51
|
Danne C, Rolhion N, Sokol H. Recipient factors in faecal microbiota transplantation: one stool does not fit all. Nat Rev Gastroenterol Hepatol 2021; 18:503-513. [PMID: 33907321 DOI: 10.1038/s41575-021-00441-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
Faecal microbiota transplantation (FMT) is a promising therapy for chronic diseases associated with gut microbiota alterations. FMT cures 90% of recurrent Clostridioides difficile infections. However, in complex diseases, such as inflammatory bowel disease, irritable bowel syndrome and metabolic syndrome, its efficacy remains variable. It is accepted that donor selection and sample administration are key determinants of FMT success, yet little is known about the recipient factors that affect it. In this Perspective, we discuss the effects of recipient parameters, such as genetics, immunity, microbiota and lifestyle, on donor microbiota engraftment and clinical efficacy. Emerging evidence supports the possibility that controlling inflammation in the recipient intestine might facilitate engraftment by reducing host immune system pressure on the newly transferred microbiota. Deciphering FMT engraftment rules and developing novel therapeutic strategies are priorities to alleviate the burden of chronic diseases associated with an altered gut microbiota such as inflammatory bowel disease.
Collapse
Affiliation(s)
- Camille Danne
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France.,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France
| | - Nathalie Rolhion
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France.,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France
| | - Harry Sokol
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France. .,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France. .,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France. .,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France. .,AP-HP Fecal Microbiota transplantation Center, Saint Antoine Hospital, Paris, France.
| |
Collapse
|
52
|
Wu Y, Wang CZ, Wan JY, Yao H, Yuan CS. Dissecting the Interplay Mechanism between Epigenetics and Gut Microbiota: Health Maintenance and Disease Prevention. Int J Mol Sci 2021; 22:6933. [PMID: 34203243 PMCID: PMC8267743 DOI: 10.3390/ijms22136933] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota exists throughout the full life cycle of the human body, and it has been proven to have extensive impacts on health and disease. Accumulating evidence demonstrates that the interplay between gut microbiota and host epigenetics plays a multifaceted role in health maintenance and disease prevention. Intestinal microflora, along with their metabolites, could regulate multiple epigenetic pathways; e.g., DNA methylation, miRNA, or histone modification. Moreover, epigenetic factors can serve as mediators to coordinate gut microbiota within the host. Aiming to dissect this interplay mechanism, the present review summarizes the research profile of gut microbiota and epigenetics in detail, and further interprets the biofunctions of this interplay, especially the regulation of intestinal inflammation, the improvement of metabolic disturbances, and the inhibition of colitis events. This review provides new insights into the interplay of epigenetics and gut microbiota, and attempts to reveal the mysteries of health maintenance and disease prevention from this new perspective.
Collapse
Affiliation(s)
- Yuqi Wu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chong-Zhi Wang
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
| | - Jin-Yi Wan
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Haiqiang Yao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
53
|
Schubert N, Nichols HJ, Winternitz JC. How can the MHC mediate social odor via the microbiota community? A deep dive into mechanisms. Behav Ecol 2021. [DOI: 10.1093/beheco/arab004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Abstract
Genes of the major histocompatibility complex (MHC) have long been linked to odor signaling and recently researchers’ attention has focused on MHC structuring of microbial communities and how this may in turn impact odor. However, understanding of the mechanisms through which the MHC could affect the microbiota to produce a chemical signal that is both reliable and strong enough to ensure unambiguous transmission of behaviorally important information remains poor. This is largely because empirical studies are rare, predictions are unclear, and the underlying immunological mechanisms governing MHC–microbiota interactions are often neglected. Here, we review the immunological processes involving MHC class II (MHC-II) that could affect the commensal community. Focusing on immunological and medical research, we provide background knowledge for nonimmunologists by describing key players within the vertebrate immune system relating to MHC-II molecules (which present extracellular-derived peptides, and thus interact with extracellular commensal microbes). We then systematically review the literature investigating MHC–odor–microbiota interactions in animals and identify areas for future research. These insights will help to design studies that are able to explore the role of MHC-II and the microbiota in the behavior of wild populations in their natural environment and consequently propel this research area forward.
Collapse
Affiliation(s)
- Nadine Schubert
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
| | - Hazel J Nichols
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
- Department of Biosciences, Swansea University, Singleton Park, Swansea, UK
| | - Jamie C Winternitz
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
| |
Collapse
|
54
|
Gonçalves E, Guillén Y, Lama JR, Sanchez J, Brander C, Paredes R, Combadière B. Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness. Front Immunol 2021; 12:657162. [PMID: 34040607 PMCID: PMC8141841 DOI: 10.3389/fimmu.2021.657162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
The identification of new biomarkers is essential to predict responsiveness to vaccines. We investigated the whole-blood transcriptome and microbiome prior to immunization, in order to assess their involvement in induction of humoral responses two months later. We based our analyses on stool and skin microbiota, and blood transcriptome prior to immunization, in a randomized clinical study in which participants were vaccinated with the MVA-HIV clade B vaccine (MVA-B). We found that the levels of neutralizing antibody responses were correlated with abundance of Eubacterium in stool and Prevotella in skin. In addition, genus diversity and bacterial species abundance were also correlated with the expression of genes involved in B cell development prior to immunization and forecast strong responders to MVA-B. To our knowledge, this is the first study integrating host blood gene expression and microbiota that might open an avenue of research in this field and to optimize vaccination strategies and predict responsiveness to vaccines.
Collapse
Affiliation(s)
- Elena Gonçalves
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Yolanda Guillén
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Javier R Lama
- Asociacion Civil Impacta Salud y Educacion, Lima, Peru
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain.,Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), Vic, Spain.,Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Paredes
- Infectious Diseases Department, Hospital Universitari Germans Trias, Barcelona, Spain
| | - Behazine Combadière
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| |
Collapse
|
55
|
Tsuji S, Akagawa S, Akagawa Y, Yamaguchi T, Kino J, Yamanouchi S, Kimata T, Hashiyada M, Akane A, Kaneko K. Idiopathic nephrotic syndrome in children: role of regulatory T cells and gut microbiota. Pediatr Res 2021; 89:1185-1191. [PMID: 32570267 DOI: 10.1038/s41390-020-1022-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND We investigated whether an association exists between regulatory T cells (Tregs) during initial presentation in children with idiopathic nephrotic syndrome (INS) and later development of frequently relapsing INS. METHODS Blood samples were obtained at onset and at remission from 25 patients (median age, 4.0 years) with INS; eight did not show relapse after initial response (non-relapsing [NR]), whereas 17 showed frequent relapses (frequently relapsing [FR]). Tregs were measured by flow cytometry; increases were compared between groups. Fecal samples were obtained at onset from 20 patients with INS, as well as from 20 age-matched healthy children. Gut microbiota composition was assessed using 16S ribosomal RNA (rRNA) sequencing (ion PGM). RESULTS The rate of increase in Tregs from onset to remission was significantly lower in the FR group (124.78%) than in the NR group (879.16%; P < 0.001). Additionally, 16S rRNA sequencing of gut microbiota showed that the proportion of butyric acid-producing bacteria was significantly lower in the FR group (7.08%) than in the healthy children (17.45%; P < 0.001). CONCLUSIONS In children with INS, small increases in Tregs in response to steroid treatment were associated with subsequent increased risk of frequent relapses. In addition, the FR group had a greater degree of dysbiosis at onset. IMPACT A low rate of Tregs increase is associated with subsequent frequent relapses of INS. The increase in Tregs in response to steroid treatment was small when dysbiosis was present in patients with INS, particularly when the proportion of butyrate-producing bacteria was considerably reduced We presume that improvement of dysbiosis by administration of probiotics and prebiotics may enhance the rate of Tregs' increase, thus preventing frequent relapse.
