Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples

Area of Science:

• Microbiology
• Immunology
• Genomics

Background:

• The exact cause of sarcoidosis remains unknown, with microbial agents being a suspected factor.
• Identifying specific microbial triggers is crucial for understanding sarcoidosis pathogenesis.

Purpose of the Study:

• To identify bacterial, fungal, or viral lineages in sarcoidosis patient specimens compared to controls.
• To develop and apply improved methods for filtering environmental DNA contamination in metagenomic samples.

Main Methods:

• Metagenomic DNA sequencing of various specimen types (lymph node biopsies, BAL, Kveim reagent, spleen) from sarcoidosis patients and controls.
• Utilized bacterial 16S and fungal ITS rRNA gene sequencing, alongside shotgun sequencing for viral particles and whole genomes.
• Implemented advanced statistical methods to account for and filter environmental contamination.

Main Results:

• Enrichment of Cladosporiaceae fungi in one set of sarcoidosis tissues and various bacterial lineages in another.
• Limited enrichment of Aspergillus fungi in bronchoalveolar lavage (BAL) samples.
• Detection of microbial lineages like Cladosporium in Kveim reagent and spleen, but no single lineage was consistently enriched across multiple sample types.

Conclusions:

• Metagenomic sequencing identified microbe enrichment in specific sarcoidosis sample types, but with low concordance between them.
• Effective statistical analysis to control for environmental contamination was critical for accurate results.
• Further research is needed to elucidate the role of specific microbes in sarcoidosis etiology.