Microbiome and Human Health: Effects and Future Uses

The various microorganisms that live on and inside a living organism are not just a simple collection of microbes. The term microbiome describes all the components of microorganisms, their community, genome, and metabolism. The study of the microbiome has changed the concept of microorganisms as a single cell to the microorganisms with complex grouping interaction roles in human, animal, and plant health.

The term microbiome was coined by Joshua Lederberg in 2001 and called for “a more ecologically- informed metaphor” to understand the relationship between humans and microbes. Nonetheless, the studies regarding commensal microbes on the host started in the seventieth century. The development of the first microscope allowed humans to explore the unknown world. The earliest focus of the microscope was on the microbes causing infectious diseases. But, only a small proportion of microbes can cause disease and are pathogenic. The majority is essential for a healthy ecosystem, found interacting with other microbes and the host organisms.

People often confuse the term microbiome with the term microbiota. Microbiota is the microbial taxa that has association with humans, plants, and animals, whereas the microbiome includes a community of microorganisms and their actions. Microorganisms residing in the host are also called normal flora or commensals.

Origin of the microbiome in Human

Human acquires the microbiome from the environment since birth. The womb was thought to be sterile, but recent studies have shown that it is where the microbiome begins. Microorganisms start colonizing the body as soon as the fetus passes out of the birthing canal. The gut microbiome is established well after weaning a baby.

Human Microbiomes

The microbiome is a vital part of humans. The figure above shows human microbes at various locations with their functions.

The diversity of the human microbiome was first studied by Antonie van Leeuwenhoek, in the 1680s by comparing his oral and fecal microbiota. His study predicted that different microbes are found in various habitat /body sites. The microbial species also vary in healthy and in diseased conditions.

Microbes are present all over the body, like the nose, mouth, lungs, stomach, colon, sexual organs, and on the skin of human beings.

Find more about ‘Normal Flora of the Skin-Skin Microbiome

The greatest variety of microorganisms is present in the gut region, especially in the colon, due to its warm, eutrophic, and stable environment. In addition to bacteria, archeas, eukaryotes, and viruses are also present, but in a smaller number.

Humans are identical, i.e., 99.9% to one another in their host genome. The microbiome is diverse over the period. It is believed that there is a core set of microbes we share. An adult human consists of over 100 trillion microorganisms, outnumbering human cells.

Once established in humans, microbes are relatively constant and depend on the external environment, antibiotics, diet, lifestyles, and genetic factors.

Effects of Microbiome on Health

Researchers are studying to understand the role of the symbionts on human health. These microbes are not invaders but colonize, benefiting us in many things. The microbiome is considered our last organ as it is a non-excludable part of the human body.

Some reports suggest that autoimmune disease and diabetes occur due to a less diverse gut microbiome. Similarly, the immune system of infants living in homes with dogs and dust is less likely to develop a response to childhood allergies and asthma. It is because of the change in gut microbe composition. Likewise, babies born from normal delivery are more resistant to respiratory diseases and allergies than those born after surgery. All such studies show the importance of microorganisms in the human body.

Although the human body is teeming with microorganisms, it has several sterile areas, like blood, cerebrospinal fluid, bone marrow, other internal body fluids, and some internal organs. Similarly, urine is primarily sterile, but it mixes with microbes dwelling on the organs of the lower urinary tract while urinating. There is a massive balance between sterile and non-sterile regions in a healthy human being. The loss in the balance between sterile and non-sterile areas results in the entry of bacteria into the body leading to different infections.

Beneficial effects

Some of the advantageous effects of the microbiome are:

  • The microbiome plays an essential role in food digestion. The gut microbe provides extra nutrition for the host, degrading protein and sugar.
  • The microbiome assists the production of short-chain fatty acids, bile acids, amino acids, vitamins, and various enzymes and metabolites, which affect host metabolism. Clostridium scindens could convert primary to secondary bile salts to prevent C. difficile colitis.
  • Our body needs vitamin B and K for immunity development and immune system build-up, supplied by gut microbes.
  • Microbiome aids in blood coagulation.
  • The microbiome is also important in immune system regulation.
  • Microbiome bears colonization resistance to pathogens. Healthy commensals regraded to the resistance to pathogen infection, called colonization resistance. It occurs through microbial competition for nutrients and the production of metabolites or bacteriocin or inducing host immune responses. For example, B. thuringiensis secretes bacteriocin targets spore-forming bacilli and clostridia. Bifidobacterium speices.
  • The microbiome produces organic acids and peptides that impair the growth and adhesion of pathogenic Escherichia coli to enterocytes.
  • Also, viruses stimulate interferon production in the gut and enhance colonization resistance to viral infection.
  • The microbiome also contributes host homeostasis in different locations.
  • The microbiome helps in fat storage regulation.
  • The plant microbiome supports increasing soil fertility, nutrient absorption, and carbon sequestration.
  • Microbiome detoxifies hazardous substances ingested by the host.

