1
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Gouzerh F, Vigo G, Dormont L, Buatois B, Hervé MR, Mancini M, Maraver A, Thomas F, Ganem G. Urinary VOCs as biomarkers of early stage lung tumour development in mice. Cancer Biomark 2024; 39:113-125. [PMID: 37980646 PMCID: PMC11002722 DOI: 10.3233/cbm-230070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/05/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Lung cancer is the primary cause of cancer-induced death. In addition to prevention and improved treatment, it has increasingly been established that early detection is critical to successful remission. OBJECTIVE The aim of this study was to identify volatile organic compounds (VOCs) in urine that could help diagnose mouse lung cancer at an early stage of its development. METHODS We analysed the VOC composition of urine in a genetically engineered lung adenocarcinoma mouse model with oncogenic EGFR doxycycline-inducible lung-specific expression. We compared the urinary VOCs of 10 cancerous mice and 10 healthy mice (controls) before and after doxycycline induction, every two weeks for 12 weeks, until full-blown carcinomas appeared. We used SPME fibres and gas chromatography - mass spectrometry to detect variations in cancer-related urinary VOCs over time. RESULTS This study allowed us to identify eight diagnostic biomarkers that help discriminate early stages of cancer tumour development (i.e., before MRI imaging techniques could identify it). CONCLUSION The analysis of mice urinary VOCs have shown that cancer can induce changes in odour profiles at an early stage of cancer development, opening a promising avenue for early diagnosis of lung cancer in other models.
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Affiliation(s)
- Flora Gouzerh
- CREEC/MIVEGEC, Centre de Recherches Ecologiques et Evolutives sur le Cancer/Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Gwenaëlle Vigo
- CREEC/MIVEGEC, Centre de Recherches Ecologiques et Evolutives sur le Cancer/Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Laurent Dormont
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Bruno Buatois
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Maxime R. Hervé
- IGEPP, Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes, Rennes, France
| | - Maicol Mancini
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-ICM-Université Montpellier, Montpellier, France
| | - Antonio Maraver
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-ICM-Université Montpellier, Montpellier, France
| | - Frédéric Thomas
- CREEC/MIVEGEC, Centre de Recherches Ecologiques et Evolutives sur le Cancer/Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Guila Ganem
- ISEM, Institut des Sciences de l’Evolution, UMR 5554, Université Montpellier, CNRS, IRD, Montpellier, France
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2
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Bowen M, Miles C, Hegseth R, Anderson CM, Brandon CS, Langford ML, Wolovich CK. The potential interplay between the glandular microbiome and scent marking behavior in owl monkeys (Aotus nancymaae). Am J Primatol 2021; 83:e23324. [PMID: 34492124 DOI: 10.1002/ajp.23324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 08/18/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
In mammals, scent marking behavior is a pervasive form of chemical communication that regulates social interactions within and between groups. Glandular microbiota consist of bacterial communities capable of producing chemical cues used in olfactory communication. Despite countless studies on scent marking in primates, few have examined the microbiota associated with glandular secretions. Nancy Ma's owl monkeys (Aotus nancymaae) are nocturnal, socially monogamous primates that frequently scent mark using their subcaudal glands. Previous analyses revealed that unique chemical signatures of Aotus may convey information about sex and age. We used positive reinforcement to sample the subcaudal glands of 23 captive owl monkeys to describe their glandular microbiomes and examine how patterns in these bacterial communities vary with age, sex, rearing environment and/or social group (pair identity). We coupled these analyses with behavioral observations to examine patterns in their scent marking behavior. We isolated 31 bacterial species from Phyla Firmicutes, Proteobacteria, and Actinobacteria, consistent with the dermal and glandular microbiomes of other primates. Several bacterial taxa we identified produce volatile organic compounds, which may contribute to olfactory communication. These bacterial communities are best predicted by an interaction between sex, rearing environment and pair identity rather than any of these variables alone. Within mated pairs of A. nancymaae, males and females scent mark their nest boxes at similar frequencies. In some pairs, rates of scent marking by males and females fluctuated over time in a similar manner. Pairs that had been together longer tended to exhibit the greatest similarities in their rates of scent marking. Together, these findings suggest that scent marking behavior and close social interactions with pair mates in Aotus may influence bacterial transmission and their glandular microbiomes. Chemical communication, including coordinated scent marking, may play a role in strengthening pair bonds, signaling pair status and/or in mate guarding in this socially monogamous primate.
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Affiliation(s)
- Malique Bowen
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
| | - Carly Miles
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
| | - Ryan Hegseth
- Department of Biology, Florida Southern College, Lakeland, Florida, USA
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3
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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.
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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
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4
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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.
