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      Glycan-based shaping of the microbiota during primate evolution

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          Abstract

          Genes encoding glycosyltransferases can be under relatively high selection pressure, likely due to the involvement of the glycans synthesized in host-microbe interactions. Here, we used mice as an experimental model system to investigate whether loss of α−1,3-galactosyltransferase gene ( GGTA1) function and Galα1-3Galβ1-4GlcNAcβ1-R (αGal) glycan expression affects host-microbiota interactions, as might have occurred during primate evolution. We found that Ggta1 deletion shaped the composition of the gut microbiota. This occurred via an immunoglobulin (Ig)-dependent mechanism, associated with targeting of αGal-expressing bacteria by IgA. Systemic infection with an Ig-shaped microbiota inoculum elicited a less severe form of sepsis compared to infection with non-Ig-shaped microbiota. This suggests that in the absence of host αGal, antibodies can shape the microbiota towards lower pathogenicity. Given the fitness cost imposed by bacterial sepsis, we infer that the observed reduction in microbiota pathogenicity upon Ggta1 deletion in mice may have contributed to increase the frequency of GGTA1 loss-of-function mutations in ancestral primates that gave rise to humans.

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          Most cited references74

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          The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3).

          Definitions of sepsis and septic shock were last revised in 2001. Considerable advances have since been made into the pathobiology (changes in organ function, morphology, cell biology, biochemistry, immunology, and circulation), management, and epidemiology of sepsis, suggesting the need for reexamination.
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            QIIME allows analysis of high-throughput community sequencing data.

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              Structure, Function and Diversity of the Healthy Human Microbiome

              Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                19 May 2021
                2021
                : 10
                : e67450
                Affiliations
                [1]Instituto Gulbenkian de Ciência OeirasPortugal
                University of California, San Francisco United States
                Pennsylvania State University United States
                University of California, San Francisco United States
                UCSD United States
                University of Montreal Canada
                Author notes
                [‡]

                Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, United States.

                [§]

                Champalimaud Centre for the Unknown, Lisbon, Portugal.

                [#]

                Department for Biomedical Research, Inselspital, University of Bern, Bern, Switzerland.

                [¶]

                Universidade Nova de Lisboa, Caparica, Portugal.

                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-1826-0180
                https://orcid.org/0000-0003-3955-0117
                https://orcid.org/0000-0002-9314-4833
                Article
                67450
                10.7554/eLife.67450
                8133779
                34009123
                90e3f667-8b19-4906-bd99-31f60bc00bf5
                © 2021, Singh et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 11 February 2021
                : 04 May 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001871, Fundação para a Ciência e a Tecnologia;
                Award ID: SFRH/BD/52177/2013
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001871, Fundação para a Ciência e a Tecnologia;
                Award ID: SFRH/BPD/112135/2015
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001704, European Society of Clinical Microbiology and Infectious Diseases;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100005635, Fundação Calouste Gulbenkian;
                Award ID: 5723/2014 and FEDER029411
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000865, Bill and Melinda Gates Foundation;
                Award ID: OPP1148170
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100010434, “la Caixa” Foundation;
                Award ID: HR18-00502
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Evolutionary Biology
                Immunology and Inflammation
                Custom metadata
                Ggta1 deletion in mice shapes and reduces the microbiota pathogenicity and probably contributed to the natural selection of GGTA1 loss-of-function mutations in the ancestral primates that gave rise to humans.

                Life sciences
                immunology,alpha-gal,primate evolution,microbiota,sepsis,mouse
                Life sciences
                immunology, alpha-gal, primate evolution, microbiota, sepsis, mouse

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