Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low–Microbial Content Samples
| Autor: | Leslie A. Litzky, Casey E. Hofstaedter, Ayannah S. Fitzgerald, Anna Dubaniewicz, Ronald G. Collman, Michael Feldman, Wojciech Biernat, Milton D. Rossman, Erik L. Clarke, Young Hwang, Bartlomiej Rekawiecki, Karen C. Patterson, Ize Imai, Abigail Lauder, Hanna Majewska, Frederic D. Bushman, Kyle Bittinger |
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| Rok vydání: | 2018 |
| Předmět: |
DNA
Bacterial Male 0301 basic medicine Pulmonary and Respiratory Medicine Sarcoidosis Metagenomic dna Kveim Test Spleen Biology Critical Care and Intensive Care Medicine Sensitivity and Specificity Microbiology 03 medical and health sciences Reference Values medicine Humans Microbiome Internal transcribed spacer Lymph node Tissue Embedding Shotgun sequencing Microbiota Biopsy Needle Editorials medicine.disease Immunohistochemistry 030104 developmental biology medicine.anatomical_structure Metagenomics Case-Control Studies Immunology Metagenome Female |
| Zdroj: | American Journal of Respiratory and Critical Care Medicine. 197:225-234 |
| ISSN: | 1535-4970 1073-449X |
| Popis: | The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers.We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA sequencing. Because DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination.We analyzed specimens from subjects with sarcoidosis (n = 93), control subjects without sarcoidosis (n = 72), and various environmental controls (n = 150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, BAL, Kveim reagent, and fresh granulomatous spleen from a patient with sarcoidosis. All specimens were analyzed by bacterial 16S and fungal internal transcribed spacer ribosomal RNA gene sequencing. In addition, BAL was analyzed by shotgun sequencing of fractions enriched for viral particles, and Kveim and spleen were subjected to whole-genome shotgun sequencing.In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared with nonsarcoidosis tissues; in the other tissue set, we detected enrichment of several bacterial lineages in sarcoidosis but not Cladosporiaceae. BAL showed limited enrichment of Aspergillus fungi. Several microbial lineages were detected in Kveim and spleen, including Cladosporium. No microbial lineage was enriched in more than one sample type after correction for multiple comparisons.Metagenomic sequencing revealed enrichment of microbes in single types of sarcoidosis samples but limited concordance across sample types. Statistical analysis accounting for environmental contamination was essential to avoiding false positives. |
| Databáze: | OpenAIRE |
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