic J. Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors. Front Microbiol 2019; 10:2305. [PMID: 31649646 PMCID: PMC6795088 DOI: 10.3389/fmicb.2019.02305] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Microbial metabolites, including B complex vitamins contribute to diverse aspects of human health. Folate, or vitamin B9, refers to a broad category of biomolecules that include pterin, para-aminobenzoic acid (pABA), and glutamate subunits. Folates are required for DNA synthesis and epigenetic regulation. In addition to dietary nutrients, the gut microbiota has been recognized as a source of B complex vitamins, including folate. This study evaluated the predicted folate synthesis capabilities in the genomes of human commensal microbes identified in the Human Microbiome Project and folate production by representative strains of six human intestinal bacterial phyla. Bacterial folate synthesis genes were ubiquitous across 512 gastrointestinal reference genomes with 13% of the genomes containing all genes required for complete de novo folate synthesis. An additional 39% of the genomes had the genetic capacity to synthesize folates in the presence of pABA, an upstream intermediate that can be obtained through diet or from other intestinal microbes. Bacterial folate synthesis was assessed during exponential and stationary phase growth through the evaluation of expression of select folate synthesis genes, quantification of total folate production, and analysis of folate polyglutamylation. Increased expression of key folate synthesis genes was apparent in exponential phase, and increased folate polyglutamylation occurred during late stationary phase. Of the folate producers, we focused on the commensal Lactobacillus reuteri to examine host-microbe interactions in relation to folate and examined folate receptors in the physiologically relevant human enteroid model. RNAseq data revealed segment-specific folate receptor distribution. Treatment of human colonoid monolayers with conditioned media (CM) from wild-type L. reuteri did not influence the expression of key folate transporters proton-coupled folate transporter (PCFT) or reduced folate carrier (RFC). However, CM from L. reuteri containing a site-specific inactivation of the folC gene, which prevents the bacteria from synthesizing a polyglutamate tail on folate, significantly upregulated RFC expression. No effects were observed using L. reuteri with a site inactivation of folC2, which results in no folate production. This work sheds light on the contributions of microbial folate to overall folate status and mammalian host metabolism.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Christina N. Morra
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Röth
- Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Kristen Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Jennifer K. Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Sridevi Devaraj
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Department of Medicine – Gastroenterology, Hepatology and Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, United States
- Mass Spectrometry and Proteomics Core, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
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55
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George MM, Rahman M, Connors J, Stadnyk AW. Opinion: Are Organoids the End of Model Evolution for Studying Host Intestinal Epithelium/Microbe Interactions? Microorganisms 2019; 7:microorganisms7100406. [PMID: 31569537 PMCID: PMC6843211 DOI: 10.3390/microorganisms7100406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
In the pursuit to understand intestinal epithelial cell biology in health and disease, researchers have established various model systems, from whole animals (typically rodents) with experimentally induced disease to transformed human carcinomas. The obvious limitation to the ex vivo or in vitro cell systems was enriching, maintaining, and expanding differentiated intestinal epithelial cell types. The popular concession was human and rodent transformed cells of mainly undifferentiated cells, with a few select lines differentiating along the path to becoming goblet cells. Paneth cells, in particular, remained unculturable. The breakthrough came in the last decade with the report of conditions to grow mouse intestinal organoids. Organoids are 3-dimensional ex vivo “mini-organs” of the organ from which the stem cells were derived. Intestinal organoids contain fully differentiated epithelial cells in the same spatial organization as in the native epithelium. The cells are suitably polarized and produce and secrete mucus onto the apical surface. This review introduces intestinal organoids and provide some thoughts on strengths and weaknesses in the application of organoids to further advance our understanding of the intestinal epithelial–microbe relationship.
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Affiliation(s)
- Michelle M George
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Mushfiqur Rahman
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Jessica Connors
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
| | - Andrew W Stadnyk
- Department of Pediatrics, Division of Gastroenterology & Nutrition, Dalhousie University, 5850 University Avenue, Halifax, NS B3K 6R8, Canada.
- Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
- Department of Pathology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
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Estes MK, Ettayebi K, Tenge VR, Murakami K, Karandikar U, Lin SC, Ayyar BV, Cortes-Penfield NW, Haga K, Neill FH, Opekun AR, Broughman JR, Zeng XL, Blutt SE, Crawford SE, Ramani S, Graham DY, Atmar RL. Human Norovirus Cultivation in Nontransformed Stem Cell-Derived Human Intestinal Enteroid Cultures: Success and Challenges. Viruses 2019; 11:E638. [PMID: 31336765 PMCID: PMC6669637 DOI: 10.3390/v11070638] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Noroviruses, in the genus Norovirus, are a significant cause of viral gastroenteritis in humans and animals. For almost 50 years, the lack of a cultivation system for human noroviruses (HuNoVs) was a major barrier to understanding virus biology and the development of effective antiviral strategies. This review presents a historical perspective of the development of a cultivation system for HuNoVs in human intestinal epithelial cell cultures. Successful cultivation was based on the discovery of genetically-encoded host factors required for infection, knowledge of the site of infection in humans, and advances in the cultivation of human intestinal epithelial cells achieved by developmental and stem cell biologists. The human stem cell-derived enteroid cultivation system recapitulates the multicellular, physiologically active human intestinal epithelium, and allows studies of virus-specific replication requirements, evaluation of human host-pathogen interactions, and supports the pre-clinical assessment of methods to prevent and treat HuNoV infections.
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Affiliation(s)
- Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Medicine, Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Medicine, Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Victoria R Tenge
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kosuke Murakami
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Virology II, National Institute of Infectious Diseases, Musashi-murayama, Tokyo 208-0011, Japan
| | - Umesh Karandikar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Vijayalakshmi Ayyar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Kei Haga
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antone R Opekun
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Broughman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Y Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
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Guthrie L, Kelly L. Bringing microbiome-drug interaction research into the clinic. EBioMedicine 2019; 44:708-715. [PMID: 31151933 PMCID: PMC6604038 DOI: 10.1016/j.ebiom.2019.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the scope and clinical relevance of gut microbiota metabolism of drugs is limited to relatively few biotransformations targeting a subset of therapeutics. Translating microbiome research into the clinic requires, in part, a mechanistic and predictive understanding of microbiome-drug interactions. This review provides an overview of microbiota chemistry that shapes drug efficacy and toxicity. We discuss experimental and computational approaches that attempt to bridge the gap between basic and clinical microbiome research. We highlight the current landscape of preclinical research focused on identifying microbiome-based biomarkers of patient drug response and we describe clinical trials investigating approaches to modulate the microbiome with the goal of improving drug efficacy and safety. We discuss approaches to aggregate clinical and experimental microbiome features into predictive models and review open questions and future directions toward utilizing the gut microbiome to improve drug safety and efficacy.
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Affiliation(s)
- Leah Guthrie
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, United States of America
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, United States of America; Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, United States of America.
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58
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Chandra L, Borcherding DC, Kingsbury D, Atherly T, Ambrosini YM, Bourgois-Mochel A, Yuan W, Kimber M, Qi Y, Wang Q, Wannemuehler M, Ellinwood NM, Snella E, Martin M, Skala M, Meyerholz D, Estes M, Fernandez-Zapico ME, Jergens AE, Mochel JP, Allenspach K. Derivation of adult canine intestinal organoids for translational research in gastroenterology. BMC Biol 2019; 17:33. [PMID: 30975131 PMCID: PMC6460554 DOI: 10.1186/s12915-019-0652-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Large animal models, such as the dog, are increasingly being used for studying diseases including gastrointestinal (GI) disorders. Dogs share similar environmental, genomic, anatomical, and intestinal physiologic features with humans. To bridge the gap between commonly used animal models, such as rodents, and humans, and expand the translational potential of the dog model, we developed a three-dimensional (3D) canine GI organoid (enteroid and colonoid) system. Organoids have recently gained interest in translational research as this model system better recapitulates the physiological and molecular features of the tissue environment in comparison with two-dimensional cultures. Results Organoids were derived from tissue of more than 40 healthy dogs and dogs with GI conditions, including inflammatory bowel disease (IBD) and intestinal carcinomas. Adult intestinal stem cells (ISC) were isolated from whole jejunal tissue as well as endoscopically obtained duodenal, ileal, and colonic biopsy samples using an optimized culture protocol. Intestinal organoids were comprehensively characterized using histology, immunohistochemistry, RNA in situ hybridization, and transmission electron microscopy, to determine the extent to which they recapitulated the in vivo tissue characteristics. Physiological relevance of the enteroid system was defined using functional assays such as optical metabolic imaging (OMI), the cystic fibrosis transmembrane conductance regulator (CFTR) function assay, and Exosome-Like Vesicles (EV) uptake assay, as a basis for wider applications of this technology in basic, preclinical and translational GI research. We have furthermore created a collection of cryopreserved organoids to facilitate future research. Conclusions We establish the canine GI organoid systems as a model to study naturally occurring intestinal diseases in dogs and humans, and that can be used for toxicology studies, for analysis of host-pathogen interactions, and for other translational applications. Electronic supplementary material The online version of this article (10.1186/s12915-019-0652-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lawrance Chandra
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | - Dawn Kingsbury
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | - Todd Atherly
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | | | - Wang Yuan
- Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Michael Kimber
- Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Yijun Qi
- Departments of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Qun Wang
- Departments of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Michael Wannemuehler
- Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | | | | | - Melissa Skala
- Biomedical Engineering, University of Wisconsin, Madison, WI, USA
| | - David Meyerholz
- Division of Comparative Pathology, University of Iowa Carver College of Medicine, Iowa City, USA
| | - Mary Estes
- Baylor College of Medicine, Houston, TX, USA
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Albert E Jergens
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | - Karin Allenspach
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA.