Harmful effects

The harmful effect starts with entering the microbiome in the sterile areas and causing infections. Some of the detrimental effects associated with the microbiome are:

  • Bloodstream infection occurs possibly from the gut microbiome, like Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus epidermidis.
  • Disrupting the intestinal barrier comprising epithelium and mucus layer may lead to severe infection.
  • Vaginal microbiome imbalance promotes sepsis. Lactobacillus develops a risk of preterm labor and rupture of fetal membranes resulting in neonatal sepsis.
  • Dysfunction of the microbiome leads to autoimmune diseases like rheumatoid arthritis, diabetes, multiple sclerosis, and fibromyalgia. It is found that such diseases are passed to offspring not through genes but by inheriting the parents’ microbiome.
  • Pathogenic change in normal flora by acquiring pathogenic genes leads to severe infections.
  • Microbiome dysbiosis promotes opportunistic infections when the body’s immune system is degraded—for example, multiple infections in cancer and AIDS patients with low immune status. The second example is Clostridium defficile infection after antibiotic therapy.
  • Disruption of normal metabolism sometimes links with a specific change in the microbiome. Metabolic diseases like diabetes, obesity, liver diseases, and tumors are associated with host abnormalities due to the microbiome.
  • More microbial load in specific sites can cause infection. For example, lack of brushing and oral hygiene may lead to dental caries by streptococcal species, otherwise harmless.
  • CONS produce specific peptides which kill Staphylococcus aureus and cause damage to the skin barrier and promote skin inflammation
  • Microbiome also sometimes hampers immune regulation, reducing recruitment and migration of immune cells and inhibiting differentiation of T and B cells.

Microbiome for the Treatment and Future Prospective

Microbiomes can prevent, detect, and treat various diseases and diet-related non-communicable diseases. The main working principle is replacing harmful bacteria with good ones. Analysis of the genome is informative in individual microorganisms and whole microbial communities in natural habitats, which can serve as a roadmap for the treatment.

Probiotics can be an effective therapeutic tool for different gastrointestinal diseases. When administered in sufficient amounts, these live microorganisms will be heath benefits. Species of Lactobacillus, Bifidobacterium, and Streptococcus serves that purpose. Probiotic treatment is the natural form of treatment that can replace antibiotic treatment as it has lesser side effects. Although antibiotics mainly combat pathogens, broad-spectrum antibiotics also inhibit the normal microbiota.

Healthy bacteria in the colon can also be restored by fecal microbiota transplantation, thereby curing many intestinal diseases like Clostridium defficile infections, irritable bowel syndrome, colitis, and constipation.

Synthetic biology, like genetic engineering, modifies microbes to new strains. Such strains have complex and unique functions to sense and record certain signals inside the body to reflect the host’s health status. It will help treat various infectious and non-infectious diseases.

Engineered microbes can be used as next-generation probiotics due to their specific and versatile nature. Microbiomes can be modulated to regulate homeostasis and metabolism to treat disease. E.g., toxins to treat cancer.

Microbiome gives vital information to synthesize personalized medicines and vaccines. As a microbiome determines how a person responds to medications, it can also design personalized medicines and tumor-engineered microbes for the effective treatment, mainly of cancer and other infectious diseases.

However, mapping human genes and discovering species and genes is challenging as it requires the proper knowledge and skills.

Plant and animal microbiomes can replace inorganic fertilizers and pesticides, improve biofuel production, and improve waste treatment.


The microbiome is essential in metabolism and immune regulation and promotes and inhibits diseases.

Since diverse groups of microbiota are found in the human body, the functions of different microbiota are also different. It is necessary to know the genome of such microbial groups to discover why the varieties in microbiota exist.

Understanding the microbiome is possible because of the rapid development of sequencing methods and analytical techniques. Studying the microbiome at a molecular level can be fruitful for effective treatments. Such studies also empower researchers to transform the microbiome for therapeutic tools and other clinical and environmental applications supporting human development.


Srijana Khanal

Hello, I am Srijana Khanal. Former faculty teacher in Microbiology Department at National College, NIST. Involved in the field of teaching for almost 10 years. I am very passionate about writing (academic as well as creative). My areas of interest are basic science, immunology, genetics, and research methodology.

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