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Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.

التفاصيل البيبلوغرافية
العنوان: Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.
المؤلفون: Stewart DB Sr; Department of Surgery, University of Arizona, Tucson, Arizona, USA., Wright JR; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA.; Contamination Source Identification, LLC, Huntingdon, Pennsylvania, USA., Fowler M; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., McLimans CJ; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA.; Contamination Source Identification, LLC, Huntingdon, Pennsylvania, USA., Tokarev V; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA.; Contamination Source Identification, LLC, Huntingdon, Pennsylvania, USA., Amaniera I; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., Baker O; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., Wong HT; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., Brabec J; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., Drucker R; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA., Lamendella R; Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA LAMENDELLA@juniata.edu.; Contamination Source Identification, LLC, Huntingdon, Pennsylvania, USA.
المصدر: MSphere [mSphere] 2019 Aug 28; Vol. 4 (4). Date of Electronic Publication: 2019 Aug 28.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 101674533 Publication Model: Electronic Cited Medium: Internet ISSN: 2379-5042 (Electronic) Linking ISSN: 23795042 NLM ISO Abbreviation: mSphere Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Washington, DC : American Society for Microbiology, [2015]-
مواضيع طبية MeSH: Gastrointestinal Microbiome* , Metagenomics* , Transcriptome*, Clostridioides difficile/*genetics , Clostridium Infections/*microbiology , Fungi/*genetics, Adult ; Aged ; Aged, 80 and over ; Biofilms ; Diarrhea/microbiology ; Feces/microbiology ; Humans ; Metabolic Networks and Pathways ; Middle Aged ; Sequence Analysis, DNA
مستخلص: There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from 49 inpatients (18 of whom tested positive for CDI) under stringent inclusion criteria. We utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative cooccurring relationships with several bacterial taxa, including the Oscillospira , Comamonadaceae , Microbacteriaceae , and Cytophagaceae Metatranscriptomics revealed enriched pathways in CDI patients associated with biofilm production primarily driven by Escherichia coli and Pseudomonas , quorum-sensing proteins, and two-component systems related to functions such as osmotic regulation, linoleic acid metabolism, and flagellar assembly. Differential expression of functional pathways unveiled a mechanism by which the causal dysbiosis of CDI may self-perpetuate, potentially contributing to treatment failures. We propose that CDI has a distinct fungus-associated bacteriome, and this first description of metatranscriptomics in human subjects with CDI demonstrates that inflammation, osmotic changes, and biofilm production are key elements of CDI pathophysiology. IMPORTANCE Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome.
(Copyright © 2019 Stewart et al.)
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فهرسة مساهمة: Keywords: Clostridioides difficile; metagenomics; metatranscriptomics; microbiome; mycobiome
تواريخ الأحداث: Date Created: 20190830 Date Completed: 20200220 Latest Revision: 20201209
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC6714892
DOI: 10.1128/mSphere.00454-19
PMID: 31462412
قاعدة البيانات: MEDLINE
الوصف
تدمد:2379-5042
DOI:10.1128/mSphere.00454-19