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Reese AT, Phillips SR, Owens LA, Venable EM, Langergraber KE, Machanda ZP, Mitani JC, Muller MN, Watts DP, Wrangham RW, Goldberg TL, Emery Thompson M, Carmody RN. Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life. Curr Biol 2020; 31:613-620.e3. [PMID: 33232664 DOI: 10.1016/j.cub.2020.10.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/24/2020] [Accepted: 10/26/2020] [Indexed: 01/26/2023]
Abstract
Survival in primates is facilitated by commensal gut microbes that ferment otherwise indigestible plant matter, resist colonization by pathogens, and train the developing immune system.1,2 However, humans are unique among primates in that we consume highly digestible foods, wean early, mature slowly, and exhibit high lifelong investments in maintenance.3-6 These adaptations suggest that lifetime trajectories of human-microbial relationships could differ from those of our closest living relatives. Here, we profile the gut microbiota of 166 wild chimpanzees aged 8 months to 67 years in the Kibale National Park, Uganda and compare the patterns of gut microbial maturation to those previously observed in humans. We found that chimpanzee gut microbial alpha-diversity, composition, density, interindividual variation, and within-individual change over time varied significantly with age. Notably, gut microbial signatures in infants <2 years old were distinct across all five metrics. Infant chimpanzee guts were enriched in some of the same taxa prevalent in infant humans (e.g., Bifidobacterium, Streptococcus, and Bacteroides), and chimpanzee gut microbial communities, like those of humans, exhibited higher interindividual variation in infancy versus later in life. However, in direct contrast to human infants, chimpanzee infants harbored surprisingly high-diversity rather than low-diversity gut bacterial communities compared with older conspecifics. These data indicate differential trajectories of gut microbiota development in humans and chimpanzees that are consistent with interspecific differences in lactation, diet, and immune function. Probing the phenotypic consequences of differential early-life gut microbial diversity in chimpanzees and other primates will illuminate the life history impacts of the hominid-microbiome partnership.
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Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Sarah R Phillips
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA
| | - Leah A Owens
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Emily M Venable
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; Ngogo Chimpanzee Project, Waltham, MA, USA; Institute of Human Origins, Tempe, AZ, USA
| | - Zarin P Machanda
- Department of Anthropology, Tufts University, Medford, MA, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - John C Mitani
- Ngogo Chimpanzee Project, Waltham, MA, USA; Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - David P Watts
- Ngogo Chimpanzee Project, Waltham, MA, USA; Department of Anthropology, Yale University, New Haven, CT, USA
| | - Richard W Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA; Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA; Department of Zoology, Makerere University, Kampala, Uganda
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Beura LK, Hamilton SE, Bi K, Schenkel JM, Odumade OA, Casey KA, Thompson EA, Fraser KA, Rosato PC, Filali-Mouhim A, Sekaly RP, Jenkins MK, Vezys V, Haining WN, Jameson SC, Masopust D. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 2016; 532:512-6. [PMID: 27096360 PMCID: PMC4871315 DOI: 10.1038/nature17655] [Citation(s) in RCA: 772] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
Abstract
Our current understanding of immunology was largely defined in laboratory mice, partly because they are inbred and genetically homogeneous, can be genetically manipulated, allow kinetic tissue analyses to be carried out from the onset of disease, and permit the use of tractable disease models. Comparably reductionist experiments are neither technically nor ethically possible in humans. However, there is growing concern that laboratory mice do not reflect relevant aspects of the human immune system, which may account for failures to translate disease treatments from bench to bedside. Laboratory mice live in abnormally hygienic specific pathogen free (SPF) barrier facilities. Here we show that standard laboratory mouse husbandry has profound effects on the immune system and that environmental changes produce mice with immune systems closer to those of adult humans. Laboratory mice--like newborn, but not adult, humans--lack effector-differentiated and mucosally distributed memory T cells. These cell populations were present in free-living barn populations of feral mice and pet store mice with diverse microbial experience, and were induced in laboratory mice after co-housing with pet store mice, suggesting that the environment is involved in the induction of these cells. Altering the living conditions of mice profoundly affected the cellular composition of the innate and adaptive immune systems, resulted in global changes in blood cell gene expression to patterns that more closely reflected the immune signatures of adult humans rather than neonates, altered resistance to infection, and influenced T-cell differentiation in response to a de novo viral infection. These data highlight the effects of environment on the basal immune state and response to infection and suggest that restoring physiological microbial exposure in laboratory mice could provide a relevant tool for modelling immunological events in free-living organisms, including humans.
