The first case of Covid-19 in the US made scientists sit up. On January 30, a 35-year-old man came to an urgent care clinic in Washington, with a four-day history of cough and low-grade fever. His vital signs remained largely stable, but on the ninth day of illness, he reported abdominal discomfort and passed loose stool. Genetic sequencing revealed virus genes in stool specimens. This was the first case that indicated a link between Covid-19 and the gut (New England Journal of Medicine, January 31, 2020). A range of scientific studies since then has shown that the respiratory virus SARS-CoV-2 is using both the lung and the gut microbiome to gain a toehold in the body; that, the virus is prompting a rise in opportunistic, negative bacteria and depleting the ‘good’ bacteria in the gut microbiome; that, the virus is pauperising the gut microbiome by diminishing its richness and diversity; that, it is provoking dysbiosis of the gut microbiome in its victims.
A breakthrough study by scientists of the Center for Gut Microbiota Research, The Chinese University of Hong Kong, reports that Covid-19 becomes severe because the immune system goes into an excessive overdrive (Gut, January 2021). The Gut study is one of the first to show that the gut microbiome of people with and without Covid-19 are significantly different. Covid-19 patients seem to have higher numbers of noxious bacteria, than people without the infection. For instance, bacterium R. gnavus (linked to inflammatory bowel diseases) normally occupies <0.1 percent of a healthy gut, but flourishes during Covid-19. Similarly, R. torques (autism, sleep disorders and frailty in the elderly), surges up; same with bacteria B.dorei (chronic kidney disease and autoimmune diabetes).
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All of them produce potent chemicals that directly induce an inflammatory response from the immune system. The ‘good’ bacteria, that can influence the immune system response positively, are woefully low in Covid-19 patients. For instance, Bifidobacterium and F. prausnitzii. In a subset of recovered patients, numbers of beneficial these bacteria remain low long after they are cleared of the virus. This is what the researchers call, “Long-haul Covid symptoms”—fatigue, breathlessness and joint pains. “We posit that the dysbiotic gut microbiome could contribute to immune-related health problems post-COVID-19,” they write. The Covid-19 outbreak, the flood of coronavirus research, the intense communication across countries and continents, the unusual level of collaboration, the unprecedented amount of knowledge generated, are transforming how and what scientists study.
The recognition that human health and the health of the biosphere rely on consortia of microbes, has led to a research network, Microbiome Centers Consortium, to promote collaboration across universities.
Not all microbes in your gut are equal: some are good, some bad, some neutral, some hostile. Most are symbiotic—meaning both you and the microbes benefit from the relationship—some can promote diseases. Going by the data from the Human Microbiome Project, 2008-2016, a healthy person has about 80-85 percent good and neutral bacteria and 15-20 percent bad bacteria. These ratios, however, can reverse due to a variety of reasons, including lifestyle and ageing. Take, for instance, bacteria Firmicutes, dominant in the gut. They love sugar, trick the brain to crave sugars, then generate inflammation, kill off surrounding microbes and feed on their sugar store.
Firmicutes are ‘bad guys,’ responsible for a range of diseases: obesity to diabetes, allergic asthma to dermatitis. Now consider very beneficial Bifidobacteria, which prevent infections and tumours, lower cholesterol, boost brain health and more. What if Firmicutes counts become high and Bifidobacteria low in your gut? “Shifts in microbial composition and variety is a process called dysbiosis,” says Dr Govind K Makharia, professor of gastroenterology at All India Institute of Medical Sciences (AIIMS), Delhi, “when bacteria do not live in mutual accord and the ‘good’ bacteria do not successfully control the ‘bad’ ones.” It can destroy the balance of gut microbiome, make it dysfunctional, trigger inflammation and compromise human health, he adds.
Dysbiosis is linked to autoimmune disorders, inflammatory bowel disease, metabolic disorders like obesity, type 2 diabetes, allergies, heart disease, hypertension, chronic kidney disease, and neurological disorders. What can bring on dysbiosis? Many things, but primarily the modern diet, lifestyle and infectious agents, he explains. A National Microbiome Data Collaborative has come up in the US, to empower the research community to more effectively harness microbiome data. The potential to revolutionise healthcare through the microbiome is attracting both biotech startups and some of the pharma industry’s biggest players. One of the most active in the microbiome space is Janssen, the pharmaceutical division of Johnson & Johnson, which has created the Janssen Human Microbiome Institute to accelerate innovation in microbiome science.
How a Respiratory Virus Uses the Gut to Infect and Kill
Covid-19 and our messed-up microbiome
January 2020: A respiratory virus China confirms that a novel coronavirus is behind the outbreak of respiratory illness
February: Exploiting the gut The first case in the US. Doctors find virus lurking in patient stool. First hint at the surprising role of the gut microbiome.
March: Role of the gut at centre stage Research shows the virus entry points are abundant, not just in the lungs, but also the gut
May: Rise of the bad guys Reports of high levels of ‘bad’ bacteria and reduced levels of ‘good’ bacteria in patients with severe Covid-19 symptoms
June-September: The changing gut Covid-19 sets the gut microbiome off kilter: much less bacterial diversity, much more opportunistic, harmful pathogens, much less beneficial bacteria
January 2021: The cytokine storm Severe deterioration of some Covid patients from excessive immune response is closely linked to the microbial imbalance in the gut, say researchers