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5
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Grogan KE, Harris RL, Boulet M, Drea CM. Genetic variation at MHC class II loci influences both olfactory signals and scent discrimination in ring-tailed lemurs. BMC Evol Biol 2019; 19:171. [PMID: 31438845 PMCID: PMC6704550 DOI: 10.1186/s12862-019-1486-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 07/21/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Diversity at the Major Histocompatibility Complex (MHC) is critical to health and fitness, such that MHC genotype may predict an individual's quality or compatibility as a competitor, ally, or mate. Moreover, because MHC products can influence the components of bodily secretions, an individual's body odors may signal its MHC composition and influence partner identification or mate choice. Here, we investigated MHC-based signaling and recipient sensitivity by testing for odor-gene covariance and behavioral discrimination of MHC diversity and pairwise dissimilarity in a strepsirrhine primate, the ring-tailed lemur (Lemur catta). METHODS First, we coupled genotyping of the MHC class II gene, DRB, with gas chromatography-mass spectrometry of genital gland secretions to investigate if functional genetic diversity is signaled by the chemical diversity of lemur scent secretions. We also assessed if the chemical similarity between individuals correlated with their MHC-DRB similarity. Next, we assessed if lemurs discriminated this chemically encoded, genetic information in opposite-sex conspecifics. RESULTS We found that both sexes signaled overall MHC-DRB diversity and pairwise MHC-DRB similarity via genital secretions, but in a sex- and season-dependent manner. Additionally, the sexes discriminated absolute and relative MHC-DRB diversity in the genital odors of opposite-sex conspecifics, suggesting that lemur genital odors function to advertise genetic quality. CONCLUSIONS In summary, genital odors of ring-tailed lemurs provide honest information about an individual's absolute and relative MHC quality. Complementing evidence in humans and Old World monkeys, we suggest that reliance on scent signals to communicate MHC quality may be important across the primate lineage.
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Affiliation(s)
- Kathleen E Grogan
- University Program in Ecology, Duke University, Durham, NC, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.
- Department of Psychology, Emory University, Atlanta, GA, USA.
- Pennsylvania State University, 516 Carpenter Building, University Park, PA, 16802, USA.
| | - Rachel L Harris
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Marylène Boulet
- Department of Biological Sciences, Bishop's University, Sherbrooke, Canada
| | - Christine M Drea
- University Program in Ecology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, USA
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6
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Weger BD, Rawashdeh O, Gachon F. At the Intersection of Microbiota and Circadian Clock: Are Sexual Dimorphism and Growth Hormones the Missing Link to Pathology? Bioessays 2019; 41:e1900059. [DOI: 10.1002/bies.201900059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/28/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin D. Weger
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanne CH‐1015 Switzerland
| | - Oliver Rawashdeh
- School of Biomedical Science, Faculty of MedicineThe University of QueenslandSt. Lucia QLD‐4072 Australia
| | - Frédéric Gachon
- Institute for Molecular BioscienceThe University of QueenslandSt. Lucia QLD‐4072 Australia
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7
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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.
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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
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8
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Kentner AC, Khan U, MacRae M, Dowd SE, Yan S. The effect of antibiotics on social aversion following early life inflammation. Physiol Behav 2018; 194:311-318. [DOI: 10.1016/j.physbeh.2018.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/10/2018] [Accepted: 06/06/2018] [Indexed: 01/23/2023]
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9
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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]
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10
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Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, Stumpf R, White B, Nelson KE, Baden AL, Tecot SR. Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. J Anim Ecol 2017; 87:388-399. [PMID: 29205327 DOI: 10.1111/1365-2656.12781] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/21/2017] [Indexed: 01/12/2023]
Abstract
Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time. Red-bellied lemurs were found to have gut microbiota with slight temporal fluctuations and strong social group-specific composition. Contrary to expectations, individual sociality was negatively associated with gut microbial diversity. However, position within the social network predicted gut microbial composition. These results emphasize the role of the social environment in determining the microbiota of adult animals. Since social transmission of gut microbiota has the potential to enhance immunity, microbiota might have played an escalating role in the evolution of sociality.
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Affiliation(s)
- Aura Raulo
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Lasse Ruokolainen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Avery Lane
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Katherine Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Steven Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Rebecca Stumpf
- Department of Anthropology, University of Colorado, Boulder, CO, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Bryan White
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.,Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | | | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York, NY, USA.,Departments of Anthropology & Biology, The Graduate Center of City University of New York, New York, NY, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, USA
| | - Stacey R Tecot
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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11
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Quantitative inheritance of volatile pheromones and darcin and their interaction in olfactory preferences of female mice. Sci Rep 2017; 7:2094. [PMID: 28522864 PMCID: PMC5437034 DOI: 10.1038/s41598-017-02259-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/24/2017] [Indexed: 11/10/2022] Open
Abstract
In this study, we examined how urine-borne volatile compounds (UVCs) and darcin of male mice are inherited from parents and interact to modulate the olfactory preferences of females using two inbred strains of mice, C57Bl/6 (C57) and BALB/c (BALB), and their reciprocal hybrids (BC = BALB♀× C57♂; CB = C57♀ × BALB♂). Chemical analysis revealed that the UVCs of C57BL/6 males were quantitatively distinguishable from those of BALB/c males. Darcin was detected in C57 urine, but not in BALB urine. The levels of UVCs and darcin in both BC and CB were intermediate between those of C57 and BALB. Behaviourally, C57 females consistently preferred BALB male urine over C57 or CB males despite that there are trace amounts of darcin in BALB urine. However, the preference for BALB urine disappeared in contact two-choice tests of BALB vs. BC pairs, and restored when recombinant darcin was added to BALB male urine. Our results suggested that both UVCs and darcin in male mice are quantitatively inherited and interact to affect the olfactory preferences of females.
