Rationale: The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers. Objective: We sought to identify bacterial, fungal or viral lineages in specimens from sarcoidosis patients enriched relative to controls using metagenomic DNA sequencing. Since DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination. Methods: We analyzed specimens from sarcoidosis subjects (n=93), non-sarcoidosis control subjects (n=72) and various environmental controls (n=150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, bronchoalveolar lavage (BAL), Kveim reagent, and fresh granulomatous spleen from a sarcoidosis patient. All specimens were analyzed by bacterial 16S and fungal ITS rRNA 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. Measurements and Main Results: In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared to non-sarcoidosis 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. Conclusions: 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.

中文翻译：

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结节病中的微生物谱系：针对低微生物含量样品量身定制的元基因组分析

理由：结节病的病因尚不清楚，但怀疑是微生物的诱因。目的：我们试图使用宏基因组DNA测序从结节病患者的标本中鉴定出相对于对照富集的细菌，真菌或病毒谱系。由于来自环境污染的DNA对微生物真实含量低的样品的贡献不成比例，因此我们开发了改进的方法来过滤环境污染。方法：我们分析了结节病受试者（n = 93），非结节病对照受试者（n = 72）和各种环境对照组（n = 150）的标本。结节病标本由两组独立的福尔马林固定，石蜡包埋的淋巴结活检，支气管肺泡灌洗（BAL），Kveim试剂和结节病患者的新鲜肉芽肿性脾脏组成。所有标本均通过细菌16S和真菌ITS rRNA基因测序进行分析。另外，通过shot弹枪测序富集了病毒颗粒的级分对BAL进行了分析，并对Kveim和脾脏进行了全基因组shot弹枪测序。测量和主要结果：在一组组织中，与非结节病组织相比，枝孢科的真菌富含结节病。在其他组织中，我们在结节病中检测到了几个细菌谱系的富集，但没有检出枝形亚科。BAL显示出曲霉真菌的富集有限。在克维姆和脾脏中发现了几种微生物谱系，包括枝孢菌。进行多次比较校正后，没有一种微生物谱系富集超过一种样品类型。结论：元基因组测序揭示了结节病单一类型样品中微生物的富集，但样品类型之间的一致性有限。对环境污染进行统计分析对于避免误报至关重要。