in the literature, there are several studies of the gut virome and microbiome, for instance Reyes et al. on Nature (https://www.nature.com/articles/nature09199?error=cookies_not_supported&code=f5201dbe-3cda-4e09-ba17-688d0352ef81). Now, it makes sense to find bacteria (hence phages) in stools. However, there are other studies reporting bacteria from tissue, for instance Kostic et al. on Genome res ( Article Genomic analysis identifies association of Fusobacterium wit... ). In this specific case, the identified bacterium (Fusobacterium nucleatum) is an endocellular parasite and has virulence factors that allows it to penetrate tissues. But my question is more general: Would be normal to identify bacteria and bacteriophages INSIDE human tissues? In particular, would whole genome sequencing metagenomic experiments be likely to identify bacteria genome from human tissues? And if yes, how can we explain the presence of bacteria inside loci that are supposed to be sterile? Thank you
Per my comment to the question, here is an answer to the same question asked on ResearchGate:
Whole genome sequencing of human tissue samples often results in reads aligning to bacterial references, and this is actually a method used in the diagnoses of infectious diseases.
However, because pathogen DNA may be present at a much lower abundance than host DNA, it may be difficult to distinguish true infections from contamination and false positives. Steven Salzberg addresses these concerns and offers a computational solution in a recent publication:
"Usually, the vast majority of the reads match (typically 95–99%) the host, and sometimes fewer than 100 reads out of many millions of reads are matched to the target species. Common skin bacteria from the patient or lab personnel and other contamination from sample collection or preparation can easily generate a similar number of reads, and thus mask the signal from the pathogen."
To expand on this answer, it is important to realize that accurate identification of low-abundance organisms in metagenomic reads requires very good reference genomes. A separate paper from the Salzberg group discusses a startling discovery: many high-copy repeats in the human genome have been incorrectly annotated as bacterial proteins in the NCBI RefSeq database.
This suggests that researchers should be careful when attempting to infer the presence of low-abundance bacteria or phage in human tissue sequencing data, particularly when the presence of those organisms is not corroborated by other analyses.
NERVES and BRAIN
After chickenpox infection, some Herpes viruses travel along the nerves and may remain dormant in the dorsal root ganglia of the spinal nerves...they can be activated later and cause shingles.
According to (jvi.asm.org):
Herpes simplex virus 1 (HSV-1) establishes latency in neurons of the brains and sensory ganglia of humans and experimentally infected mice.
Our findings further validated the presence of low-virulence anaerobic bacteria in degenerated IVDs, and P. acnes was the most frequent bacterium.