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12
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Eisthen HL, Theis KR. Animal-microbe interactions and the evolution of nervous systems. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150052. [PMID: 26598731 DOI: 10.1098/rstb.2015.0052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Animals ubiquitously interact with environmental and symbiotic microbes, and the effects of these interactions on animal physiology are currently the subject of intense interest. Nevertheless, the influence of microbes on nervous system evolution has been largely ignored. We illustrate here how taking microbes into account might enrich our ideas about the evolution of nervous systems. For example, microbes are involved in animals' communicative, defensive, predatory and dispersal behaviours, and have likely influenced the evolution of chemo- and photosensory systems. In addition, we speculate that the need to regulate interactions with microbes at the epithelial surface may have contributed to the evolutionary internalization of the nervous system.
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Affiliation(s)
- Heather L Eisthen
- Department of Integrative Biology, Michigan State University, 288 Farm Lane Rm 203, East Lansing, MI 48824, USA BEACON Center for the Study of Evolution in Action, 567 Wilson Road Rm 1441, East Lansing, MI 48824, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, 567 Wilson Road Rm 1441, East Lansing, MI 48824, USA Department of Internal Medicine, University of Michigan Medical School, 1150 West Medical Center Drive, MSRB I Rm 1510A, Ann Arbor, MI 48109, USA
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13
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Buie T. Potential Etiologic Factors of Microbiome Disruption in Autism. Clin Ther 2016; 37:976-83. [PMID: 26046240 DOI: 10.1016/j.clinthera.2015.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE The primary purpose of this article was to consider the candidate disruptors of the development of a healthy microbiome in patients with autism. The reported abnormalities in the microbiome of individuals with autism are discussed. METHODS This selected review used data from published articles related to the assessment of microbiota in autism. Evidence-based support of factors known to affect the intestinal microbiome in individuals with autism are presented. Proposed interventions are evaluated and discussed. FINDINGS Studies that have investigated the intestinal microbiome in patients with autism have reported significant differences versus unaffected controls. Increased clostridial species in autism have been reported in several studies. These differences may have resulted from a number of environmental factors. Microbiome alterations that might contribute to the development of autism include altered immune function and bacterial metabolites. IMPLICATIONS Efforts to modify microbial imbalances through a variety of interventions are addressed. Focusing on mechanisms that drive imbalances in the microbiome may affect the development of disease. Altered intestinal health may contribute to the development of autistic behaviors or autism itself. Interventions aimed at improving intestinal health may favorably affect the microbiome and autism.
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Affiliation(s)
- Timothy Buie
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
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14
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Neuman H, Debelius JW, Knight R, Koren O. Microbial endocrinology: the interplay between the microbiota and the endocrine system. FEMS Microbiol Rev 2015; 39:509-21. [PMID: 25701044 DOI: 10.1093/femsre/fuu010] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2014] [Indexed: 12/27/2022] Open
Abstract
The new field of microbiome research studies the microbes within multicellular hosts and the many effects of these microbes on the host's health and well-being. We now know that microbes influence metabolism, immunity and even behavior. Essential questions, which are just starting to be answered, are what are the mechanisms by which these bacteria affect specific host characteristics. One important but understudied mechanism appears to involve hormones. Although the precise pathways of microbiota-hormonal signaling have not yet been deciphered, specific changes in hormone levels correlate with the presence of the gut microbiota. The microbiota produces and secretes hormones, responds to host hormones and regulates expression levels of host hormones. Here, we summarize the links between the endocrine system and the gut microbiota. We categorize these interactions by the different functions of the hormones, including those affecting behavior, sexual attraction, appetite and metabolism, gender and immunity. Future research in this area will reveal additional connections, and elucidate the pathways and consequences of bacterial interactions with the host endocrine system.
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Affiliation(s)
- Hadar Neuman
- Faculty of medicine, Bar-Ilan University, 1311502 Safed, Israel
| | - Justine W Debelius
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Omry Koren
- Faculty of medicine, Bar-Ilan University, 1311502 Safed, Israel
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15
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Kuduk K, Babik W, Bellemain E, Valentini A, Zedrosser A, Taberlet P, Kindberg J, Swenson JE, Radwan J. No evidence for the effect of MHC on male mating success in the brown bear. PLoS One 2014; 9:e113414. [PMID: 25470381 PMCID: PMC4254848 DOI: 10.1371/journal.pone.0113414] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
Mate choice is thought to contribute to the maintenance of the spectacularly high polymorphism of the Major Histocompatibility Complex (MHC) genes, along with balancing selection from parasites, but the relative contribution of the former mechanism is debated. Here, we investigated the association between male MHC genotype and mating success in the brown bear. We analysed fragments of sequences coding for the peptide-binding region of the highly polymorphic MHC class I and class II DRB genes, while controlling for genome-wide effects using a panel of 18 microsatellite markers. Male mating success did not depend on the number of alleles shared with the female or amino-acid distance between potential mates at either locus. Furthermore, we found no indication of female mating preferences for MHC similarity being contingent on the number of alleles the females carried. Finally, we found no significant association between the number of MHC alleles a male carried and his mating success. Thus, our results provided no support for the role of mate choice in shaping MHC polymorphism in the brown bear.