Collapse
Affiliation(s)
- Shoji Tsuji
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Shohei Akagawa
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Yuko Akagawa
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | | | - Jiro Kino
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | | | - Takahisa Kimata
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Masaki Hashiyada
- Department of Legal Medicine, Kansai Medical University, Osaka, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, Osaka, Japan
| | - Kazunari Kaneko
- Department of Pediatrics, Kansai Medical University, Osaka, Japan.
| |
Collapse
|
56
|
Sottas C, Schmiedová L, Kreisinger J, Albrecht T, Reif J, Osiejuk TS, Reifová R. Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance. BMC Ecol Evol 2021; 21:41. [PMID: 33691625 PMCID: PMC7948333 DOI: 10.1186/s12862-021-01773-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that divergence in the gut microbiota composition between incipient species could contribute to their reproductive isolation. Nevertheless, empirical evidence for the role of gut microbiota in speciation is scarce. Moreover, it is still largely unknown to what extent closely related species in the early stages of speciation differ in their gut microbiota composition, especially in non-mammalian taxa, and which factors drive the divergence. Here we analysed the gut microbiota in two closely related passerine species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). The ranges of these two species overlap in a secondary contact zone, where both species occasionally hybridize and where interspecific competition has resulted in habitat use differentiation. Results We analysed the gut microbiota from the proximal, middle and distal part of the small intestine in both sympatric and allopatric populations of the two nightingale species using sequencing of bacterial 16S rRNA. We found small but significant differences in the microbiota composition among the three gut sections. However, the gut microbiota composition in the two nightingale species did not differ significantly between either sympatric or allopatric populations. Most of the observed variation in the gut microbiota composition was explained by inter-individual differences. Conclusions To our knowledge, this is the first attempt to assess the potential role of the gut microbiota in bird speciation. Our results suggest that neither habitat use, nor geographical distance, nor species identity have strong influence on the nightingale gut microbiota composition. This suggests that changes in the gut microbiota composition are unlikely to contribute to reproductive isolation in these passerine birds. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01773-1.
Collapse
Affiliation(s)
- Camille Sottas
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Jiří Reif
- Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Tomasz S Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| |
Collapse
|
57
|
Darolová A, Poláček M, Krištofík J, Lukasch B, Hoi H. First Evidence of a Relationship Between Female Major Histocompatibility Complex Diversity and Eggshell Bacteria in House Sparrows (Passer domesticus). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.615667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacteria are known to exert positive and negative influences on animals’ health and fitness. Bacteria, in particular those inhabiting the skin and inner organs of vertebrates, are horizontally or vertically transmitted. Specifically, mothers of bird species can transfer bacterial strains to their offspring when the egg is passing the reproductive tract, as the eggshell rubs against the wall of the uterus. In this context, the female immune system might play an important role in influencing the vertical transmission of bacteria. Here, we investigate the relationship between the major histocompatibility complex (MHC) and cultivable eggshell bacteria originating putatively from the female urogenital tract in a captive population of house sparrows (Passer domesticus). We predict that females with a more variable MHC will transfer fewer bacteria onto the eggshells. Our results show a negative relationship between the number of functional MHC class I alleles and bacteria originating in the urinary tract and growing on a selective medium. This is the first study to find a correlation between female MHC diversity and eggshell bacteria.
Collapse
|
58
|
Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
Collapse
Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
59
|
Jia M, Sangwan N, Tzeng A, Eng C. Interplay Between Class II HLA Genotypes and the Microbiome and Immune Phenotypes in Individuals With PTEN Hamartoma Tumor Syndrome. JCO Precis Oncol 2021; 5:PO.20.00374. [PMID: 34250407 DOI: 10.1200/po.20.00374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/12/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022] Open
Abstract
We evaluate potential contributors to the development of autoimmunity and other phenotypes consistent with immune dysregulation in individuals with germline mutations in the tumor suppressor gene PTEN in this observational report. MATERIALS AND METHODS Illumina sequencing of bacterial and fungal microbes was carried out on patient-donated fecal samples in a cohort of 67 patients with pathogenic germline PTEN mutations, including 41 individuals with autoimmunity and/or phenotypes consistent with immune dysregulation (cases) and 26 individuals without (controls). From these data, we measured differences in alpha and beta diversity between cases and controls and identified differentially abundant bacterial and fungal taxa using phyloseq and MicrobiomeSeq packages in R. We analyzed correlations between these taxa and specific HLA genotypes, along with correlations between HLA diversity and microbial diversity, by conducting high-resolution HLA genotyping at four class II loci (DRB1, DRB345, DQA1, and DQB1). RESULTS We found that alpha diversity distributions for both bacterial and fungal genera were statistically different between cases and controls. We identified differentially abundant bacterial and fungal taxa between cases and controls. Network analysis of differentially abundant bacterial taxa revealed some co-varying bacterial genera. We additionally found significant correlations between certain HLA genotypes and certain taxa and significant correlations between HLA diversity and alpha diversity. CONCLUSION PTEN-associated immune phenotypes might be influenced by the gut microbiome, and class II HLA molecules, in part, crosstalk with the gut microbiome. These preliminary observations should lay the groundwork for future studies to ultimately derive clinical measures, which could use gut microbiome and HLA molecule biomarkers to predict, and perhaps prevent, immunity and inflammation in patients predisposed to cancer because of germline PTEN mutations.
Collapse
Affiliation(s)
- Margaret Jia
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Naseer Sangwan
- Center for Microbiome in Health and Disease, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Alice Tzeng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, OH.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| |
Collapse
|
60
|
Abstract
AbstractKin recognition plays an important role in social behavior and evolution, but the proximate mechanisms by which individuals recognize kin remain poorly understood. In many species, individuals form a "kin template" that they compare with conspecifics' phenotypes to assess phenotypic similarity-and, by association, relatedness. Individuals may form a kin template through self-inspection (i.e., self-referencing) and/or by observing their rearing associates (i.e., family referencing). However, despite much interest, few empirical studies have successfully disentangled self-referencing and family referencing. Here, we employ a novel set of breeding crosses using the Trinidadian guppy (Poecilia reticulata) to disentangle referencing systems by manipulating exposure to kin from conception onward. We show that guppies discriminate among their full and maternal half siblings, which can be explained only by self-referencing. Additional behavioral experiments revealed no evidence that guppies incorporate the phenotypes of their broodmates or mother into the kin template. Finally, by manipulating the format of our behavioral tests, we show that olfactory communication is both necessary and sufficient for kin discrimination. These results provide robust evidence that individuals recognize kin by comparing the olfactory phenotypes of conspecifics with their own. This study resolves key questions about the proximate mechanisms underpinning kin recognition, with implications for the ontogeny and evolution of social behavior.
Collapse
|
61
|
Fleischer R, Risely A, Hoeck PEA, Keller LF, Sommer S. Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds. Ecol Evol 2020; 10:13345-13354. [PMID: 33304542 PMCID: PMC7713960 DOI: 10.1002/ece3.6934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023] Open
Abstract
The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non-mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island-averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large-scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level.
Collapse
Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Alice Risely
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | | | - Lukas F. Keller
- Zoological MuseumUniversity of ZurichZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| |
Collapse
|
62
|
Wu J, Zhao Y, Wang X, Kong L, Johnston LJ, Lu L, Ma X. Dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications. Crit Rev Food Sci Nutr 2020; 62:783-797. [PMID: 33043708 DOI: 10.1080/10408398.2020.1828813] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jianmin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xian Wang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Lingchang Kong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lee J. Johnston
- West Central Research & Outreach Centre, University of Minnesota, Morris, Minnesota, USA
| | - Lin Lu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
63
|
Kaneko K, Akagawa S, Akagawa Y, Kimata T, Tsuji S. Our Evolving Understanding of Kawasaki Disease Pathogenesis: Role of the Gut Microbiota. Front Immunol 2020; 11:1616. [PMID: 32793240 PMCID: PMC7393004 DOI: 10.3389/fimmu.2020.01616] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
Kawasaki disease (KD) was first described by Dr. Tomisaku Kawasaki in 1967. The etiology of KD has been studied comprehensively but remains largely unknown. The disease seems to result from the interplay of genetic and environmental susceptibility factors with infectious triggers, followed by a subsequent abnormal immune response characterized by increased levels of inflammatory cytokines and chemokines during the acute phase. Evidence has mounted to suggest that an imbalance between T helper 17 cells (Th17s) and regulatory T cells (Tregs) is associated with aberrant immune responses in KD. Recent advances in culture-independent techniques for detection and identification of intestinal commensal bacteria enabled the discovery that Th17 and Treg differentiation are regulated by short chain fatty acids (SCFAs), in particular butyrate, produced by the gut microbiota. This finding provided a mechanistic link between dysbiosis, defined as changes in the composition of the gut microbiota, and various inflammatory diseases. On this basis, we propose that dysbiosis, with reduced production of SCFAs leading to imbalances of Th17s/Tregs, could be involved in the etiology of KD. A pilot study supported this hypothesis, as only fecal concentrations of butyrate were significantly reduced in KD patients among SCFAs. This evolving perspective prompted us to undertake metagenomic analyses of bacterial DNA from the feces of KD patients who were antibiotic-naïve at diagnosis. Simultaneous measurements of Th17s/Tregs in peripheral blood and SCFA concentrations in feces would provide valuable information regarding the association between dysbiosis and dysregulated immune responses in KD.
