Methods: Twelve primary demyelination (MS) biopsy and 15 control epilepsy surgical human brain specimens were studied. RNA was extracted and quantified from the formalin-fixed paraffin-embedded specimens, subjected to quality control, and then deep sequenced. The reads were filtered and aligned against a panmicrobial database of 1.3 million (M) sequence records representing 10,654 species. Microbial reads and human gene expression were compared between the groups.
Results: 100-300M high-quality 125 bp paired-end reads were derived from each brain specimen. 6.4M read pairs (0.1% of total), from both the MS and control specimens, aligned to the panmicrobial database. Outlier analysis, corrected for multiple comparisons, identified significantly increased microbial sequence in 11/12 MS brain specimens. 43 genera and 36 families from 11 microbial phyla (archaea 2, unclassified 1, bacteria 11, fungi 2, viruses 1) were overrepresented in at least one of the MS brain samples. Many of the MS candidate microbes are anaerobic (Alistipes, Akkermansia), noncultivable (Candidatus), or extremophiles (Lawsonia). Gene expression analysis showed that several immune system pathways are significantly increased in the MS brain specimens.
Conclusion: The sequencing data shows that most of the MS brain specimens studied contain a set of microbial sequences that are significantly different than the controls. This suggests that MS lesions may be related to the invasion of a diverse set of microbes into the brain, or to a disturbance of preexisting microbes within brain tissue. Human gene expression in these brain specimens supports a role for a bacterial pathogenesis of MS. Studies are in progress to visualize specific MS candidate microbes within the brain tissue specimens.
C. Palmer, None
K. F. Fischer, None