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Affiliation(s)
- Katarzyna Kuduk
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Eva Bellemain
- SPYGEN, Savoie Technolac - Bât. Koala 17, rue du Lac Saint-André - BP 274, 73375, Le Bourget-du-Lac Cedex, France
| | - Alice Valentini
- SPYGEN, Savoie Technolac - Bât. Koala 17, rue du Lac Saint-André - BP 274, 73375, Le Bourget-du-Lac Cedex, France
| | - Andreas Zedrosser
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway
- Institute for Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, AT-1180, Vienna, Austria
| | - Pierre Taberlet
- CNRS, LECA, F-38000, Grenoble, France
- Université Grenoble Alpes, LECA, F-38000, Grenoble, France
| | - Jonas Kindberg
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway
- Norwegian Institute for Nature Research, NO-7485, Trondheim, Norway
| | - Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
- * E-mail:
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Stagaman K, Guillemin K, Milligan-Myhre K. Tending a complex microbiota requires major immune complexity. Mol Ecol 2014; 23:4679-81. [PMID: 25263404 DOI: 10.1111/mec.12895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 01/25/2023]
Abstract
Animals maintain complex microbial communities within their guts that fill important roles in the health and development of the host. To what degree a host's genetic background influences the establishment and maintenance of its gut microbial communities is still an open question. We know from studies in mice and humans that external factors, such as diet and environmental sources of microbes, and host immune factors play an important role in shaping the microbial communities (Costello et al. ). In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake to provide evidence that another part of the adaptive immune response, the major histocompatibility complex class II (MHCII) receptors of antigen-presenting cells, may play a role in shaping the gut microbiota of the threespine stickleback, Gasterosteus aculeatus (Bolnick et al. 2014a). Bolnick et al. (2014a) provide insight into natural, interindividual variation in the diversity of both stickleback MHCII alleles and their gut microbial communities and correlate changes in the diversity of MHCII receptor alleles with changes in the microbiota.
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Affiliation(s)
- Keaton Stagaman
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR, 97403, USA
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17
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Leclaire S, Nielsen JF, Drea CM. Bacterial communities in meerkat anal scent secretions vary with host sex, age, and group membership. Behav Ecol 2014. [DOI: 10.1093/beheco/aru074] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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18
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Trojan Genes or Transparent Genomes? Sexual Selection and Potential Impacts of Genetically Modified Animals in Natural Ecosystems. Evol Biol 2013. [DOI: 10.1007/s11692-013-9268-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Daum JM, Davis LR, Bigler L, Woodhams DC. Hybrid advantage in skin peptide immune defenses of water frogs (Pelophylax esculentus) at risk from emerging pathogens. INFECTION GENETICS AND EVOLUTION 2012; 12:1854-64. [DOI: 10.1016/j.meegid.2012.07.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/30/2012] [Accepted: 07/31/2012] [Indexed: 02/08/2023]
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Moshkin M, Litvinova N, Litvinova EA, Bedareva A, Lutsyuk A, Gerlinskaya L. Scent Recognition of Infected Status in Humans. J Sex Med 2012; 9:3211-8. [DOI: 10.1111/j.1743-6109.2011.02562.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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21
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Villinger J, Waldman B. Social discrimination by quantitative assessment of immunogenetic similarity. Proc Biol Sci 2012; 279:4368-74. [PMID: 22951741 PMCID: PMC3479794 DOI: 10.1098/rspb.2012.1279] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/10/2012] [Indexed: 01/04/2023] Open
Abstract
Genes of the major histocompatibility complex (MHC) that underlie the adaptive immune system may allow vertebrates to recognize their kin. True kin-recognition genes should produce signalling products to which organisms can respond. Allelic variation in the peptide-binding region (PBR) of MHC molecules determines the pool of peptides that can be presented to trigger an immune response. To examine whether these MHC peptides also might underlie assessments of genetic similarity, we tested whether Xenopus laevis tadpoles socially discriminate between pairs of siblings with which they differed in PBR amino acid sequences. We found that tadpoles (four sibships, n = 854) associated preferentially with siblings with which they were more similar in PBR amino acid sequence. Moreover, the strength of their preference for a conspecific was directly proportional to the sequence similarity between them. Discrimination was graded, and correlated more closely with functional sequence differences encoded by MHC class I and class II alleles than with numbers of shared haplotypes. Our results thus suggest that haplotype analyses may fail to reveal fine-scale behavioural responses to divergence in functionally expressed sequences. We conclude that MHC-PBR gene products mediate quantitative social assessment of immunogenetic similarity that may facilitate kin recognition in vertebrates.