Collapse
Affiliation(s)
- Kazunari Kaneko
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Shohei Akagawa
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Yuko Akagawa
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Takahisa Kimata
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| | - Shoji Tsuji
- Department of Pediatrics, Kansai Medical University, Osaka, Japan
| |
Collapse
|
64
|
Affiliation(s)
- Mary Melissa Roland
- University of South Carolina School of Medicine, Department of Pathology, Microbiology, and Immunology, Columbia, South Carolina, United States of America
| | - Ahmed Dawood Mohammed
- University of South Carolina School of Medicine, Department of Pathology, Microbiology, and Immunology, Columbia, South Carolina, United States of America
| | - Jason Lee Kubinak
- University of South Carolina School of Medicine, Department of Pathology, Microbiology, and Immunology, Columbia, South Carolina, United States of America
| |
Collapse
|
65
|
Gu W, Liu S, Chen L, Liu Y, Gu C, Ren HQ, Wu B. Single-Cell RNA Sequencing Reveals Size-Dependent Effects of Polystyrene Microplastics on Immune and Secretory Cell Populations from Zebrafish Intestines. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3417-3427. [PMID: 32092251 DOI: 10.1021/acs.est.9b06386] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microplastics (MPs) as widespread contamination pose a high risk for aquatic organisms. However, the current understanding of MP toxicity is based on cell population-averaged measurements. Our aim was to gain a comprehensive understanding of the size-dependent effects of polystyrene MPs (PS-MPs) on intestinal cell populations in zebrafish and characterize the interplay of MPs, intestinal cells, and intestinal microbiota. Here, we used single-cell RNA sequencing to determine the transcriptome heterogeneity of 12 000 intestinal cells obtained from zebrafish exposed to 100 nm, 5 μm, and 200 μm PS-MPs for 21 days. Eight intestinal cell populations were identified. Combined with changes in intestinal microbiota, our findings highlight a previously unrecognized end point that all three sizes of PS-MPs induced dysfunction of intestinal immune cells (including effects on phagosomes and the regulation of immune system processes) and increased the abundance of pathogenic bacteria. However, only 100 nm PS-MPs altered the expression of genes related to phagocyte-produced reactive oxygen species (ROS) generation and increased mucus secretion by secretory cells. Microsize PS-MPs specifically changed the lysosome (5 μm) and cell surface receptor signaling (200 μm) processes of the macrophages. Our findings pinpoint to cell-specific and size-dependent responses to PS-MPs in fish intestine, which can provide a reference for future study directions.
Collapse
Affiliation(s)
- Weiqing Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
| | - Su Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
- Department of Environmental Science, School of Engineering, China Pharmaceutical University, Nanjing, Jiangsu 211198, P.R. China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
| | - Yuxuan Liu
- College of Environment, Hohai University, Nanjing, Jiangsu 210098, P.R. China
| | - Cheng Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
| | - Hong-Qiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, P.R. China
| |
Collapse
|
66
|
Dedrick S, Sundaresh B, Huang Q, Brady C, Yoo T, Cronin C, Rudnicki C, Flood M, Momeni B, Ludvigsson J, Altindis E. The Role of Gut Microbiota and Environmental Factors in Type 1 Diabetes Pathogenesis. Front Endocrinol (Lausanne) 2020; 11:78. [PMID: 32174888 PMCID: PMC7057241 DOI: 10.3389/fendo.2020.00078] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
Type 1 Diabetes (T1D) is regarded as an autoimmune disease characterized by insulin deficiency resulting from destruction of pancreatic β-cells. The incidence rates of T1D have increased worldwide. Over the past decades, progress has been made in understanding the complexity of the immune response and its role in T1D pathogenesis, however, the trigger of T1D autoimmunity remains unclear. The increasing incidence rates, immigrant studies, and twin studies suggest that environmental factors play an important role and the trigger cannot simply be explained by genetic predisposition. Several research initiatives have identified environmental factors that potentially contribute to the onset of T1D autoimmunity and the progression of disease in children/young adults. More recently, the interplay between gut microbiota and the immune system has been implicated as an important factor in T1D pathogenesis. Although results often vary between studies, broad compositional and diversity patterns have emerged from both longitudinal and cross-sectional human studies. T1D patients have a less diverse gut microbiota, an increased prevalence of Bacteriodetes taxa and an aberrant metabolomic profile compared to healthy controls. In this comprehensive review, we present the data obtained from both animal and human studies focusing on the large longitudinal human studies. These studies are particularly valuable in elucidating the environmental factors that lead to aberrant gut microbiota composition and potentially contribute to T1D. We also discuss how environmental factors, such as birth mode, diet, and antibiotic use modulate gut microbiota and how this potentially contributes to T1D. In the final section, we focus on existing recent literature on microbiota-produced metabolites, proteins, and gut virome function as potential protectants or triggers of T1D onset. Overall, current results indicate that higher levels of diversity along with the presence of beneficial microbes and the resulting microbial-produced metabolites can act as protectors against T1D onset. However, the specifics of the interplay between host and microbes are yet to be discovered.
Collapse
Affiliation(s)
- Sandra Dedrick
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | | | - Qian Huang
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Claudia Brady
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Tessa Yoo
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Catherine Cronin
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Caitlin Rudnicki
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Michael Flood
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Babak Momeni
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Johnny Ludvigsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Emrah Altindis
- Biology Department, Boston College, Chestnut Hill, MA, United States
| |
Collapse
|
67
|
D’Aquila P, Lynn Carelli L, De Rango F, Passarino G, Bellizzi D. Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host. Nutrients 2020; 12:E597. [PMID: 32106534 PMCID: PMC7146473 DOI: 10.3390/nu12030597] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that inhabit symbiotically on and in the human intestine. They carry out, through the production of a series of metabolites, many important metabolic functions that complement the activity of mammalian enzymes and play an essential role in host digestion. Interindividual variability of microbiota structure, and consequently of the expression of its genes (microbiome), was largely ascribed to the nutritional regime. Diet influences microbiota composition and function with short- and long-term effects. In spite of the vast literature, molecular mechanisms underlying these effects still remain elusive. In this review, we summarized the current evidence on the role exerted by gut microbiota and, more specifically, by its metabolites in the establishment of the host epigenome. The interest in this topic stems from the fact that, by modulating DNA methylation and histone modifications, the gut microbiota does affect the cell activities of the hosting organism.
Collapse
Affiliation(s)
- Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | | | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences (DIBEST), University of Calabria, 87036 Rende, Italy; (F.D.R.); (G.P.); (D.B.)
| |
Collapse
|
68
|
Sterlin D, Fadlallah J, Slack E, Gorochov G. The antibody/microbiota interface in health and disease. Mucosal Immunol 2020; 13:3-11. [PMID: 31413347 DOI: 10.1038/s41385-019-0192-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/25/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023]
Abstract
The human intestine is densely colonized with commensal microbes that stimulate the immune system. While secretory Immunoglobulin (Ig) A is known to play a crucial role in gut microbiota compartmentalization, secretory IgM, and systemic IgG have recently been highlighted in host-microbiota interactions as well. In this review, we discuss important aspects of secretory IgA biology, but rather than focusing on mechanistic aspects of IgA impact on microbiota, we stress the current knowledge of systemic antibody responses to whole gut microbiota, in particular their generation, specificities, and function. We also provide a comprehensive picture of secretory IgM biology. Finally, therapeutic and diagnostic implications of these novel findings for the treatment of various diseases are outlined.