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Affiliation(s)
- Lalit K Beura
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Sara E Hamilton
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Kevin Bi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Jason M Schenkel
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Oludare A Odumade
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Kerry A Casey
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Emily A Thompson
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Kathryn A Fraser
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Pamela C Rosato
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Ali Filali-Mouhim
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Rafick P Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Marc K Jenkins
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Vaiva Vezys
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Pediatric Hematology and Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - David Masopust
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55414, USA
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Corti-Hoekstra ER, van den Brande JMH, Peppelenbosch MP. Report from the Falk Workshop on Microscopic Colitis: creating awareness for an underappreciated disease. Gastroenterology 2012; 143:e1-e3. [PMID: 23000527 DOI: 10.1053/j.gastro.2012.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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The suckling rat as a model for immunonutrition studies in early life. Clin Dev Immunol 2012; 2012:537310. [PMID: 22899949 PMCID: PMC3415261 DOI: 10.1155/2012/537310] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 12/17/2022]
Abstract
Diet plays a crucial role in maintaining optimal immune function. Research demonstrates the immunomodulatory properties and mechanisms of particular nutrients; however, these aspects are studied less in early life, when diet may exert an important role in the immune development of the neonate. Besides the limited data from epidemiological and human interventional trials in early life, animal models hold the key to increase the current knowledge about this interaction in this particular period. This paper reports the potential of the suckling rat as a model for immunonutrition studies in early life. In particular, it describes the main changes in the systemic and mucosal immune system development during rat suckling and allows some of these elements to be established as target biomarkers for studying the influence of particular nutrients. Different approaches to evaluate these immune effects, including the manipulation of the maternal diet during gestation and/or lactation or feeding the nutrient directly to the pups, are also described in detail. In summary, this paper provides investigators with useful tools for better designing experimental approaches focused on nutrition in early life for programming and immune development by using the suckling rat as a model.
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Pérez-Cano FJ, Castellote C, González-Castro AM, Pelegrí C, Castell M, Franch A. Developmental changes in intraepithelial T lymphocytes and NK cells in the small intestine of neonatal rats. Pediatr Res 2005; 58:885-91. [PMID: 16257927 DOI: 10.1203/01.pdr.0000182187.88505.49] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The main objective of this study was to characterize developmental changes in small intestinal intraepithelial lymphocyte (IEL) subpopulations during the suckling period, thus contributing to the understanding of the development of diffuse gut-associated lymphoid tissue (GALT) and to the identification of early mechanisms that protect the neonate from the first contact with diet and gut microbial antigens. The study was performed by double labeling and flow cytometry in IEL isolated from the proximal and distal small intestine of 1- to 21-d-old Lewis rats. During the suckling period, intraepithelial natural killer (NK) cells changed from a typical systemic phenotype, CD8+, to a specific intestinal phenotype, CD8-. Analysis of CD8+ IEL revealed a progressive increase in the relative number of CD8+ IEL co-expressing TCRalphabeta, cells associated with acquired immunity, whereas the percentage of CD8+ cells expressing the NK receptor, i.e. cells committed to innate immunity, decreased. At weaning, IEL maturity was still not achieved, as revealed by a phenotypic pattern that differed from that of adult rats. Thus, late after weaning, the regulatory CD8+CD4+ T IEL population appeared and the NK population declined. In summary, the intestinal intraepithelial compartment undergoes changes in its lymphocyte composition associated with the first ingestion of food. These changes are focused on a relatively high proportion of NK cells during the suckling period, and after weaning, an expansion of the regulatory CD8+CD4+ T cells.
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Affiliation(s)
- Francisco J Pérez-Cano
- Department of Physiology, Faculty of Pharmacy, University of Barcelona, E-08028 Barcelona, Spain
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Pickard KM, Bremner AR, Gordon JN, MacDonald TT. Microbial-gut interactions in health and disease. Immune responses. Best Pract Res Clin Gastroenterol 2004; 18:271-85. [PMID: 15123069 DOI: 10.1016/j.bpg.2003.10.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The indigenous bacterial microflora colonize the gut at birth and remain there throughout life. Approximately 10(14) bacteria are present in the ileum and colon and they are clearly immunogenic. The evidence is strong that the vast majority of IgA plasma cells in normal human gut are responding to the antigens of the flora, and although the flora is also responsible for producing the large numbers of T cells which are present in the gut of healthy individuals, the types of T cell response which the flora elicits are less well understood. A major challenge for the immune system is to distinguish between the antigens of the flora and the antigens of pathogens. There is also a growing realization that the normal flora can also influence gene expression in antigen-presenting cells in the gut and so set the context in which T cells respond to food antigen and vaccines.