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Affiliation(s)
- Jandouwe Villinger
- Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, PO Box 30772-00100, Nairobi, Kenya
| | - Bruce Waldman
- Department of Ecology, PO Box 84, Lincoln University, Canterbury 7647, New Zealand
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-747, South Korea
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22
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Strandh M, Westerdahl H, Pontarp M, Canbäck B, Dubois MP, Miquel C, Taberlet P, Bonadonna F. Major histocompatibility complex class II compatibility, but not class I, predicts mate choice in a bird with highly developed olfaction. Proc Biol Sci 2012; 279:4457-63. [PMID: 22951737 DOI: 10.1098/rspb.2012.1562] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mate choice for major histocompatibility complex (MHC) compatibility has been found in several taxa, although rarely in birds. MHC is a crucial component in adaptive immunity and by choosing an MHC-dissimilar partner, heterozygosity and potentially broad pathogen resistance is maximized in the offspring. The MHC genotype influences odour cues and preferences in mammals and fish and hence olfactory-based mate choice can occur. We tested whether blue petrels, Halobaena caerulea, choose partners based on MHC compatibility. This bird is long-lived, monogamous and can discriminate between individual odours using olfaction, which makes it exceptionally well suited for this analysis. We screened MHC class I and II B alleles in blue petrels using 454-pyrosequencing and quantified the phylogenetic, functional and allele-sharing similarity between individuals. Partners were functionally more dissimilar at the MHC class II B loci than expected from random mating (p = 0.033), whereas there was no such difference at the MHC class I loci. Phylogenetic and non-sequence-based MHC allele-sharing measures detected no MHC dissimilarity between partners for either MHC class I or II B. Our study provides evidence of mate choice for MHC compatibility in a bird with a high dependency on odour cues, suggesting that MHC odour-mediated mate choice occurs in birds.
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Affiliation(s)
- Maria Strandh
- Behavioral Ecology Group, CEFE-CNRS, 1919 Route de Mende, Montpellier Cedex 5, France.
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23
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Theis KR, Schmidt TM, Holekamp KE. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Sci Rep 2012; 2:615. [PMID: 22937224 PMCID: PMC3431069 DOI: 10.1038/srep00615] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/10/2012] [Indexed: 02/01/2023] Open
Abstract
Symbiotic microbes can benefit their animal hosts by enhancing the diversity of communication signals available to them. The fermentation hypothesis for chemical recognition posits that 1) fermentative bacteria in specialized mammalian scent glands generate odorants that mammals co-opt to communicate with one another, and 2) that variation in scent gland odors is due to underlying variation in the structure of bacterial communities within scent glands. For example, group-specific social odors are suggested to be due to members of the same social group harboring more similar bacterial communities in their scent glands than do members of different social groups. We used 16S rRNA gene surveys to show that 1) the scent secretions of spotted hyenas are densely populated by fermentative bacteria whose closest relatives are well-documented odor producers, and that 2) these bacterial communities are more similar among hyenas from the same social group than among those from different groups.
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Affiliation(s)
- Kevin R Theis
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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24
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Charpentier MJE, Barthes N, Proffit M, Bessière JM, Grison C. Critical thinking in the chemical ecology of mammalian communication: roadmap for future studies. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.01998.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Nicolas Barthes
- CEFE-CNRS UMR 5175; 1919; Route de Mende, 34293 Montpellier Cedex 5; France
| | - Magali Proffit
- Chemical Ecology Group; Swedish University of Agricultural Sciences; 230 53; Alnarp; Sweden
| | | | - Claude Grison
- CEFE-CNRS UMR 5175; 1919; Route de Mende, 34293 Montpellier Cedex 5; France
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25
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Sin YW, Buesching CD, Burke T, Macdonald DW. Molecular characterization of the microbial communities in the subcaudal gland secretion of the European badger (Meles meles). FEMS Microbiol Ecol 2012; 81:648-59. [PMID: 22530962 DOI: 10.1111/j.1574-6941.2012.01396.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/30/2022] Open
Abstract
Many mammals possess specialized scent glands, which convey information about the marking individual. As the chemical profile of scent marks is likely to be affected by bacteria metabolizing the primary gland products, the variation in bacterial communities between different individuals has been proposed to underpin olfactory communication. However, few studies have investigated the dependency of microbiota residing in the scent organs on the host's individual-specific parameters. Here, we used terminal restriction fragment length polymorphism analysis of the PCR-amplified 16S rRNA gene and clone library construction to investigate the microbial communities in the subcaudal gland secretion of the European badger (Meles meles). As the secretion has been shown to encode individual-specific information, we investigated the correlation of the microbiota with different individual-specific parameters (age, sex, body condition, reproductive status, and season). We discovered a high number of bacterial species (56 operational taxonomic units from four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes), dominated by Actinobacteria (76.0%). The bacterial communities of cubs and adults differed significantly. Cubs possessed considerably more diverse communities dominated by Firmicutes, while in adults the communities were less diverse and dominated by Actinobacteria, suggesting that the acquisition of a 'mature bacterial community' is an ontogenetic process related to physiological changes during maturation.
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Affiliation(s)
- Yung Wa Sin
- Wildlife Conservation Research Unit, Department of Zoology, Recanati-Kaplan Centre, University of Oxford, Tubney, Abingdon, Oxfordshire, UK.
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26
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Barribeau SM, Villinger J, Waldman B. Ecological immunogenetics of life-history traits in a model amphibian. Biol Lett 2011; 8:405-7. [PMID: 22114322 PMCID: PMC3367720 DOI: 10.1098/rsbl.2011.0845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Major histocompatibility complex (MHC) genes determine immune repertoires and social preferences of vertebrates. Immunological regulation of microbial assemblages associated with individuals influences their sociality, and should also affect their life-history traits. We exposed Xenopus laevis tadpoles to water conditioned by adult conspecifics. Then, we analysed tadpole growth, development and survivorship as a function of MHC class I and class II peptide-binding region amino acid sequence similarities between tadpoles and frogs that conditioned the water to which they were exposed. Tadpoles approached metamorphosis earlier and suffered greater mortality when exposed to immunogenetically dissimilar frogs. The results suggest that developmental regulatory cues, microbial assemblages or both are specific to MHC genotypes. Tadpoles may associate with conspecifics with which they share microbiota to which their genotypes are well adapted.
