Evidence for the Existence of a Bacterial Etiology for Alzheimer’s Disease and for a Temporal-Spatial Development of a Pathogenic Microbiome in the Brain

Background Over the last few decades, a growing body of evidence suggests a role for various infectious agents in Alzheimer’s Disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, or fungi) being detected in AD subjects’ brains, most research has focused on individual pathogens and only a few studies investigated the hypothesis of a bacterial brain microbiome. We profiled the bacterial communities present in non-demented controls and AD subjects’ brains. Results We obtained post-mortem samples from the brains of 32 individual subjects, comprising 16 AD and 16 control aged-matched subjects with a total of 130 samples from the frontal and temporal lobes and entorhinal cortex. We used full-length 16S rRNA gene amplification with Pacific Biosciences sequencing technology to identify the bacteria. We detected bacteria in the brains of both cohorts with the principal bacteria comprising Propionibacterium acnes (recently renamed Cutibacterium acnes) and two species each of Acinetobacter and Comamonas genera. We used a hierarchical Bayesian method to detect differences in relative abundance among AD and control groups. Because of large abundance variances we also employed an unconventional analysis approach that utilized Latent Dirichlet Allocation, often used in computational linguistics. This allowed us to identify 5 classes of samples, each revealing a different microbiome. Assuming that samples represented infections that potentially began at different times, we ordered these classes in time, finding that the last class exclusively explained the existence or non-existence of AD. Conclusions The AD-related pathogenicity of the brain microbiome seems to be based on a complex polymicrobial dynamic. The time ordering revealed a rise and fall of the abundance of Propionibacterium acnes with pathogenicity occurring for an off-peak abundance level in association with at least one other bacterium from a set of genera that included: Methylobacterium, Bacillus, Caulobacter, Delftia, and Variovorax. P. acnes may also be involved with outcompeting the Comamonas species, which were strongly associated with non-demented brain microbiome, whose early destruction could be the first stage of the disease. The statistical results are also consistent with a leaky blood brain barrier or lymphatic network that allows bacteria, viruses, fungi, or other pathogens to enter the brain. ### Competing Interest Statement The authors have declared no competing interest. * AD : Alzheimer’s disease AMC : Age-matched controls CCS : Circular consensus sequence Clr : centered log ratio DMM : Dirichlet-multinomial model LDA : Latent Dirichlet allocation MLDA : Modified latent Dirichlet allocation MCSMRT : Microbiome Classifier using Single Molecule Real-time Sequencing OTU : Operational taxonomic unit PacBio : Pacific Biosciences PCA : Principal component analysis