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Affiliation(s)
- Karen M Pickard
- Division of Infection, Inflammation and Repair, University of Southampton School of Medicine, Mailpoint 813, Level E, South Block, Southampton General Hospital, Southampton SO16 6YD, UK
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Olafsdottir E, Aksnes L, Fluge G, Berstad A. Faecal calprotectin levels in infants with infantile colic, healthy infants, children with inflammatory bowel disease, children with recurrent abdominal pain and healthy children. Acta Paediatr 2002. [PMID: 11883817 DOI: 10.1111/j.1651-2227.2002.tb01638.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
UNLABELLED This study investigated faecal calprotectin concentration, a measure of intestinal inflammation, in infants and children with abdominal pain. Faecal calprotectin was measured by an enzyme-linked immunosorbent assay kit in spot stool samples in 76 infants with typical infantile colic, 7 infants with transient lactose intolerance and 27 healthy infants. All infants were 2-10 wk of age. In addition, 19 children with recurrent abdominal pain (RAP; mean age 11.5 y), 17 with inflammatory bowel disease (IBD; mean age 11.1 y; 10 had Crohn's disease and 7 ulcerative colitis) and 24 healthy children (mean age 5.3 y) were studied. In infants with infantile colic the mean faecal calprotectin concentration was not different from that in healthy infants (278 +/- 105 vs 277 +/- 109 mg kg(-1), p = 0.97) or in infants with transient lactose intolerance (300.3 +/- 124 mg kg(-1), p = 0.60). The calprotectin level was similar in boys and girls and fell significantly with age (p = 0.04). Children with IBD had faecal calprotectin levels (293 +/- 218 mg kg(-1)) much higher than healthy children (40 +/- 28 mg kg(-1), p < 0.0001) and children with RAP without identified organic disease (18 +/- 24 mg kg(-1), p < 0.0001). CONCLUSION Faecal calprotectin may differentiate between functional abdominal pain and IBD in school-aged children. In young infants high faecal calprotectin levels are normal.
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Affiliation(s)
- E Olafsdottir
- Department of Paediatrics, University of Bergen, Norway.
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Roccabianca P, Woo J, Moore P. Characterization of the diffuse mucosal associated lymphoid tissue of feline small intestine. Vet Immunol Immunopathol 2000; 75:27-42. [PMID: 10889297 PMCID: PMC7119714 DOI: 10.1016/s0165-2427(00)00181-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Characterization of the feline intestinal mucosal associated lymphoid tissue (MALT) will facilitate investigation of intestinal disease in the cat and promote the cat as an animal model for a range of human diseases which involve the intestinal lymphoid tissue. This includes inflammatory bowel disease, viral and non-viral associated intestinal lymphomas and immunodeficiency associated syndromes. Morphologic and phenotypic characterization of the normal small intestinal diffuse MALT in 22 SPF cats was performed using flow cytometry and cytology on isolated intestinal leukocytes from the intra-epithelial and lamina proprial compartments, as well as immunohistology on tissues from the feline duodenum, jejunum and ileum. The intra-epithelial compartment (IEC) was dominated by lymphocytes (>85%) which frequently contained intracytoplasmic granules. The most striking findings in the IEC were the elevated percentages of CD8 alpha+ lymphocytes (40%), presumed to express CD8 alpha alpha chains, and CD4-/CD8- (double negative) lymphocytes (44%), and the consistent presence of a minor subpopulation of CD3+/CD11d+ IELs (6%). Small percentages of CD4+ lymphocytes (10%) were observed such that the IEL CD4:CD8 ratio (0.25) was low. The LPC also contained a majority of T cells and few plasma cells. However, this compartment had reduced percentages of CD8 alpha+ lymphocytes (28%) and increased percentages of CD4+ lymphocytes (27%) relative to the IEC. However, the LPL CD4:CD8 ratio (1.0) remained low compared with the ratio in peripheral blood. In feline MALT, MHC class II expression was lower than in other peripheral lymphoid compartments. The results of this study provide important reference values for future investigations involving feline intestinal lymphocytes and demonstrates that the leukocyte distribution and phenotypic characteristics of the feline diffuse MALT appear largely similar to the murine, rat and human counterparts.
