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

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    $\begingroup$ Do you mean in healthy or diseased tissues? There are some bacteria, viruses or parasites in healthy tissues. $\endgroup$ – Jan May 6 '19 at 11:53
  • $\begingroup$ in both cases, there are differences in abundances and species between diseased and healthy tissues but in general, in the absence of an obvious infection, tissues should be sterile. Or not? $\endgroup$ – Gigiux May 6 '19 at 13:15
  • $\begingroup$ Tissues within the organs are usually sterile, but not necessary 100%. Theoretically, sterile means zero microbes, but in practice, sterile means no microbes detected by usual medical tests. So, yes, there can be few microbes in healthy tissues. And there are a lot of microbes in the gut, saliva, on the skin as part of normal flora. But you are probably asking if there are microbes "in the tissues" not only "on" the skin or in the body cavities. $\endgroup$ – Jan May 6 '19 at 13:25
  • $\begingroup$ correct, I am talking deep solid tissues such as muscles $\endgroup$ – Gigiux May 6 '19 at 14:11
  • $\begingroup$ @Gigiux If there is not enough specificity in your question such that you need to clarify your intents in the comments, your question is not specific enough and you should edit it. $\endgroup$ – Bryan Krause May 6 '19 at 15:02

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.

Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases

Identification of low abundance microbiome in clinical samples using whole genome sequencing

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:

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

"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.

Human contamination in bacterial genomes has created thousands of spurious proteins

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.



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.

  • $\begingroup$ sorry, I should have specified that I was referring to tissues not directly in contact with the environment, such as brain and muscles - blood is out because there is compelling evidence for viruses in the bloodstream such as Anelloviridae. $\endgroup$ – Gigiux May 6 '19 at 14:15
  • $\begingroup$ OK, what about Herpes simplex virus in the nerve ganglia after chickenpox infection? I updated my answer. $\endgroup$ – Jan May 6 '19 at 14:17
  • $\begingroup$ sure, those I know about. My data from WGS from tissues indicates the presence of non-human viruses and plenty of bacteriophages. Would it be normal to find them inside tissues? $\endgroup$ – Gigiux May 7 '19 at 7:42
  • $\begingroup$ Most people probably have Herpes simplex viruses latent in their nerves and, some, even in the brain, as I wrote in my answer. Other possible candidates are Mycobacterium tuberculosis (in latent tuberculosis), Epstein-Barr virus (in chronic infectious mononucleosis), Borrelia burgdorferi (Lyme disease). I mean, these bacteria can persist inside the brain, bone or other tissues after healing. It's called latent asymptomatic infection. $\endgroup$ – Jan May 7 '19 at 7:51

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