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Affiliation(s)
- Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, Zürich 8092, Switzerland
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27
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From models to mechanisms: Odorant communication as a key determinant of social behavior in rodents during illness-associated states. Neurosci Biobehav Rev 2011; 35:1916-28. [DOI: 10.1016/j.neubiorev.2011.03.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 11/22/2022]
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28
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29
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Litvinova EA, Moshkin MP, Gerlinskaya LA, Nagatomi R, Zhang X, Matsuo K, Shikano S. Female scent mobilizes leukocytes to airways in BALB/c male mice. Integr Zool 2011; 4:285-93. [PMID: 21392301 DOI: 10.1111/j.1749-4877.2009.00162.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The scent of receptive females as a signal to reproduction stimulates male mice to olfactory search of a potential breeding partner. This searching behavior is coupled with infection risk due to bacterial contamination of the fecal and urine scent marks. We hypothesized that sniffing of female soiled bedding induced the migration of immuno-competent cells into airways as a possible adaptation to breeding-related infection. Using bronchoalveolar lavage in a study on mice, we found the number of leukocytes to be significantly higher in male mice that were provided new portions of soiled bedding daily from female cages, in comparison with male mice that were kept in isolation from female scent. The number of leukocytes in blood was equal in both groups. However, monocytes were fewer in number in male mice exposed to female scent than in male mice isolated from female mice. Scent-induced migration of leukocytes was accompanied by typical behavioral (increased sniffing activity and aggressiveness) and morphological (increase preputial glands and seminal vesicles) responses to olfactory sexual stimulus.
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Affiliation(s)
- Ekatherina A Litvinova
- Laboratory of Physiological Adaptation of Animals, Institute of Systematics and Ecology of Animals, Siberian Branch of Russian academy of sciences, Novosibirsk, Russia.
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30
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Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. The mind-body-microbial continuum. DIALOGUES IN CLINICAL NEUROSCIENCE 2011. [PMID: 21485746 PMCID: PMC3139398 DOI: 10.31887/dcns.2011.13.1/agonzalez] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent "metagenomic" techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A central question in psychiatry is the relative role of genes and environment in shaping behavior. The human microbiome serves as the interface between our genes and our history of environmental exposures; explorations of our microbiomes thus offer the possibility of providing new insights into our neurodevelopment and our behavioral phenotypes by affecting complex processes such as inter- and intra personal variations in cognition, personality, mood, sleep, and eating behavior, and perhaps even a variety of neuropsychiatric diseases ranging from affective disorders to autism. Better understanding of microbiome-encoded pathways for xenobiotic metabolism also has important implications for improving the efficacy of pharmacologic interventions with neuromodulatory agents.
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Affiliation(s)
- Antonio Gonzalez
- Department of Computer Science, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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31
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Supaphol S, Jenkins SN, Intomo P, Waite IS, O'Donnell AG. Microbial community dynamics in mesophilic anaerobic co-digestion of mixed waste. BIORESOURCE TECHNOLOGY 2011; 102:4021-7. [PMID: 21196114 DOI: 10.1016/j.biortech.2010.11.124] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 11/27/2010] [Accepted: 11/30/2010] [Indexed: 05/16/2023]
Abstract
This paper identifies key components of the microbial community involved in the mesophilic anaerobic co-digestion (AD) of mixed waste at Rayong Biogas Plant, Thailand. The AD process is separated into three stages: front end treatment (FET); feed holding tank and the main anaerobic digester. The study examines how the microbial community structure was affected by the different stages and found that seeding the waste at the beginning of the process (FET) resulted in community stability. Also, co-digestion of mixed waste supported different bacterial and methanogenic pathways. Typically, acetoclastic methanogenesis was the major pathway catalysed by Methanosaeta but hydrogenotrophs were also supported. Finally, the three-stage AD process means that hydrolysis and acidogenesis is initiated prior to entering the main digester which helps improve the bioconversion efficiency. This paper demonstrates that both resource availability (different waste streams) and environmental factors are key drivers of microbial community dynamics in mesophilic, anaerobic co-digestion.
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Affiliation(s)
- Savaporn Supaphol
- Department of Soil Science, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
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32
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Tourlomousis P, Kemsley EK, Ridgway KP, Toscano MJ, Humphrey TJ, Narbad A. PCR-denaturing gradient gel electrophoresis of complex microbial communities: a two-step approach to address the effect of gel-to-gel variation and allow valid comparisons across a large dataset. MICROBIAL ECOLOGY 2010; 59:776-786. [PMID: 19953241 DOI: 10.1007/s00248-009-9613-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 10/26/2009] [Indexed: 05/28/2023]
Abstract
Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis software package (TL120 v2006, Phoretix 1D Advanced) followed by a simple interpolation step in Matlab minimized the effect of gel-to-gel variation, allowing for comparisons between large numbers of samples with a high degree of confidence. At the same time, data were obtained in the form of whole densitometric curves, rather than as band presence/absence or intensity information, and could be readily analyzed by a collection of well-established multivariate methods. This work clearly demonstrates that there is still room for significant improvements as to the way large DGGE datasets are processed and statistically interrogated.