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Stewart CJ, Fatemizadeh R, Parsons P, Lamb CA, Shady DA, Petrosino JF, Hair AB. Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue. BMC Microbiol 2019; 19:52. [PMID: 30832576 PMCID: PMC6398254 DOI: 10.1186/s12866-019-1426-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared. Results Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively. Conclusions Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls. Electronic supplementary material The online version of this article (10.1186/s12866-019-1426-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. .,Institute of Cellular Medicine, Newcastle University, Medical School, Leech Building, M3.121, Newcastle upon Tyne, NE2 4HH, UK.
| | - Roxana Fatemizadeh
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Pamela Parsons
- Texas Medical Center Digestive Diseases Center, Core B Cellular and Molecular Morphology, Houston, TX, USA
| | - Christopher A Lamb
- Institute of Cellular Medicine, Newcastle University, Medical School, Leech Building, M3.121, Newcastle upon Tyne, NE2 4HH, UK.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Deborah A Shady
- Texas Medical Center Digestive Diseases Center, Core B Cellular and Molecular Morphology, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Amy B Hair
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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60
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Nagpal R, Wang S, Solberg Woods LC, Seshie O, Chung ST, Shively CA, Register TC, Craft S, McClain DA, Yadav H. Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces. Front Microbiol 2018; 9:2897. [PMID: 30555441 PMCID: PMC6283898 DOI: 10.3389/fmicb.2018.02897] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Gut microbiome plays a fundamental role in several aspects of host health and diseases. There has been an exponential surge in the use of animal models that can mimic different phenotypes of the human intestinal ecosystem. However, data on host species-specific signatures of gut microbiome and its metabolites like short-chain fatty acids (SCFAs; i.e., acetate, propionate, and butyrate) and lactate in these models and their similarities/differences from humans remain limited, due to high variability in protocols and analyses. Here, we analyze the fecal microbiota composition and the fecal levels of SCFAs and lactate in three of the most-widely used animal models, i.e., mice, rats, and non-human primates (NHPs) and compare them with human subjects, using data generated on a single platform with same protocols. The data show several species-specific similarities and differences in the gut microbiota and fecal organic acids between these species groups. Based on β-diversity, the gut microbiota in humans seems to be closer to NHPs than to mice and rats; however, among rodents, mice microbiota appears to be closer to humans than rats. The phylum-level analyses demonstrate higher Firmicutes-Bacteroidetes ratio in humans and NHPs vs. mice and rats. Human microbiota is dominated by Bacteroides followed by Ruminococcaceae and Clostridiales. Mouse gut is predominated by members of the family S24-7 followed by those from the order Clostridiales, whereas rats and NHPs have higher abundance of Prevotella compared with mice and humans. Also, fecal levels of lactate are higher in mice and rats vs. NHPs and humans, while acetate is highest in human feces. These data of host species-specific gut microbiota signatures in some of the most widely used animal models in context to the human microbiota might reflect disparities in host factors, e.g., diets, genetic origin, gender and age, and hence call for prospective studies investigating the features of gut microbiome in such animal models by controlling for these host elements.
