Richard Sprague

My personal website

Coronavirus and the microbiome

Created: 2020-03-23 ; Updated: 2020-04-30

There is considerable evidence for a link between the microbiome and the SARS-COV2 virus.

Front-line COVID19 clinicians have long noted that gastrointestinal issues – often a clue to microbiome dysbiosis – are one of the unusual underlying symptoms of a SARS-COV2 infection. Furthermore, it is well known that SARS-COV2 can be detected in human fecal samples, often many weeks after the symptoms of infection have subsided:


Figure 1: Source:

In fact, a stool test may turn out to be the best way to detect the true end of an infection. Researchers at Chinese University of Hong Kong found evidence of the virus in all samples of people who had previously been known to be infected, even when no traces were found in respiratory samples.

A relationship with smell?

Another intriguing clue that the microbiome is involved comes from the nose.

The New York Times (Mar 22, Roni Caryn Rabin) wonders if Lost Sense of Smell May Be Peculiar Clue to Coronavirus Infection. Among the evidence:

"A study from South Korea, where widespread testing has been done, found that 30 percent of some 2,000 patients who tested positive for the coronavirus reported experiencing anosmia.

There is a clear association between the microbiome and smell. Both Alzheimers and Parkinsons researchers have long noted that changes in smell precede symptoms of those diseases. Researchers from the University of Graz in Austria published a small study (n=67) in 2018 The nasal microbiome mirrors and potentially shapes olfactory function in Nature Scientific Reports. There were clear differences between those with normal sense of smell (n=29) and those without (n=10). In particular, “butyric acid-producing microorganisms were found to be associated with impaired olfactory function”

Here are the microbes most associated with poor ability to smell:

Full table here:

For what it’s worth, in my several dozen nose microbiome tests, I tend to have a lot of Corynebacterium (one of the items on the list) but lots of Moraxella (not on the list) too. My sense of smell seems just fine, but if it starts to fade I’m going to pay attention.

The nasopharynx of patients with respiratory tract infections is also known to be enriched in bacteriological pathogens1, specifically anaerobes and Prevotella spp. Furthermore, “certain bacteria seem to be associated with symptomatic manifestations, such as Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus, which are known to cause an excess of mortality due to secondary infection.”

Other viruses

A 2011 study of another coronavirus, (HCoV-NL63), found “increased adherence of Streptococcus pneumoniae to virus-infected cell lines and fully differentiated primary human airway epithelium cultures”2

More information

Megan Molteni wrote more in 04.29.2020 Wired: Microbe Mappers Are Tracking Covid-19’s Invisible Traces

respiratory viruses, including influenza, can bind directly to several species of bacteria, which makes both the bacteria and the virus better at grabbing on to human cells.