Collapse
Affiliation(s)
- Delphine Sterlin
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP Hôpital Pitié-Salpêtrière, 75013, Paris, France.,Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 Inserm, F-75015, Paris, France
| | - Jehane Fadlallah
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), EA3518, 75010, Paris, France
| | - Emma Slack
- Institute of Food Sciences, Nutrition and Health, ETH Zurich, 8093, Zürich, Switzerland.
| | - Guy Gorochov
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), AP-HP Hôpital Pitié-Salpêtrière, 75013, Paris, France.
| |
Collapse
|
69
|
Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ, Preziosi RF. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 2019; 88:1684-1695. [PMID: 31325164 PMCID: PMC6899969 DOI: 10.1111/1365-2656.13065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
Abstract
Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.
Collapse
Affiliation(s)
- Sarah M. Griffiths
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Donald C. Behringer
- Fisheries and Aquatic SciencesUniversity of FloridaGainesvilleFLUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Mark J. Butler
- Department of Biological SciencesOld Dominion UniversityNorfolkVAUSA
| | - Richard F. Preziosi
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| |
Collapse
|
70
|
Whittaker DJ, Slowinski SP, Greenberg JM, Alian O, Winters AD, Ahmad MM, Burrell MJE, Soini HA, Novotny MV, Ketterson ED, Theis KR. Experimental evidence that symbiotic bacteria produce chemical cues in a songbird. ACTA ACUST UNITED AC 2019; 222:jeb.202978. [PMID: 31537652 DOI: 10.1242/jeb.202978] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022]
Abstract
Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here, we tested whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second experiment, we cultured bacteria from junco preen oil, and found that all of the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both experiments, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals.
Collapse
Affiliation(s)
- Danielle J Whittaker
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA
| | - Samuel P Slowinski
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jonathan M Greenberg
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Osama Alian
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.,Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Madison M Ahmad
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Mikayla J E Burrell
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Institute for Pheromone Research, Indiana University, Bloomington, IN 47405-7102, USA
| | - Helena A Soini
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Institute for Pheromone Research, Indiana University, Bloomington, IN 47405-7102, USA
| | - Milos V Novotny
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Institute for Pheromone Research, Indiana University, Bloomington, IN 47405-7102, USA
| | - Ellen D Ketterson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| |
Collapse
|
71
|
Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, de Pooter R, Antonopoulos DA, Golovkina T, Chervonsky A. Polymorphic Immune Mechanisms Regulate Commensal Repertoire. Cell Rep 2019; 29:541-550.e4. [PMID: 31618625 PMCID: PMC6904226 DOI: 10.1016/j.celrep.2019.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/28/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Environmental influences (infections and diet) strongly affect a host's microbiota. However, host genetics may influence commensal communities, as suggested by the greater similarity between the microbiomes of identical twins compared to non-identical twins. Variability of human genomes and microbiomes complicates the understanding of polymorphic mechanisms regulating the commensal communities. Whereas animal studies allow genetic modifications, they are sensitive to influences known as "cage" or "legacy" effects. Here, we analyze ex-germ-free mice of various genetic backgrounds, including immunodeficient and major histocompatibility complex (MHC) congenic strains, receiving identical input microbiota. The host's polymorphic mechanisms affect the gut microbiome, and both innate (anti-microbial peptides, complement, pentraxins, and enzymes affecting microbial survival) and adaptive (MHC-dependent and MHC-independent) pathways influence the microbiota. In our experiments, polymorphic mechanisms regulate only a limited number of microbial lineages (independently of their abundance). Our comparative analyses suggest that some microbes may benefit from the specific immune responses that they elicit.
Collapse
Affiliation(s)
- Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Leonid Yurkovetskiy
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Kelly O'Grady
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Joseph M Pickard
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Renée de Pooter
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Dionysios A Antonopoulos
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tatyana Golovkina
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
| | - Alexander Chervonsky
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
72
|
Metcalf CJE, Koskella B. Protective microbiomes can limit the evolution of host pathogen defense. Evol Lett 2019; 3:534-543. [PMID: 31636945 PMCID: PMC6791398 DOI: 10.1002/evl3.140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
The evolution of host immunity occurs in the context of the microbiome, but little theory exists to predict how resistance against pathogens might be influenced by the need to tolerate and regulate commensal microbiota. We present a general model to explore the optimal investment in host immunity under conditions in which the host can, versus cannot easily distinguish among commensal versus pathogenic bacteria, and when commensal microbiota can, versus cannot protect the host against the impacts of pathogen infection. We find that a loss of immune vigilance associated with innate immunity over evolutionary time can occur due to the challenge of discriminating between pathogenic and other microbe species. Further, we find the greater the protective effect of microbiome species, acting either directly or via competition with a pathogen, or the higher the costs of immunity, the more likely the loss of immune vigilance is. Conversely, this effect can be reversed when pathogens increase host mortality. Generally, the magnitude of costs of immunity required to allow evolution of decreased immune vigilance are predicted to be lowest when microbiome and pathogen species most resemble each other (in terms of host recognition), and when immune effects on the pathogen are weak. Our model framework makes explicit the core trade‐offs likely to shape the evolution of immunity in the context of microbiome/pathogen discrimination. We discuss how this informs interpretation of patterns and process in natural systems, including vulnerability to pathogen emergence.
Collapse
Affiliation(s)
- C Jessica E Metcalf
- Department of Ecology and Evolutionary Princeton University Princeton New Jersey 08540
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley Berkeley California 94720
| |
Collapse
|
73
|
Santos PSC, Mezger M, Kolar M, Michler FU, Sommer S. The best smellers make the best choosers: mate choice is affected by female chemosensory receptor gene diversity in a mammal. Proc Biol Sci 2019; 285:20182426. [PMID: 30963892 DOI: 10.1098/rspb.2018.2426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The products of the genes of the major histocompatibility complex (MHC) are known to be drivers of pathogen resistance and sexual selection enhancing offspring genetic diversity. The MHC further influences individual odour types and social communication. However, little is known about the receptors and their volatile ligands that are involved in this type of chemical communication. Here, we have investigated chemosensory receptor genes that ultimately enable females to assess male genes through odour cues. As a model, we used an invasive population of North American raccoons ( Procyon lotor) in Germany. We investigated the effect of two groups of chemosensory receptor genes-trace amine-associated receptors (TAARs) and olfactory receptors (ORs)-on MHC-dependent mate choice. Females with more alleles of the TAAR or OR loci were more likely to choose a male with a diverse MHC. We additionally found that MHC class I genes have a stronger effect on mate choice than the recently reported effect for MHC class II genes, probably because of their immunological relevance for viral resistance. Our study is among the first to show a genetic link between behaviour and chemosensory receptor genes. These results contribute to understanding the link between genetics, olfaction and associated life-history decisions.
Collapse
Affiliation(s)
- Pablo S C Santos
- 1 Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm , Ulm , Germany
| | - Maja Mezger
- 1 Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm , Ulm , Germany
| | - Miriam Kolar
- 1 Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm , Ulm , Germany
| | - Frank-Uwe Michler
- 2 Institute of Forest Botany and Forest Zoology, Technical University of Dresden , Tharandt , Germany
| | - Simone Sommer
- 1 Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm , Ulm , Germany
| |
Collapse
|
74
|
Russell JT, Roesch LFW, Ördberg M, Ilonen J, Atkinson MA, Schatz DA, Triplett EW, Ludvigsson J. Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome. Nat Commun 2019; 10:3621. [PMID: 31399563 PMCID: PMC6689114 DOI: 10.1038/s41467-019-11460-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Susceptibility to many human autoimmune diseases is under strong genetic control by class II human leukocyte antigen (HLA) allele combinations. These genes remain by far the greatest risk factors in the development of type 1 diabetes and celiac disease. Despite this, little is known about HLA influences on the composition of the human gut microbiome, a potential source of environmental influence on disease. Here, using a general population cohort from the All Babies in Southeast Sweden study, we report that genetic risk for developing type 1 diabetes autoimmunity is associated with distinct changes in the gut microbiome. Both the core microbiome and beta diversity differ with HLA risk group and genotype. In addition, protective HLA haplotypes are associated with bacterial genera Intestinibacter and Romboutsia. Thus, general population cohorts are valuable in identifying potential environmental triggers or protective factors for autoimmune diseases that may otherwise be masked by strong genetic control.
