New Insights Into The Gut Microbiome: These Bacteria Influence Your Health More Than You Might Suspect!

Credit: NIAID

The bacteria, archaea, viruses, fungi and protozoa living in the gut, collectively called the gut microbiome, have been linked to several diseases including obesity, heart disease, depression, type 2 diabetes, and rheumatoid arthritis. Human studies have linked specific microbiome compositions to specific diseases but often the directionality of the correlation is not known. Does the microbiome cause the disease or does the disease cause the changed microbiome?

To answer this question researchers have changed the microbiome in laboratory mice and found that this had an influence on the onset, severity or progression of several diseases. Preliminary small experiments with ‘gut microbiome transplantation’ in humans have observed some positive effects like weight loss in obese people. However, for many diseases listed above the evidence remains limited to observed correlations between the microbiome and disease rather than proven causation.

Most of the research on the gut microbiome so far has focused on the role of bacteria in health and disease. The role of viruses, fungi and protozoa is less clear. While we are just beginning to understand the role of our microbiome in health it seems clear that there are three broad categories of bacteria:

Humans have a multitude of different microbes living on and in us

(i) those that are beneficial to their host

(ii) those that are harmful to their host 

(iii) those who can be either beneficial or harmful depending on environmental conditions (or maybe even the genetic makeup of their host)


Beneficial bacteria help us to break down our food, make vitamins (like B and K), and suppress the growth of harmful bacteria. In a previous Longevity Reporter article we reported a beautiful example of a beneficial bacterial species that is able to break down toxic dietary Maillard reaction products and convert them to the health promoting compound butyric acid (see our article about this here). The size of the human microbiome is immense. For example, the human bacterial microbiome is made up of about an equal number of cells as the number of human cells in our body (approximately 39 trillion cells). Also the viral microbiome (called the virome) is large with an estimated 100 million to 1 billion viruses per gram of human feces.  

In April two papers were published side by side in the journal Science, one by Belgian researchers (Falony et al., 2016) and one from the Netherlands (Zhernakova et al., 2016). Both papers investigated the composition of the normal human gut microbiome and sought to determine factors which influence the bacterial composition. Outside of the usual suspects like diet, gender, disease status, and age many other factors were found including medication use, smoking status, and stool consistency. Some may recall a study from 2013 that showed that metformin extends lifespan in the roundworm C. elegans by influencing the metabolism of the bacteria on which the worm feeds. When worms in the absence of bacteria were given metformin their lifespan was actually decreased! This is a nice example of the interrelationship between the gut microbiome, health and drug use. 

Germ-free mice facility at the National Institute of Allergy and Infectious Diseases (NIAID). Credit: NIAID

Most mice used in biomedical research live in specific-pathogen-free (SPF) conditions. Compare it to living in an operating theater. Most often each cage of mice has its own filtered air supply, cages are autoclaved before use, as is the bedding and food. Living in such sterile conditions leaves these mice deprived of the normal microbiome. However, it should be pointed out that SPF mice are not completely sterile. In contrast, mice born and raised in even more rigoreus sterile conditions are known as germ-free mice. SPF mice, as the name suggests, are only free from a limited number of known mouse pathogens but still carry a microbiome while germ free mice are completely free from any bacteria. Germ-free mice have been very instrumental in helping us understand the role of the microbiome in health and disease. Firstly, by studying germ-free mice researchers have discovered that such mice have abnormalities in the development of their immune system (especially the gut immune system). Secondly, researchers can inoculate these germ-free mice with specific bacteria and hence study the health effects of specific bacterial species.

One example of this research is that mice that have a genetic susceptibility for autoimmune arthritis (inflammation of the joints) have a much less severe presentation of the disease when raised in germ-free conditions compared to normal conditions. Furthermore introduction of a single bacterial species (segmented filamentous bacteria) in these germ-free mice can induce arthritis. Another interesting example is a study from 2013 in which the human gut microbiome from a twin was transplanted into germ-free mice. One twin donor was obese and the other was lean. Interestingly, the mice who had received the transplant from the obese twin donor became obese themselves while the mice who had received the transplant from the lean twin remained lean themselves. Even more, when the mice who had received the transplant from the obese twin were cohoused with the mice who had received the transplant from the lean twin, they all remained lean.  