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Affiliation(s)
- Panagiotis Tourlomousis
- Integrated Biology of GI Tract Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
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Kwak J, Willse A, Preti G, Yamazaki K, Beauchamp GK. In search of the chemical basis for MHC odourtypes. Proc Biol Sci 2010; 277:2417-25. [PMID: 20356897 DOI: 10.1098/rspb.2010.0162] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mice can discriminate between chemosignals of individuals based solely on genetic differences confined to the major histocompatibility complex (MHC). Two different sets of compounds have been suggested: volatile compounds and non-volatile peptides. Here, we focus on volatiles and review a number of publications that have identified MHC-regulated compounds in inbred laboratory mice. Surprisingly, there is little agreement among different studies as to the identity of these compounds. One recent approach to specifying MHC-regulated compounds is to study volatile urinary profiles in mouse strains with varying MHC types, genetic backgrounds and different diets. An unexpected finding from these studies is that the concentrations of numerous compounds are influenced by interactions among these variables. As a result, only a few compounds can be identified that are consistently regulated by MHC variation alone. Nevertheless, since trained animals are readily able to discriminate the MHC differences, it is apparent that chemical studies are somehow missing important information underlying mouse recognition of MHC odourtypes. To make progress in this area, we propose a focus on the search for behaviourally relevant odourants rather than a random search for volatiles that are regulated by MHC variation. Furthermore, there is a need to consider a 'combinatorial odour recognition' code whereby patterns of volatile metabolites (the basis for odours) specify MHC odourtypes.
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Affiliation(s)
- Jae Kwak
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA.
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34
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BEJA‐PEREIRA ALBANO, OLIVEIRA RITA, ALVES PAULOC, SCHWARTZ MICHAELK, LUIKART GORDON. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 2009; 9:1279-301. [DOI: 10.1111/j.1755-0998.2009.02699.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ALBANO BEJA‐PEREIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
| | - RITA OLIVEIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - PAULO C. ALVES
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - MICHAEL K. SCHWARTZ
- USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - GORDON LUIKART
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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35
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Yao M, Rosenfeld J, Attridge S, Sidhu S, Aksenov V, Rollo CD. The Ancient Chemistry of Avoiding Risks of Predation and Disease. Evol Biol 2009. [DOI: 10.1007/s11692-009-9069-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Zomer S, Dixon SJ, Xu Y, Jensen SP, Wang H, Lanyon CV, O'Donnell AG, Clare AS, Gosling LM, Penn DJ, Brereton RG. Consensus multivariate methods in gas chromatography mass spectrometry and denaturing gradient gel electrophoresis: MHC-congenic and other strains of mice can be classified according to the profiles of volatiles and microflora in their scent-marks. Analyst 2008; 134:114-23. [PMID: 19082183 DOI: 10.1039/b807061j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
House mice (Mus domesticus) communicate using scent-marks, and the chemical and microbial composition of these 'extended phenotypes' are both influenced by genetics. This study examined how the genes of the major histocompatibility complex (MHC) and background genes influence the volatile compounds (analysed with Gas Chromatography Mass Spectrometry or GC/MS) and microbial communities (analysed using Denaturating Gradient Gel Electrophoresis or DGGE) in scent-marks produced by congenic strains of mice. The use of Consensus Principal Components Analysis is described and shows relationships between the two types of fingerprints (GC/MS and DGGE profiles). Classification methods including Support Vector Machines and Discriminant Partial Least Squares suggest that mice can be classified according to both background strain and MHC-haplotype. As expected, the differences among the mice were much greater between strains that vary at both MHC and background loci than the congenics, which differ only at the MHC. These results indicate that the volatiles in scent-marks provide information about genetic similarity of the mice, and support the idea that the production of these genetically determined volatiles is influenced by commensal microflora. This paper describes the application of consensus methods to relate two blocks of analytical data.
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Affiliation(s)
- Simeone Zomer
- Centre for Chemometrics, School of Chemistry, University of Bristol, Cantocks Close, Bristol, UKBS8 1TS
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37
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Garms AI, Zenkova MA, Moshkin MP, Vlasov VV. Behavioral and endocrine effects of pUC19 plasmid DNA in mice. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2008; 423:379-381. [PMID: 19213413 DOI: 10.1134/s0012496608060033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- A I Garms
- Institute of Systematics and Ecology, Siberian Branch, Russian Academy of Sciences, ul. Frunze 11, Novosibirsk, 630091 Russia
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38
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Abstract
Self/non-self recognition mechanisms underlie the development, immunology and social behaviour of virtually all living organisms, from bacteria to humans. Indeed, recognition processes lie at the core of how social cooperation evolved. Much evidence suggests that the major histocompatibility complex (MHC) both facilitates nepotistic interactions and promotes inbreeding avoidance. Social discrimination based on MHC differences has been demonstrated in many vertebrates but whether the labels used in discrimination are directly associated with the MHC, rather than with other genes with which it covaries, has remained problematic. Furthermore, effects of familiarity on natural preferences have not been controlled in most previous studies. Here we show that African clawed frog (Xenopus laevis) tadpoles discriminate among familiar full siblings based on MHC haplotype differences. Subjects (N=261) from four parental crosses preferred siblings with which they shared MHC haplotypes to those with no MHC haplotypes in common. Using only full siblings in experimental tests, we controlled for genetic variation elsewhere in the genome that might influence schooling preferences. As test subjects were equally familiar with stimulus groups, we conclude that tadpole discrimination involves a self-referent genetic recognition mechanism whereby individuals compare their own MHC type with those of conspecifics.