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Affiliation(s)
- P. Roccabianca
- Istituto di Anatomia Patologica Veterinaria e Patologia Aviare, Facoltaı́ di Medicina Veterinaria, Via Celoria n. 10, 20133 Milan, Italy
| | - J.C. Woo
- Department of Veterinary Pathology, Immunology and Microbiology, School of Veterinary Medicine, University of California at Davis, Davis, CA 95616, USA
| | - P.F. Moore
- Department of Veterinary Pathology, Immunology and Microbiology, School of Veterinary Medicine, University of California at Davis, Davis, CA 95616, USA
- Corresponding author. Tel.: +1-530-752-6611; fax: +1-530-752-3349
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Thompson FM, Catto-Smith AG, Moore D, Davidson G, Cummins AG. Epithelial growth of the small intestine in human infants. J Pediatr Gastroenterol Nutr 1998; 26:506-12. [PMID: 9586760 DOI: 10.1097/00005176-199805000-00004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Findings in studies in rodents have suggested that epithelial growth of the small intestine is dependent on activation of the immune system. The purpose of this study was to compare changes of postnatal epithelial growth with immunologic activity in humans. METHODS Duodenal biopsies were obtained by endoscopy from 74 infants. Villus area, crypt length, and mitotic count were measured, using a microdissection technique. Enterocyte height, intraepithelial lymphocytes and mucosal mast cells were recorded in histologic sections, and soluble interleukin-2 receptor levels were measured in sera. These data were compared with those from 77 adult control subjects. RESULTS Mean +/- SD villus area was similar in infants compared with that in adults (0.364 +/- 0.108 mm2 vs. 0.339 +/- 0.1 mm2); but mean crypt length was 31% longer (270 +/- 56 microm vs. 206 +/- 29 microm; p < 0.0001), and mitotic count was 68% higher (4.2 +/- 2.8 vs. 2.5 +/- 1 per crypt; p < 0.0001) in infants. Enterocyte height was lower during infancy (27.0 +/- 3.4 microm vs. 30.9 +/- 4.6 microm; p < 0.0001). There was no evidence of a trophic effect on the small intestine of breast feeding compared with the effect of bottle feeding. Counts of intraepithelial lymphocytes but not mucosal mast cells were significantly less in infants. Mean soluble interleukin-2 receptor levels peaked during early infancy, compared with levels in adults (1,820 +/- 596 U/ml vs. 695 +/- 359 U/ml). CONCLUSION These results indicate that epithelial proliferation is increased during infancy at an age when immunologic activity is high.
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Affiliation(s)
- F M Thompson
- Gastroenterology Unit, The Queen Elizabeth Hospital, Woodville South, SA, Australia
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Cummins AG, Thompson FM. Postnatal changes in mucosal immune response: a physiological perspective of breast feeding and weaning. Immunol Cell Biol 1997; 75:419-29. [PMID: 9429889 DOI: 10.1038/icb.1997.67] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
There are profound changes of immune activity during infancy from suppression during breast feeding, activation with weaning, and later intrinsic down-regulation after weaning. Breast feeding, as well as protecting against infections, seems to have a fundamental role in modifying the immune system against certain disease states. Transforming growth factor (TGF)beta in breast milk may mediate this immunosuppressive effect. Although the infant immune system is not in an adult state, the notion that the infant immune system is immature is difficult to reconcile with evidence that most infants respond appropriately to immunization and to infections. The systemic immune system of neonates may be subject to Th2 immune deviation, while the mucosal immune system, particularly of the gastrointestinal tract and probably the respiratory tract, is up-regulated with physiological inflammation during infancy. Weaning is associated with a peak of intestinal immune activation which includes mucosal mast cells and T cells. The physiological effects of this activation are promotion of epithelial growth of the small intestine and initial activation of mechanisms leading to subsequent down-regulation of the physiological heightened immune activity. This coincides with the development of mucosal (oral) tolerance to food and bacterial antigens.
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Affiliation(s)
- A G Cummins
- Gastroenterology Unit, Queen Elizabeth Hospital, Australia.
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