Collapse
Affiliation(s)
- Jordan T Russell
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences University of Florida, Gainesville, 32611-0700, FL, USA
| | - Luiz F W Roesch
- Biological Sciences, Universidade Federal do Pampa, São Gabriel, 97300-000, Brazil
| | - Malin Ördberg
- Crown Princess Victoria's Children's Hospital, Region Östergötland, Division of Pediatrics, Linköping University, Linköping, SE 58185, Sweden
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, and Clinical Microbiology, Turku University Hospital, Turku, 20521, Finland
| | - Mark A Atkinson
- Department of Pathology, University of Florida Diabetes Institute, Gainesville, 32610, FL, USA
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, 32610, FL, USA
| | - Desmond A Schatz
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, 32610, FL, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences University of Florida, Gainesville, 32611-0700, FL, USA.
| | - Johnny Ludvigsson
- Crown Princess Victoria's Children's Hospital, Region Östergötland, Division of Pediatrics, Linköping University, Linköping, SE 58185, Sweden
| |
Collapse
|
75
|
Pan H, Guo R, Ju Y, Wang Q, Zhu J, Xie Y, Zheng Y, Li T, Liu Z, Lu L, Li F, Tong B, Xiao L, Xu X, Leung ELH, Li R, Yang H, Wang J, Zhou H, Jia H, Liu L. A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis. MICROBIOME 2019; 7:107. [PMID: 31315667 PMCID: PMC6637628 DOI: 10.1186/s40168-019-0719-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/03/2019] [Indexed: 05/04/2023]
Abstract
Background Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfactory. The microbial disorder in rheumatoid arthritis (RA) patients is significantly reversed with effective treatment. Modulating aberrant gut microbiomes into a healthy state is a potential therapeutic approach for preventing bone damage. Results By using metagenomic shotgun sequencing and a metagenome-wide association study, we assessed the effect of Lactobacillus casei (L. casei) on the induction of arthritis as well as on the associated gut microbiota and immune disorders in adjuvant-induced arthritis (AIA) rats. Treatment of AIA rats with L. casei inhibited joint swelling, lowered arthritis scores, and prevented bone destruction. Along with the relief of arthritis symptoms, dysbiosis in the microbiome of arthritic rats was significantly reduced after L. casei intervention. The relative abundance of AIA-decreased Lactobacillus strains, including Lactobacillus hominis, Lactobacillus reuteri, and Lactobacillus vaginalis, were restored to normal and Lactobacillus acidophilus was upregulated by the administration of L. casei to the AIA rats. Moreover, L. casei downregulated the expression of pro-inflammatory cytokines, which are closely linked to the effect of the L. casei treatment-associated microbes. Functionally, the maintenance of the redox balance of oxidative stress was involved in the improvement in the L. casei-treated AIA rats. Conclusion A single bacterium, L. casei (ATCC334), was able to significantly suppress the induction of AIA and protect bones from destruction in AIA rats by restoring the microbiome dysbiosis in the gut, indicating that using probiotics may be a promising strategy for treating RA, especially in the early stage of the disease. Electronic supplementary material The online version of this article (10.1186/s40168-019-0719-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hudan Pan
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Ruijin Guo
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Yanmei Ju
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Qi Wang
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China
| | - Jie Zhu
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Ying Xie
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Yanfang Zheng
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
- Fujian University of Traditional Chinese Medicine, No.1, Qiuyang Road, Minhoushangjie, Fuzhou, 350122 Fujian China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Zhongqiu Liu
- International Institute for Translational Research of Traditional Chinese Medicine of Guangzhou University of Chinese Medicine, Guangzhou, 510006 Guangdong China
| | - Linlin Lu
- International Institute for Translational Research of Traditional Chinese Medicine of Guangzhou University of Chinese Medicine, Guangzhou, 510006 Guangdong China
| | - Fei Li
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China
| | - Bin Tong
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Runze Li
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058 China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058 China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, 518083 China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120 China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China
| |
Collapse
|
76
|
Abstract
Studies over the last decade have transformed our previously simplistic view of
microbes, having only a pathogenic role in disease to a more robust understanding
that they are critical for maintaining human health. Indeed, our microbiota—the
collection of commensal organisms that live in and on each of us—contributes to
nearly every facet of host physiology, from ontogeny of the immune system to
neurological function to metabolism. Although the specific details of these
host–microbe interactions are still being elucidated for most diseases, the coupling
of clinical samples with animal models of disease have provided key insights. This
review provides some general background on the microbiota, highlights a few examples
of how the microbiota influences diseases of the central nervous system, and provides
a perspective for how these findings may be clinically translatable.
Collapse
Affiliation(s)
- Neeraj K Surana
- Departments of Pediatrics, Molecular Genetics, Microbiology and Immunology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
77
|
Cohen LJ, Cho JH, Gevers D, Chu H. Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases. Gastroenterology 2019; 156:2174-2189. [PMID: 30880022 PMCID: PMC6568267 DOI: 10.1053/j.gastro.2019.03.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBDs) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa, influencing inflammatory responses in the gut. Therefore, strategies to manipulate the microbiome might be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to the development of microbe-based therapies for IBD.
Collapse
Affiliation(s)
- Louis J. Cohen
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Correspondence:
(L.J.C.),
(H.C.)
| | - Judy H. Cho
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai; The Charles Bronfman Institute for Personalized
Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, 10029,
USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research &
Development, Cambridge, MA, 02142, USA
| | - Hiutung Chu
- Department of Pathology, University of California-San Diego, La Jolla, California; Chiba University and University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California.
| |
Collapse
|
78
|
Does MHC heterozygosity influence microbiota form and function? PLoS One 2019; 14:e0215946. [PMID: 31095603 PMCID: PMC6522005 DOI: 10.1371/journal.pone.0215946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host’s microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.
Collapse
|
79
|
Persisting enteropathy and disturbed adaptive mucosal immunity due to MHC class II deficiency. Clin Immunol 2019; 203:125-133. [PMID: 31028919 DOI: 10.1016/j.clim.2019.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
Abstract
Intestinal epithelial cells (IECs) form a fundamental mucosal barrier and actively participate in tolerance and immunity against intestinal contents. Major histocompatibility complex class II (MHC II) and invariant chain (Ii) molecules are essential for adaptive immune response. MHC II deficiency often presents with gastrointestinal disorders. Intestinal biopsy samples revealed an absence of HLA-DR, Ii, and local immunoglobulins in both hematopoietic immune cells and IECs accompanied by a lack of faecal sIgA. After successful hematopoietic stem cell transplantation (HSCT) absent HLA-DR and Ii expression persisted in IECs and faecal stool analysis indicated inflammation and high microbial activity. We describe multifaceted disturbance of adaptive mucosal immunity in MHC II deficient patients suffering from enteropathy. HLA-DR and Ii expression on enterocytes is not restored by HSCT. This may account for increased susceptibility to enteric infections and intestinal inflammation leading to prolonged enteropathy reported in MHC II deficient patients.
Collapse
|
80
|
Cross talk between neutrophils and the microbiota. Blood 2019; 133:2168-2177. [PMID: 30898860 DOI: 10.1182/blood-2018-11-844555] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 12/18/2022] Open
Abstract
The microbiota has emerged as an important regulator of the host immunity by the induction, functional modulation, or suppression of local and systemic immune responses. In return, the host immune system restricts translocation and fine tunes the composition and distribution of the microbiota to maintain a beneficial symbiosis. This paradigm applies to neutrophils, a critical component of the innate immunity, allowing their production and function to be influenced by microbial components and metabolites derived from the microbiota, and engaging them in the process of microbiota containment and regulation. The cross talk between neutrophils and the microbiota adjusts the magnitude of neutrophil-mediated inflammation on challenge while preventing neutrophil responses against commensals under steady state. Here, we review the major molecular and cellular mediators of the interactions between neutrophils and the microbiota and discuss their interplay and contribution in chronic inflammatory diseases and cancer.
Collapse
|
81
|
Leclaire S, Strandh M, Dell'Ariccia G, Gabirot M, Westerdahl H, Bonadonna F. Plumage microbiota covaries with the major histocompatibility complex in blue petrels. Mol Ecol 2019; 28:833-846. [PMID: 30582649 DOI: 10.1111/mec.14993] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023]
Abstract
To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour-producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds.