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Affiliation(s)
- Jandouwe Villinger
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Kwak J, Opiekun MC, Matsumura K, Preti G, Yamazaki K, Beauchamp GK. Major histocompatibility complex-regulated odortypes: peptide-free urinary volatile signals. Physiol Behav 2008; 96:184-8. [PMID: 18957300 DOI: 10.1016/j.physbeh.2008.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 09/09/2008] [Accepted: 10/01/2008] [Indexed: 11/17/2022]
Abstract
Major histocompatibility complex (MHC) genes influence urinary odors (odortypes) of mice. That volatile odorants are involved is supported by the observation that odortype identity can be detected from a distance. Furthermore, chemical analyses of urines have revealed numerous volatile odorants that differ in relative abundance between mice that differ only in MHC genotypes. In addition, urines from MHC-different mice evoke distinct odor-induced activity maps in the main olfactory bulbs. However, recent studies report that non-volatile MHC class I peptides may directly act as MHC-associated signals and may thereby be seen to call into question the evidence for a volatile MHC signal. To evaluate this question, we designed a procedure to collect peptide-free urinary volatiles and tested these volatiles for their ability to mediate chemosensory discrimination of MHC-congenic mice differing in their MHC genotype. The headspace volatiles from urines of C57BL/6 congenic mice (haplotypes H2(b) and H2(k)) were collected by solid phase microextraction (SPME). These volatiles were then desorbed into a gas chromatograph (GC) and the entire chromatographic eluate was collected into a buffer solution. Our results conclusively demonstrate that mice trained to discriminate between unadulterated urinary signals of the congenic mice generalize the discrimination, without reward or training, to the buffer solution containing the peptide-free urinary volatiles (p<0.001, binomial test). Thus volatile signals, perhaps along with non-volatile ones, are capable of mediating behavioral discriminations of mice of different MHC genotypes.
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Affiliation(s)
- Jae Kwak
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA.
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Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008; 6:776-88. [PMID: 18794915 PMCID: PMC2664199 DOI: 10.1038/nrmicro1978] [Citation(s) in RCA: 1052] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.
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Affiliation(s)
- Ruth E Ley
- Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
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Abstract
In several species, including rodents and fish, it has been shown that the Major Histocompatibility Complex (MHC) influences mating preferences and, in some cases, that this may be mediated by preferences based on body odour. In humans, the picture has been less clear. Several studies have reported a tendency for humans to prefer MHC-dissimilar mates, a sexual selection that would favour the production of MHC-heterozygous offspring, who would be more resistant to pathogens, but these results are unsupported by other studies. Here, we report analyses of genome-wide genotype data (from the HapMap II dataset) and HLA types in African and European American couples to test whether humans tend to choose MHC-dissimilar mates. In order to distinguish MHC-specific effects from genome-wide effects, the pattern of similarity in the MHC region is compared to the pattern in the rest of the genome. African spouses show no significant pattern of similarity/dissimilarity across the MHC region (relatedness coefficient, R = 0.015, p = 0.23), whereas across the genome, they are more similar than random pairs of individuals (genome-wide R = 0.00185, p<10−3). We discuss several explanations for these observations, including demographic effects. On the other hand, the sampled European American couples are significantly more MHC-dissimilar than random pairs of individuals (R = −0.043, p = 0.015), and this pattern of dissimilarity is extreme when compared to the rest of the genome, both globally (genome-wide R = −0.00016, p = 0.739) and when broken into windows having the same length and recombination rate as the MHC (only nine genomic regions exhibit a higher level of genetic dissimilarity between spouses than does the MHC). This study thus supports the hypothesis that the MHC influences mate choice in some human populations. There has been a longstanding hypothesis that selection may have led to mating patterns that encourage heterozygosity at Major Histocompatibility Complex (MHC) loci because of improved immune response to pathogens in the offspring of such matings, and, indeed, this has been observed in several model systems. However, in humans, previous studies regarding the role of the MHC in mate choice or preference, both directly in couples and also indirectly in “sweaty T-shirts” experiments, have reported conflicting results. Here, by using genome-wide genotype data and HLA types in African and European American couples, we test whether humans tend to choose MHC-dissimilar mates. This approach allows us to distinguish MHC-specific effects from genome-wide effects. In the African sample, the patterns at MHC loci is confounded by genome-wide effects, possibly resulting from demographic processes relating to the social organization of this population, and no tendency to choose MHC-dissimilar mates is detected. On the other hand, the sampled European Americans appear to have favoured MHC-dissimilar mates, supporting the hypothesis that MHC influences mate choice in some human populations. Thus, this study suggests that, in some cases, humans may rely on biological factors, in addition to social factors, when choosing a mate.
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Affiliation(s)
- Raphaëlle Chaix
- Department of Statistics, University of Oxford, Oxford, United Kingdom.
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