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      Altered Microbiota, Impaired Quality of Life, Malabsorption, Infection, and Inflammation in CVID Patients With Diarrhoea

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          Abstract

          Background: Diarrhoea is the commonest gastrointestinal symptom in patients with common variable immunodeficiency (CVID).

          Objective: The aim of this study was to describe the prevalence and clinical presentation of chronic and recurrent diarrhoea in the Royal-Free-Hospital (RFH) London CVID cohort, including symptoms, infections, level of inflammation, and microbial diversity.

          Methods: A cross-sectional study of adult CVID patients (139 out of 172 diagnosed with CVID completed the screening questionnaire). Those with diarrhoea ≥6 days/month had stool and blood samples analysed and completed the short Inflammatory Bowel Disease Questionnaire (sIBDQ). BMI, spleen-size, lymphocytes and gut-microbial diversity were compared. Due to logistical and clinical restraints, not all patients could be analysed on all measures.

          Results: 46/139 (33.1%) patients had current significant diarrhoea. In patients with past or present diarrhoea, BMI was lower (median 23.7 vs. 26, p = 0.005), malabsorption more common (57.97 vs. 35.71%, p = 0.011). CD4+ lymphocytes were higher in patients with diarrhoea ( p = 0.028; n = 138), but CD4+ naïve lymphocytes were significantly higher in non-diarrhoea patients ( p = 0.009, N = 28). Nine patients had confirmed or probable current gastrointestinal infections. Calprotectin was >60 μg/g in 13/29 with significant diarrhoea including 9 without infection. SIBDQ revealed a low median score of 4.74. Microbial alpha diversity was significantly lower in CVID patients compared to healthy household controls. There was no significant difference in alpha diversity in relation to antibiotic intake during the 6 weeks prior to providing samples.

          Conclusion: Patients with CVID and significant diarrhoea had infections, raised calprotectin, malabsorption, a lower BMI, an impaired quality of life (comparable to active IBD), and they differed from non-diarrhoea patients in their lymphocyte phenotyping. Furthermore, microbial diversity was altered. These findings strongly imply that there may be an inflammatory nature and a systemic predisposition to diarrhoea in CVID, which necessitates further investigation.

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          Most cited references58

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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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            Diet rapidly and reproducibly alters the human gut microbiome

            Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut 1–5 , but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals 2 , reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease 6 . In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
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              Linking long-term dietary patterns with gut microbial enterotypes.

              Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
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                Author and article information

                Contributors
                Journal
                Front Immunol
                Front Immunol
                Front. Immunol.
                Frontiers in Immunology
                Frontiers Media S.A.
                1664-3224
                31 July 2020
                2020
                : 11
                : 1654
                Affiliations
                [1] 1Institute of Immunity and Transplantation, Royal Free Hospital, University College London , London, United Kingdom
                [2] 2Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Institute for Immunodeficiency, Albert-Ludwigs-University Freiburg , Freiburg, Germany
                [3] 3Freiburg Center for Data Analysis and Modeling (FDM), IMBI/ZKS , Freiburg, Germany
                [4] 4DZIF – German Center for Infection Research, Satellite Center Freiburg , Freiburg, Germany
                [5] 5CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-University Freiburg , Freiburg, Germany
                [6] 6RESIST – Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg , Freiburg, Germany
                Author notes

                Edited by: Antonio Condino-Neto, University of São Paulo, Brazil

                Reviewed by: Neil Romberg, Children's Hospital of Philadelphia, United States; Mark Ballow, University of South Florida, United States

                *Correspondence: David M. Lowe d.lowe@ 123456ucl.ac.uk

                This article was submitted to Primary Immunodeficiencies, a section of the journal Frontiers in Immunology

                Article
                10.3389/fimmu.2020.01654
                7412961
                32849570
                4f17a17e-6058-483f-9b21-054d18ad9c04
                Copyright © 2020 van Schewick, Nöltner, Abel, Burns, Workman, Symes, Guzman, Proietti, Bulashevska, Moreira, Soetedjo, Lowe and Grimbacher.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 25 April 2020
                : 22 June 2020
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 61, Pages: 13, Words: 7941
                Funding
                Funded by: Deutsche Forschungsgemeinschaft 10.13039/501100001659
                Award ID: CIBSS — EXC-2189 — Project ID 390939984
                Award ID: GR1617/14-1/iPAD
                Award ID: RESIST — EXC 2155 — Project ID 39087428
                Award ID: SFB1160/IMPATH
                Funded by: Jeffrey Modell Foundation 10.13039/100001245
                Award ID: center award
                Funded by: Bundesministerium für Bildung und Forschung 10.13039/501100002347
                Award ID: GAIN_ 01GM1910A
                Categories
                Immunology
                Original Research

                Immunology
                cvid,diarrhoea,calprotectin,norovirus,microbiome,ibdq,lymphocytes,quality of life
                Immunology
                cvid, diarrhoea, calprotectin, norovirus, microbiome, ibdq, lymphocytes, quality of life

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