Collapse
Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution & Diversité Biologique, UMR 5174 (CNRS, Université Paul Sabatier, ENFA), Toulouse, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Maria Strandh
- Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Gaia Dell'Ariccia
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Marianne Gabirot
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | | | - Francesco Bonadonna
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| |
Collapse
|
82
|
Le Roy T, Debédat J, Marquet F, Da-Cunha C, Ichou F, Guerre-Millo M, Kapel N, Aron-Wisnewsky J, Clément K. Comparative Evaluation of Microbiota Engraftment Following Fecal Microbiota Transfer in Mice Models: Age, Kinetic and Microbial Status Matter. Front Microbiol 2019; 9:3289. [PMID: 30692975 PMCID: PMC6339881 DOI: 10.3389/fmicb.2018.03289] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
The intestinal microbiota and its functions are intricately interwoven with host physiology. Colonizing rodents with donor microbiota provides insights into host-microbiota interactions characterization and the understanding of disease physiopathology. However, a better assessment of inoculation methods and recipient mouse models is needed. Here, we compare the engraftment at short and long term of genetically obese mice microbiota in germ-free (GF) mice and juvenile and adult specific pathogen free (SPF) mice. We also tested the effects of initial microbiota depletion before microbiota transfer. In the present work, donor microbiota engraftment was better in juvenile SPF mice than in adult SPF mice. In juvenile mice, initial microbiota depletion using laxatives or antibiotics improved donor microbiota engraftment 9 weeks but not 3 weeks after microbiota transfer. Microbiota-depleted juvenile mice performed better than GF mice 3 weeks after the microbiota transfer. However, 9 weeks after transfer, colonized GF mice microbiota had the lowest Unifrac distance to the donor microbiota. Colonized GF mice were also characterized by a chronic alteration in intestinal absorptive function. With these collective results, we show that the use of juvenile mice subjected to initial microbiota depletion constitutes a valid alternative to GF mice in microbiota transfer studies.
Collapse
Affiliation(s)
- Tiphaine Le Roy
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France
| | - Jean Debédat
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France
| | - Florian Marquet
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France
| | - Carla Da-Cunha
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France
| | - Farid Ichou
- ICANalytics Facility Core, Institut de Cardiométabolisme et Nutrition (ICAN), Paris, France
| | | | - Nathalie Kapel
- Department of Functional Coprology, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Judith Aron-Wisnewsky
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France.,Department of Nutrition, CRNH Ile de France, Pitié-Salpêtrière Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Karine Clément
- NutriOmics Team, INSERM, ICAN, Sorbonne Université, Paris, France.,Department of Nutrition, CRNH Ile de France, Pitié-Salpêtrière Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| |
Collapse
|
83
|
Abstract
Acute anterior uveitis (AAU) and the spondyloarthritis (SpA) subtypes ankylosing spondylitis, reactive arthritis and psoriatic arthritis are among the inflammatory diseases affected by the biology of the intestinal microbiome. In this Review, the relationship between AAU, SpA and the microbiome is discussed, with a focus on the major SpA risk gene HLA-B*27 and how it is associated with both intestinal tolerance and the loss of ocular immune privilege that can accompany AAU. We provide four potential mechanisms to account for how dysbiosis, barrier function and immune response contribute to the development of ocular inflammation and the pathogenesis of AAU. Finally, potential therapeutic avenues to target the microbiota for the clinical management of AAU and SpA are outlined.
Collapse
Affiliation(s)
- James T Rosenbaum
- Departments of Ophthalmology, Medicine and Cell Biology, Oregon Health and Science University, Portland, OR, USA
- Legacy Devers Eye Institute, Portland, OR, USA
| | - Mark Asquith
- Department of Medicine, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
84
|
Severance EG, Yolken RH. Deciphering microbiome and neuroactive immune gene interactions in schizophrenia. Neurobiol Dis 2018; 135:104331. [PMID: 30471416 DOI: 10.1016/j.nbd.2018.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
The body's microbiome represents an actively regulated network of novel mechanisms that potentially underlie the etiology and pathophysiology of a wide range of diseases. For complex brain disorders such as schizophrenia, understanding the cellular and molecular pathways that intersect the bidirectional gut-brain axis is anticipated to lead to new methods of treatment. The means by which the microbiome might differ across neuropsychiatric and neurological disorders are not known. Brain disorders as diverse as schizophrenia, major depression, Parkinson's disease and multiple sclerosis appear to share a common pathology of an imbalanced community of commensal microbiota, often measured in terms of a leaky gut phenotype accompanied by low level systemic inflammation. While environmental factors associated with these disease states might contribute to intestinal pathologies, products from a perturbed microbiome may also directly promote specific signs, symptoms and etiologies of individual disorders. We hypothesize that in schizophrenia, it is the putatively unique susceptibility related to genes that modulate the immune system and the gut-brain pleiotropy of these genes which leads to a particularly neuropathological response when challenged by a microbiome in dysbiosis. Consequences from exposure to this dysbiosis may occur during pre- or post-natal time periods and thus may interfere with normal neurodevelopment in those who are genetically predisposed. Here, we review the evidence from the literature which supports the idea that the intersection of the microbiome and immune gene susceptibility in schizophrenia is relevant etiologically and for disease progression. Figuring prominently at both ends of the gut-brain axis and at points in between are proteins encoded by genes found in the major histocompatibility complex (MHC), including select MHC as well as non-MHC complement pathway genes.
Collapse
Affiliation(s)
- Emily G Severance
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| | - Robert H Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
85
|
Derakhshani H, Plaizier JC, De Buck J, Barkema HW, Khafipour E. Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation. MICROBIOME 2018; 6:203. [PMID: 30419937 PMCID: PMC6233267 DOI: 10.1186/s40168-018-0586-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/29/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation. RESULTS Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the BoLA-DRB3. In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included Staphylococcus, Ruminococcaceae, and Clostridiales within the bacterial community and Alternaria, Aspergillus, Candida, and Cryptococcus within the fungal community. Comparing the composition of intramammary microbiota between identified BoLA-DRB3.2 variants (n = 2) revealed distinct clustering pattern on day 0, whereas this effect was not significant on the microbiota of milk samples collected on subsequent days. On day 0, proportions of several non-aureus Staphylococcus (NAS) OTUs, including those aligned to Staphylococcus equorum, Staphylococcus gallinarum, Staphylococcus sciuri, and Staphylococcus haemolyticus, were enriched within the microbiota of one of the BoLA-DRB3.2 variants, whereas lactic acid bacteria (LAB) including Lactobacillus and Enterococcus were enriched within the colostrum microbiota of the other variant. CONCLUSION Our results suggest a potential role for BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows. Determining whether BoLA-mediated shifts in the composition of colostrum microbiota are regulated directly by immune system or indirectly by microbiota-derived colonization resistant can have important implications for future development of preventive/therapeutic strategies for controlling mastitis.
Collapse
Affiliation(s)
- Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jan C Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 225 Animal Science Bldg., Winnipeg, MB, R3T 2N2, Canada.
| |
Collapse
|
86
|
Derakhshani H, Fehr KB, Sepehri S, Francoz D, De Buck J, Barkema HW, Plaizier JC, Khafipour E. Invited review: Microbiota of the bovine udder: Contributing factors and potential implications for udder health and mastitis susceptibility. J Dairy Sci 2018; 101:10605-10625. [PMID: 30292553 DOI: 10.3168/jds.2018-14860] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/05/2018] [Indexed: 12/13/2022]
Abstract
Various body sites of vertebrates provide stable and nutrient-rich ecosystems for a diverse range of commensal, opportunistic, and pathogenic microorganisms to thrive. The collective genomes of these microbial symbionts (the microbiome) provide host animals with several advantages, including metabolism of indigestible carbohydrates, biosynthesis of vitamins, and modulation of innate and adaptive immune systems. In the context of the bovine udder, however, the relationship between cow and microbes has been traditionally viewed strictly from the perspective of host-pathogen interactions, with intramammary infections by mastitis pathogens triggering inflammatory responses (i.e., mastitis) that are often detrimental to mammary tissues and cow physiology. This traditional view has been challenged by recent metagenomic studies indicating that mammary secretions of clinically healthy quarters can harbor genomic markers of diverse bacterial groups, the vast majority of which have not been associated with mastitis. These observations have given rise to the concept of "commensal mammary microbiota," the ecological properties of which can have important implications for understanding the pathogenesis of mastitis and offer opportunities for development of novel prophylactic or therapeutic products (or both) as alternatives to antimicrobials. Studies conducted to date have suggested that an optimum diversity of mammary microbiota is associated with immune homeostasis, whereas the microbiota of mastitic quarters, or those with a history of mastitis, are considerably less diverse. Whether disruption of the diversity of udder microbiota (dysbiosis) has a role in determining mastitis susceptibility remains unknown. Moreover, little is known about contributions of various biotic and abiotic factors in shaping overall diversity of udder microbiota. This review summarizes current understanding of the microbiota within various niches of the udder and highlights the need to view the microbiota of the teat apex, teat canal, and mammary secretions as interconnected niches of a highly dynamic microbial ecosystem. In addition, host-associated factors, including physiological and anatomical parameters, as well as genetic traits that may affect the udder microbiota are briefly discussed. Finally, current understanding of the effect of antimicrobials on the composition of intramammary microbiota is discussed, highlighting the resilience of udder microbiota to exogenous perturbants.