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Affiliation(s)
- Ravinder Nagpal
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States.,Department of Microbiology and Immunology, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States
| | - Shaohua Wang
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States.,Department of Microbiology and Immunology, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States
| | - Leah C Solberg Woods
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States.,Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Osborne Seshie
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States
| | - Stephanie T Chung
- Diabetes, Endocrinology and Obesity Branch, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Carol A Shively
- Department of Pathology-Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Thomas C Register
- Department of Pathology-Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Suzanne Craft
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Donald A McClain
- Department of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Hariom Yadav
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States.,Department of Microbiology and Immunology, Wake Forest School of Medicine, Center for Diabetes, Obesity and Metabolism, Winston-Salem, NC, United States
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61
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Pearce SC, Coia HG, Karl JP, Pantoja-Feliciano IG, Zachos NC, Racicot K. Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors. Front Physiol 2018; 9:1584. [PMID: 30483150 PMCID: PMC6240795 DOI: 10.3389/fphys.2018.01584] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 12/16/2022] Open
Abstract
The gut microbiome is extremely important for maintaining homeostasis with host intestinal epithelial, neuronal, and immune cells and this host-microbe interaction is critical during times of stress or disease. Environmental, nutritional, and cognitive stress are just a few factors known to influence the gut microbiota and are thought to induce microbial dysbiosis. Research on this bidirectional relationship as it pertains to health and disease is extensive and rapidly expanding in both in vivo and in vitro/ex vivo models. However, far less work has been devoted to studying effects of host-microbe interactions on acute stressors and performance, the underlying mechanisms, and the modulatory effects of different stressors on both the host and the microbiome. Additionally, the use of in vitro/ex vivo models to study the gut microbiome and human performance has not been researched extensively nor reviewed. Therefore, this review aims to examine current evidence concerning the current status of in vitro and ex vivo host models, the impact of acute stressors on gut physiology/microbiota as well as potential impacts on human performance and how we can parlay this information for DoD relevance as well as the broader scientific community. Models reviewed include widely utilized intestinal cell models from human and animal models that have been applied in the past for stress or microbiology research as well as ex vivo organ/tissue culture models and new innovative models including organ-on-a-chip and co-culture models.
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Affiliation(s)
- Sarah C Pearce
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Heidi G Coia
- National Research Council, The National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States.,711th Human Performance Wing, Airforce Research Laboratory, Airman Systems Directorate, Human-Centered ISR Division, Molecular Mechanisms Branch, Wright-Patterson Air Force Base, Dayton, OH, United States
| | - J P Karl
- Military Nutrition Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA, United States
| | - Ida G Pantoja-Feliciano
- Soldier Protection and Optimization Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kenneth Racicot
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
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62
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Harris VC. The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications. Drugs 2018; 78:1063-1072. [PMID: 29943376 PMCID: PMC6061423 DOI: 10.1007/s40265-018-0941-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite unprecedented advances in understanding the intestinal microbiome, its potential to improve fields such as vaccinology has yet to be realized. This review briefly outlines the immunologic potential of the intestinal microbiome for vaccinology and highlights areas where the microbiome holds specific promise in vaccinology. Oral rotavirus vaccine effectiveness in low-income countries is used as a case study to describe how the intestinal microbiome may be employed to improve a vaccine's immunogenicity. A top-down, evidence-based approach is proposed to identify effective microbiota-based applications for vaccine improvement. Applying evidence from field studies in pertinent populations that correlate microbiome composition with vaccine effectiveness to appropriate experimental platforms will lead to the identification of safe, vaccine-supporting microbiota targets that are relevant to populations in need of improvement in vaccine-induced immunity.
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Affiliation(s)
- Vanessa C Harris
- Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands.
- Department of Medicine, Division of Infectious Diseases and Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center, Amsterdam, The Netherlands.
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63
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Ramani S, Crawford SE, Blutt SE, Estes MK. Human organoid cultures: transformative new tools for human virus studies. Curr Opin Virol 2018; 29:79-86. [PMID: 29656244 PMCID: PMC5944856 DOI: 10.1016/j.coviro.2018.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 12/23/2022]
Abstract
Studies of human infectious diseases have been limited by the paucity of functional models that mimic normal human physiology and pathophysiology. Recent advances in the development of multicellular, physiologically active organotypic cultures produced from embryonic and pluripotent stem cells, as well as from stem cells isolated from biopsies and surgical specimens are allowing unprecedented new studies and discoveries about host-microbe interactions. Here, we summarize recent developments in the use of organoids for studying human viral pathogens, including intestinal infections with human rotavirus, norovirus, enteroviruses and adenoviruses (intestinal organoids and enteroids), neuronal infections with Zika virus (cerebral organoids) and respiratory infections with respiratory syncytial virus in (lung bud organoids). Biologic discovery of host-specific genetic and epigenetic factors affecting infection, and responses to infection that lead to disease are possible with the use of organoid cultures. Continued development to increase the complexity of these cultures by including components of the normal host tissue microenvironment such as immune cells, blood vessels and microbiome, will facilitate studies on human viral pathogenesis, and advance the development of platforms for pre-clinical evaluation of vaccines, antivirals and therapeutics.
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Affiliation(s)
- Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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