Metabolome of Microbiome

There is a dynamic relationship between the microbiome and the human health. However, to understand this dynamic relationship, researchers need to have a closer look at the metabolome.

The Microbiome

In the past decade or so, there has been increased research surrounding human genetics and diseases. The discovery of the endocrine system which has been found to be crucial in regulating metabolism and fighting infection is a great step towards understanding the human body. This endocrine system can be damaged by antibiotics and be restored using capsules that have been filled with fecal matter.

This endocrine system is also what scientist call as the microbiome. It is large and complex. The human body is taught to contain as many microbes as the number of cells. There are as many as 160 different species of microbes found in the different parts of the body like the skin, intestines, and the mouth. In a study done by the European MetaHIT consortium, there were found to be 1,000 different bacteria species containing 3.3 million unique genes which, is 150 higher than the genes found in humans.

Understanding Microbes

The microbiome is being treated by scientists as the organ on its own, with its different necessary functions. Making sense of these diverse microbes in the human body has not been easy. Scientists have had to revisit an approach that was used over 20 years ago. Genetic sequencing, which is the study of the genome, has helped scientists understand the microbes better.

The scientists have been able to catalog and characterize the microbes by sequencing their genome. This has helped them understand how they work and their unique functions in the body. However, genomics alone might not give us a better understating of the link between human health and microbes. Scientists have had to dig deeper and use methods like rRNA sequencing and metagenomics to be able to identify a single microbiota.

This enables the scientists to have an estimation of the microbial activity in the human body. Scientists can tell how a certain microbiota appears and at what parts of the body. However, this method still comes short of revealing the direct relationship between the biota and the human body.


The study of a metabolome comes into play here to help understand the relationship between the microbes and the human body. The comprehensive study of the global metabolome is the study of the metabolites produced by the microbes and those of the host that has interacted with the microbes. We can understand the microbes by looking that their metabolites.

This is the language they use and having a full understanding of the metabolites will reveal the relationship between the human body and the microbes. However, it is not as simple as it appears. For the study of metabolites to be effective, scientists need to measure the different classes of metabolites produced by microbes. This is how the microbes communicate and one cannot understand the link between the human health and microbes without looking at this communication. The study of the metabolome has led to several discoveries in the area of disease research. Here are some of the recent discoveries that can help treat common diseases:

The microbiome and metabolome of infants have shown there is a link for asthma and allergy cases. A study was done of these two shows biomarkers for these two conditions. The metabolomes and microbes for different infants susceptible to allergy and asthma showed that the infants had deficiencies in certain native bacteria in the guts. The study further revealed a low amount of T cells protecting against allergy and asthma while showing a high amount of pro-inflammatory cells. The gut microbes and the difference in the immunological T cell can be used to predict the biomarkers for asthma and allergy in infants.

The metabolites have also been linked to the microbes in people with psychiatric disorders. A model mouse with autism was found to have overly high levels of two bacteria species in the gut. Scientist injected a healthy mouse with these bacteria species, and surprisingly the mouse showed autism symptoms. The elevated levels of these two bacteria microbes show a biomarker for psychiatric conditions.

The metabolomes have also been found to prevent the lethal C difficile injections, with the highest risk for difficile injections being antibiotics. The antibiotics usually wipe out a large number of the microbes in the gut, creating conditions suitable for the growth of the C difficile growth. An analysis of metabolomics showed that antibiotics kill a wide range of bacteria species. However, the difference in metabolites is very small. It is usually difficult to determine the extent of damage to the indigenous bacteria as antibiotics act differently.

Research on metabolomics has shown a link in the production of serotonin levels in the gut. The gut is where over 90% of the serotonin is produced. Gut serotonin has been linked with several conditions like irritable bowel syndrome, osteoporosis, and cardiovascular diseases. Recent studies have shown serotonin secretion in the gut is regulated by the metabolites released by the indigenous bacteria species in the gut. There are still a lot of studies going on to show the link between the metabolites and the microbiome. The studies have shown a link to most of the conditions affecting people, ranging from obesity the periodontal gum disease.

The Future Of Health

There is expected to be more discoveries as more is studied on the link between these two. The fact that scientists have been able to create a full profile of the metabolome about the microbiome in our bodies shows that it is time scientists did biomedical research on the two. Concentrations should not just be put on the microbiome alone but also on the metabolites they produce.

A metabolome approach has helped scientists to study every molecule in our bodies ranging from amino acids, hormones, co-factors, and neurotransmitters. Being able to catalog the human genome has helped biomedical research in understanding the importance of the microbiome in the human body. The metabolome has taken the research to another level, making it an important part of science. The metabolome cannot be overlooked anymore.


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