Collapse
Affiliation(s)
- Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Kelsey B Fehr
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Shadi Sepehri
- Children Hospital Research Institute of Manitoba, Winnipeg, MB, R3E 3P4 Canada
| | - David Francoz
- Département de Sciences Cliniques, Faculté de Médecine Vétérinaire, Université de Montréal, Montréal, QC, J2S 2M2 Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1 Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1 Canada
| | - Jan C Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2 Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9 Canada.
| |
Collapse
|
87
|
Wosen JE, Mukhopadhyay D, Macaubas C, Mellins ED. Epithelial MHC Class II Expression and Its Role in Antigen Presentation in the Gastrointestinal and Respiratory Tracts. Front Immunol 2018; 9:2144. [PMID: 30319613 PMCID: PMC6167424 DOI: 10.3389/fimmu.2018.02144] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
As the primary barrier between an organism and its environment, epithelial cells are well-positioned to regulate tolerance while preserving immunity against pathogens. Class II major histocompatibility complex molecules (MHC class II) are highly expressed on the surface of epithelial cells (ECs) in both the lung and intestine, although the functional consequences of this expression are not fully understood. Here, we summarize current information regarding the interactions that regulate the expression of EC MHC class II in health and disease. We then evaluate the potential role of EC as non-professional antigen presenting cells. Finally, we explore future areas of study and the potential contribution of epithelial surfaces to gut-lung crosstalk.
Collapse
Affiliation(s)
- Jonathan E Wosen
- Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Dhriti Mukhopadhyay
- Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Claudia Macaubas
- Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Elizabeth D Mellins
- Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA, United States
| |
Collapse
|
88
|
Male Scent Gland Signals Mating Status in Greater Spear-Nosed Bats, Phyllostomus hastatus. J Chem Ecol 2018; 44:975-986. [DOI: 10.1007/s10886-018-1003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/24/2022]
|
89
|
Abstract
Mammalian immune systems evolved within a diverse world dominated by microbes, making interactions between these two life-forms inevitable. Adaptive immunity protects against microbes through antigen-specific responses. In classical studies, these responses were investigated in the context of pathogenicity; however, we now know that they have significant effects on our resident microbes. In turn, microbes employ an arsenal of mechanisms to influence development and specificity of host immunity. Understanding these complex reactions will be necessary to develop microbiota-based strategies to prevent or treat disease. Here we review the literature detailing the cross talk between resident microbes with a focus on the specificity of host responses and the microbial molecules that influence them.
Collapse
Affiliation(s)
- Kyla S Ost
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Utah 84211, USA;
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Utah 84211, USA;
| |
Collapse
|
90
|
Parfrey LW, Moreau CS, Russell JA. Introduction: The host-associated microbiome: Pattern, process and function. Mol Ecol 2018; 27:1749-1765. [DOI: 10.1111/mec.14706] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Laura Wegener Parfrey
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada
- Department of Zoology; University of British Columbia; Vancouver British Columbia Canada
| | - Corrie S. Moreau
- Department of Science and Education; Field Museum of Natural History; Chicago IL USA
| | | |
Collapse
|
91
|
Kennedy AE, Ozbek U, Dorak MT. What has GWAS done for HLA and disease associations? Int J Immunogenet 2018; 44:195-211. [PMID: 28877428 DOI: 10.1111/iji.12332] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/16/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022]
Abstract
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA-DR/DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered.
Collapse
Affiliation(s)
- A E Kennedy
- Center for Research Strategy, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - U Ozbek
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M T Dorak
- Head of School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Kingston-upon-Thames, UK
| |
Collapse
|
92
|
Zhao Q, Elson CO. Adaptive immune education by gut microbiota antigens. Immunology 2018; 154:28-37. [PMID: 29338074 PMCID: PMC5904715 DOI: 10.1111/imm.12896] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 12/13/2022] Open
Abstract
Host-microbiota mutualism has been established during long-term co-evolution. A diverse and rich gut microbiota plays an essential role in the development and maturation of the host immune system. Education of the adaptive immune compartment by gut microbiota antigens is important in establishing immune balance. In particular, a critical time frame immediately after birth provides a 'window of opportunity' for the development of lymphoid structures, differentiation and maturation of T and B cells and, most importantly, establishment of immune tolerance to gut commensals. Depending on the colonization niche, antigen type and metabolic property of different gut microbes, CD4 T-cell responses vary greatly, which results in differentiation into distinct subsets. As a consequence, certain bacteria elicit effector-like immune responses by promoting the production of pro-inflammatory cytokines such as interferon-γ and interleukin-17A, whereas other bacteria favour the generation of regulatory CD4 T cells and provide help with gut homeostasis. The microbiota have profound effects on B cells also. Gut microbial exposure leads to a continuous diversification of B-cell repertoire and the production of T-dependent and -independent antibodies, especially IgA. These combined effects of the gut microbes provide an elegant educational process to the adaptive immune network. Contrariwise, failure of this process results in a reduced homeostasis with the gut microbiota, and an increased susceptibility to various immune disorders, both inside and outside the gut. With more definitive microbial-immune relations waiting to be discovered, modulation of the host gut microbiota has a promising future for disease intervention.
Collapse
Affiliation(s)
- Qing Zhao
- Department of MedicineThe University of Alabama at BirminghamBirminghamALUSA
| | - Charles O. Elson
- Department of MedicineThe University of Alabama at BirminghamBirminghamALUSA
| |
Collapse
|
93
|
Wang J, Chen L, Zhao N, Xu X, Xu Y, Zhu B. Of genes and microbes: solving the intricacies in host genomes. Protein Cell 2018; 9:446-461. [PMID: 29611114 PMCID: PMC5960464 DOI: 10.1007/s13238-018-0532-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.
Collapse
Affiliation(s)
- Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Xizhan Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yakun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
94
|
Hernández-Gómez O, Briggler JT, Williams RN. Influence of immunogenetics, sex and body condition on the cutaneous microbial communities of two giant salamanders. Mol Ecol 2018; 27:1915-1929. [PMID: 29411437 DOI: 10.1111/mec.14500] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
The complex association between hosts and microbial symbionts requires the implementation of multiple approaches to evaluate variation in host physiology. Within amphibians, heterogeneity in immunogenetic traits and cutaneous microbiota is associated with variation in disease resistance. Ozark (Cryptobranchus alleganiensis bishopi) and eastern hellbenders (C. a. alleganiensis) provide a model system to assess variation in host traits and microbial communities. Ozark hellbenders have experienced declines throughout their range, are federally endangered and experience wound retardation that is absent in the eastern subspecies. Previous microbial investigations indicate differentiation in the composition of the skin microbiota of both hellbender subspecies, but it is not clear whether these patterns are concurrent with diversity in the major histocompatibility complex (MHC) genes. We characterized the MHC IIB and the skin microbiota of hellbenders in Missouri, where both subspecies co-occur though not sympatric. We compared the microbiota composition and MHC diversity between both subspecies and investigated whether individual-level MHC diversity, sex and body condition were associated with microbiota composition. Overall, MHC IIB diversity was lower in Ozark hellbenders compared to the eastern subspecies. Multivariate statistical comparisons identified microbiota differentiation between Ozark and eastern hellbenders. MHC IIB allele presence/absence, allele divergence, body composition and sex defined grouping of hellbender microbiotas within populations. Differentiation of the cutaneous microbiotas and MHC IIB genes between eastern and Ozark hellbenders suggests that differences exist in immunity between the two subspecies. This study demonstrates how simultaneous assessments of host genetic traits and microbiotas can inform patterns of microbial community structure in natural systems.
