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      ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation

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          Abstract

          Mutations in angiotensin-converting enzyme 2 are shown to predispose mice to colitis as a consequence of neutral amino acid malabsorption and a change in the resident microbiota; these results could explain how protein malnutrition — affecting up to one billion people — leads to intestinal inflammation.

          Supplementary information

          The online version of this article (doi:10.1038/nature11228) contains supplementary material, which is available to authorized users.

          Hunger pangs: how malnutrition leads to intestinal disorders

          Malnutrition affects many millions of people in the developing world and remains a problem in wealthy nations, especially for disadvantaged groups. In many cases, it is the associated diarrhoea and intestinal inflammation that cause morbidity and death. A study published in this issue presents a molecular explanation for the increased susceptibility to intestinal inflammation in malnutrition. Angiotensin converting enzyme 2 (ACE2), which has a central role in blood-pressure regulation and has been implicated in diabetes, heart failure and viral infection, is shown to influence dietary amino-acid homeostasis, innate immunity, gut microbial ecology and susceptibility to colitis. Mice deficient in this enzyme show impaired tryptophan metabolism and develop colitis, which is alleviated by dietary tryptophan and its metabolite, nicotinamide. This surprising result explains nutritional effects that have been known for centuries and provides a molecular link between malnutrition and the intestinal microbiome.

          Supplementary information

          The online version of this article (doi:10.1038/nature11228) contains supplementary material, which is available to authorized users.

          Abstract

          Malnutrition affects up to one billion people in the world and is a major cause of mortality 1, 2 . In many cases, malnutrition is associated with diarrhoea and intestinal inflammation, further contributing to morbidity and death 2 . The mechanisms by which unbalanced dietary nutrients affect intestinal homeostasis are largely unknown. Here we report that deficiency in murine angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 ( Ace2), which encodes a key regulatory enzyme of the renin-angiotensin system (RAS), results in highly increased susceptibility to intestinal inflammation induced by epithelial damage. The RAS is known to be involved in acute lung failure 3 , cardiovascular functions 4 and SARS infections 5 . Mechanistically, ACE2 has a RAS-independent function, regulating intestinal amino acid homeostasis, expression of antimicrobial peptides, and the ecology of the gut microbiome. Transplantation of the altered microbiota from Ace2 mutant mice into germ-free wild-type hosts was able to transmit the increased propensity to develop severe colitis. ACE2-dependent changes in epithelial immunity and the gut microbiota can be directly regulated by the dietary amino acid tryptophan. Our results identify ACE2 as a key regulator of dietary amino acid homeostasis, innate immunity, gut microbial ecology, and transmissible susceptibility to colitis. These results provide a molecular explanation for how amino acid malnutrition can cause intestinal inflammation and diarrhoea.

          Supplementary information

          The online version of this article (doi:10.1038/nature11228) contains supplementary material, which is available to authorized users.

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          Most cited references44

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          Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

          The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
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            Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

            mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
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              Is Open Access

              UCHIME improves sensitivity and speed of chimera detection

              Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                p.rosenstiel@mucosa.de
                josef.penninger@imba.oeaw.ac.at
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                25 July 2012
                2012
                : 487
                : 7408
                : 477-481
                Affiliations
                [1 ]GRID grid.417521.4, ISNI 0000 0001 0008 2788, IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria, ; ,
                [2 ]The Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine and School of Medicine, 2360004 Yokohama, Japan, ,
                [3 ]GRID grid.9764.c, ISNI 0000 0001 2153 9986, Institute of Clinical Molecular Biology, University of Kiel, Schittenhelmstrasse12, 24105 Kiel, Germany, ; ,
                [4 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Department of Chemical Ecology and Ecosystem Research, , Center of Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria, ; ,
                [5 ]GRID grid.7400.3, ISNI 0000 0004 1937 0650, Institute of Physiology and Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland, ; ,
                [6 ]GRID grid.251924.9, ISNI 0000 0001 0725 8504, Department of Biological Informatics and Experimental Therapeutics, , Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita 010-8543, Japan, ; ,
                [7 ]GRID grid.20515.33, ISNI 0000 0001 2369 4728, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan, ; ,
                [8 ]GRID grid.419927.0, ISNI 0000 0000 9471 3191, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands, ; ,
                [10 ]GRID grid.7708.8, ISNI 0000 0000 9428 7911, Present Address: Present address: Department of Environmental Health Sciences, University Medical Center, Breisacher Strasse 115b, D-79106 Freiburg, Germany., ; ,
                Article
                BFnature11228
                10.1038/nature11228
                7095315
                22837003
                2da12bbb-a5ac-437b-a41a-223f7bbe7083
                © Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2012

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 7 June 2011
                : 14 May 2012
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2012

                Uncategorized
                inflammation,pathogenesis,gastrointestinal diseases,malnutrition
                Uncategorized
                inflammation, pathogenesis, gastrointestinal diseases, malnutrition

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