As discussed above the immune system of germ-free mice differs from SPF mice. But are SPF mice normal? According to a new paper published in Nature mice living in SPF conditions were found to have an immune system that is more similar to that of newborn babies. When SPF mice were co-housed with mice bought from pet stores the laboratory mice had an immune system that more closely matches that of adult humans. Next, the researchers challenged the mice by exposing them to a bacterial infection (Listeria monocytogenes) that is often used in the lab to test the immune function of mice. Three days after infection the bacterial load was more than 10,000-fold lower in pet store mice and laboratory mice co-housed with pet store mice compared to SPF mice. This experiment demonstrates that pet store mice or mice co-housed with pet stores mice are much better at controlling and fighting bacterial infection than SPF mice. 

Finally, another recent study published in Cell shows that the microbiome plays a role in autoimmunity. In this study researchers followed the development of the gut microbiome in babies born in Finland and Estonia versus Russia. Early-onset autoimmune diseases (including allergies and type 1 diabetes mellitus) are much more prevalent in Finland and Estonia compared to Russia.

Interestingly, the composition of the gut microbiome was different between children born in Finland and Estonia compared to Russia. Bacteroides species were much more abundant in babies born in Finland and Estonia compared to Russian babies. Bacteroides species have a molecule called lipopolysaccharide (or LPS for short) in their outer membrane. Exposure to LPS causes a very strong immune response. However, what was unexpected was that LPS from Bacteroides influences the immune system in a different manner than LPS from other bacterial species (such as E. coli). When white blood cells were exposed to LPS from E. coli they had a strong activation of pro-inflammatory gene expression. But when white blood cells were exposed to LPS from Bacteroides there was no response at all. Even more, when LPS from Bacteroides was added to white blood cells also exposed to LPS from E. coli, the Bacteroides LPS acted as an inhibitor of E. coli LPS induced inflammatory gene expression.

Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times. Photo by Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU

The difference in response between LPS from Bacteroides species versus E. coli is explained by a difference in the LPS structure (the lipid A carries 6 acyl groups in E. coli LPS versus 4 or 5 in LPS from Bacteroides). When cells are repeatedly exposed to LPS they develop tolerance to the LPS (exposure to LPS no longer leads to an activation of pro-inflammatory gene expression). This phenomenon is called ‘endotoxin tolerance’. However the researchers discovered that Bacteroides LPS failed to induce tolerance while E. coli LPS induced tolerance. Furthermore, exposing cells to a mix of both Bacteroides and E. coli LPS also failed to induce tolerance. Hence, the Bacteroides LPS inhibits the ability of E. coli LPS to induce tolerance in the cells. Finally, the researchers injected LPS from either Bacteroides or E. coli in animals that are genetically-engineered to develop autoimmune diabetes. Treatment with E. coli but not Bacteroides LPS caused a delay in disease onset. 



Wu H-J et al. (2010). Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 32(6): 815-827.

Cabreiro F et al. (2013). Metformin retards aging in C. elegans by altering microbial folate and methionine metabolism. Cell 153(1): 228-239. 

Ridaura VK et al. (2013). Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341(6150): 1241214. 

Virgin HW (2014). The virome in mammalian physiology and disease. Cell 157(1): 142-150. 

Sender R et al. (2016). Revised estimates for the number of human and bacteria cells in the body. doi:

Falony G et al. (2016). Population-level analysis of gut microbiome variation. Science 352: 560-564. 

Zhernakova A et al. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352: 565-569. 

Beura LK et al. (2016). Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 532: 512-516. 

Vatanen T et al. (2016). Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell 165: 842-853.