Collapse
Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | | | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
95
|
Sáez de Guinoa J, Jimeno R, Gaya M, Kipling D, Garzón MJ, Dunn-Walters D, Ubeda C, Barral P. CD1d-mediated lipid presentation by CD11c + cells regulates intestinal homeostasis. EMBO J 2018; 37:embj.201797537. [PMID: 29378774 PMCID: PMC5830915 DOI: 10.15252/embj.201797537] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/15/2017] [Accepted: 12/22/2017] [Indexed: 12/16/2022] Open
Abstract
Intestinal homeostasis relies on a continuous dialogue between the commensal bacteria and the immune system. Natural killer T (NKT) cells, which recognize CD1d‐restricted microbial lipids and self‐lipids, contribute to the regulation of mucosal immunity, yet the mechanisms underlying their functions remain poorly understood. Here, we demonstrate that NKT cells respond to intestinal lipids and CD11c+ cells (including dendritic cells (DCs) and macrophages) are essential to mediate lipid presentation within the gut ultimately controlling intestinal NKT cell homeostasis and activation. Conversely, CD1d and NKT cells participate in the control of the intestinal bacteria composition and compartmentalization, in the regulation of the IgA repertoire and in the induction of regulatory T cells within the gut. These changes in intestinal homeostasis require CD1d expression on DC/macrophage populations as mice with conditional deletion of CD1d on CD11c+ cells exhibit dysbiosis and altered immune homeostasis. These results unveil the importance of CD11c+ cells in controlling lipid‐dependent immunity in the intestinal compartment and reveal an NKT cell–DC crosstalk as a key mechanism for the regulation of gut homeostasis.
Collapse
Affiliation(s)
- Julia Sáez de Guinoa
- The Peter Gorer Department of Immunobiology, King's College London, London, UK.,The Francis Crick Institute, London, UK
| | - Rebeca Jimeno
- The Peter Gorer Department of Immunobiology, King's College London, London, UK.,The Francis Crick Institute, London, UK
| | - Mauro Gaya
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - David Kipling
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - María José Garzón
- Departamento de Genómica y Salud, Centro Superior de Investigación en Salud Pública - FISABIO, Valencia, Spain
| | | | - Carles Ubeda
- Departamento de Genómica y Salud, Centro Superior de Investigación en Salud Pública - FISABIO, Valencia, Spain.,Centers of Biomedical Research Network (CIBER) in Epidemiology and Public Health, Madrid, Spain
| | - Patricia Barral
- The Peter Gorer Department of Immunobiology, King's College London, London, UK .,The Francis Crick Institute, London, UK
| |
Collapse
|
96
|
Liang D, Leung RKK, Guan W, Au WW. Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities. Gut Pathog 2018; 10:3. [PMID: 29416567 PMCID: PMC5785832 DOI: 10.1186/s13099-018-0230-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
The commensal, symbiotic, and pathogenic microbial community which resides inside our body and on our skin (the human microbiome) can perturb host energy metabolism and immunity, and thus significantly influence development of a variety of human diseases. Therefore, the field has attracted unprecedented attention in the last decade. Although a large amount of data has been generated, there are still many unanswered questions and no universal agreements on how microbiome affects human health have been agreed upon. Consequently, this review was written to provide an updated overview of the rapidly expanding field, with a focus on revealing knowledge gaps and research opportunities. Specifically, the review covered animal physiology, optimal microbiome standard, health intervention by manipulating microbiome, knowledge base building by text mining, microbiota community structure and its implications in human diseases and health monitoring by analyzing microbiome in the blood. The review should enhance interest in conducting novel microbiota investigations that will further improve health and therapy.
Collapse
Affiliation(s)
- Dachao Liang
- Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics Hong Kong, Hong Kong SAR, China
| | - Ross Ka-Kit Leung
- 2State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Wenda Guan
- 2State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - William W Au
- 3University of Medicine and Pharmacy, Tirgu Mures, Romania.,4Shantou University Medical College, Shantou, China
| |
Collapse
|
97
|
Cai W, Ran Y, Li Y, Wang B, Zhou L. Intestinal microbiome and permeability in patients with autoimmune hepatitis. Best Pract Res Clin Gastroenterol 2017; 31:669-673. [PMID: 29566910 DOI: 10.1016/j.bpg.2017.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/16/2017] [Indexed: 01/31/2023]
Abstract
Autoimmune hepatitis (AIH) is a severe inflammatory liver disease. The underlying mechanisms remain unclear, but recent studies provided new perspectives on altered intestinal microbiome and permeability in AIH animal models and patients, highlighting gut-liver crosstalk in the pathogenesis of AIH. Transgenic AIH mice carrying HLA-DR3 showed reduced diversity and total load of gut microbiota. Germ-free mice are resistant to concanavalin A-induced liver injury, whereas enterogenouss antigens induce the activation of natural killer T cells participating in concanavalin A-induced liver injury, supporting the close relationship between microbiota and AIH. Moreover, 'molecular mimicry' provides a plausible interpretation of the immune reactions between microorganic antigens and liver autoantigens, for instance, cytochrome P4502D6, the target of cross-reactivity between virus and self. Nevertheless, direct evidence for the intestinal microbiome and permeability in AIH is still limited. The relationship between AIH susceptibilities and an intestinal microbiome shaped by drugs, diets or genes needs further study.
Collapse
Affiliation(s)
- Wangfeng Cai
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, PR China
| | - Ying Ran
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, PR China
| | - Yanni Li
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, PR China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, PR China.
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300052, PR China.
| |
Collapse
|
98
|
Roselli M, Pieper R, Rogel-Gaillard C, de Vries H, Bailey M, Smidt H, Lauridsen C. Immunomodulating effects of probiotics for microbiota modulation, gut health and disease resistance in pigs. Anim Feed Sci Technol 2017. [DOI: 10.1016/j.anifeedsci.2017.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
99
|
Abstract
Whereas strong evidence supports the notion that the microbiota promotes immune system maturation in multiple tissues, the identity of the specific microbes that elicit protective immunity to different infections is less clear. In a recent issue of Cell Host & Microbe, Thiemann et al. (2017) report the identification of specific gut bacteria that protect from Salmonella infection by priming host IFN-γ responses.
Collapse
Affiliation(s)
- Kyla S Ost
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - June L Round
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA.
| |
Collapse
|
100
|
De Re V, Magris R, Cannizzaro R. New Insights into the Pathogenesis of Celiac Disease. Front Med (Lausanne) 2017; 4:137. [PMID: 28913337 PMCID: PMC5583152 DOI: 10.3389/fmed.2017.00137] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/27/2017] [Indexed: 12/12/2022] Open
Abstract
Celiac disease (CD) is an autoimmune and multisystem gluten-related disorder that causes symptoms involving the gastrointestinal tract and other organs. Pathogenesis of CD is only partially known. It had been established that ingestion of gluten proteins present in wheat and other cereals are necessary for the disease and develops in individuals genetically predisposed carrying the DQ2 or DQ8 human leukocyte antigen haplotypes. In this review, we had pay specific attention on the last discoveries regarding the three cellular components mainly involved in the development and maintenance of CD: T-cells, B-cells, and microbioma. All of them had been showed critical for the interaction between inflammatory immune response and gluten peptides. Although the mechanisms of interaction among overall these components are not yet fully understood, recent proteomics and molecular studies had shed some lights in the pathogenic role of tissue transglutaminase 2 in CD and in the alteration of the intestinal barrier function induced by host microbiota.
Collapse
Affiliation(s)
- Valli De Re
- Immunopatologia e Biomarcatori Oncologici/Bio-Proteomics Facility, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Raffaella Magris
- Oncological Gastroenterology, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Oncological Gastroenterology, CRO Aviano National Cancer Institute, Aviano, Italy
| |
Collapse
|