Microbes are everywhere. In your body, in your bedsheets, in the air, and even in your food.

For a long time, the idea of germs and bacteria was considered a bad thing – potentially harmful to plants, animals and us. However, thanks to researchers studying the concept of microbiomes, the role bacteria play is being reevaluated and constantly modified.

The microbiome can be defined as the sum of the microbes and their genomic elements in a particular environment (Berg et al. 2020).

The ongoing microbiome research is a fascinating fast-growing discipline strongly supported by ecological and genomic perspectives.

This scientific support teaches us more about these tiny microbes, how they affect different organisms, how they modify our health, and the good and the bad guys causing these effects.

More and more, researchers are studying how the introduction of certain organisms into the human environment impacts our own microbiome. Does it increase diversity? Is this introduction positive or negative?

In this article, we’ll be looking at just that, but with a hyperfocus on the microbiome exchange between plants and people.

In this article

Key terms in the microbiome research




Microbial consortia:


The plant microbiome

Detrimental effects

Beneficial effects

The human microbiome

Commonalities between plant and human microbiomes

Plant-human microbiome interactions


Indoor environments

Tips to increase microbial diversity in an indoor environment



Key terms in the microbiome research

Before going too deep into the article, we wanted to present some key terms for definition.


A metagenome are all the genes and genomes of the microbiota, including plasmids (Berg et al. 2020).


A microbiome includes the connection between microbiota, genetics, and its environment. In this paper, we took the definition of the microbiome as the sum of the microbes and their genomic elements in a particular environment (Berg et al. 2020).


Microbiota is the collection of living microorganisms present in a given environment. The key difference between the microbiota and the microbiome is that only living organisms are considered part of the microbiota. Therefore, phages, viruses, plasmids, prions, viroids, and free DNA are usually not considered to belong to the microbiota (Berg et al. 2020).

Microbial consortia:

A group of microbes. This may include bacteria, fungi and yeast.


An artificially designed microbial consortia.

The hierarchy of the microbiome - microbiota, microbiome etc

In this sense, there is also no clear consensus as to whether extracellular DNA derived from dead cells (called "relic DNA") should be included within a microbiome.

Why is the question of its inclusion important? Relic DNA content in a sample is not negligible. It can comprise 40% - 80% of the sequenced DNA in some soil samples.

Despite everything, it has been found that the relic DNA has a minimal effect on the estimation of taxonomic and phylogenetic diversity, so it does not interfere with microbiological analysis significantly.

The plant microbiome

Contrary to many other scientific fields where human-related topics are prioritized, close attention has been paid to plants in microbiome research.

Plant microbiome studies aim to unravel microbial communities' functional and structural diversity associated with a host plant in a particular habitat.

It has been reported that plant microbial diversity depends not only on host species but also on selection pressure, that is, the external factors that affect an organism's ability to survive in a specific environment.

It also depends on developmental stages and environmental conditions. For example, pH, salinity, soil structure, climate, pathogen presence, and human practices can all have an influence.

Microbes can exert detrimental or beneficial effects on plants.

Detrimental effects

  • Disease symptoms through the production of phytotoxic compounds, proteins, and phytohormones.
  • Plant pathogens like Pseudomonas syringae produce phaseolotoxin affecting a broad host range, including tomato, tobacco, and olive.
  • Hormone production
  • Reduction of stress through the inhibition of ethylene by phosphate solubilization, nitrogen fixation, and indole acetic acid production.
  • Mechanisms involved in improved nutrient uptake, growth, and stress tolerance.

Beneficial effects

A deeper understanding of the plant microbiome is being further explored for agriculture improvements.

For example, researchers are now using a mixture of different microbial species (microbial consortia) in breeding management practices to develop beneficial microorganisms optimized for plants. Another term for these mixtures is a synthetic microbial community (SynCom).

One study evaluated rice in the presence of organic nitrogen. The comparative study evaluated growth performance based on the number of members within the provided synthetic community.

Researchers found that adding a consortium of 16-members associated with rice plant substantially lengthened the shoot and root growth of rice plants compared to a 3-membered synthetic community.

An important conclusion from this study and others like it is that higher microbial diversity leads to better plant immune systems and improved yield performance.

In contrast, the loss of microbial diversity, which is associated with domestication, weakens a plant’s defense systems or leads to undesirable traits.

Next-generation sequencing has also led to more insight about the plant microbiome. Next-generation sequencing has allowed researchers to fully identify components of a microbiome, which has then led to creating more optimized synthetic communities.

However, there are many microorganisms that cannot be cultivated under laboratory conditions (using in vitro culture techniques), so some desired microbial consortia cannot be created because of this limitation.

The human microbiome

The human microbiome field has moved from cataloging microbial diversity to deciphering the microbial molecular mechanisms influencing human health.

Microbes are known to govern infectious diseases, but the research on the human microbiome also shows us that several common health conditions such as neurological disorders and even cancer, are associated with microbiome distress (Mendes et al. 2015).

It has been estimated that 500–1000 species of bacteria exist in the human body. The gut microbiome alone houses the largest number and has the most diversity.

The gastrointestinal tract (gut) is one of the most well studied microbial systems in humans. The microbiome's composition is unique in everyone, and the differences among individuals can be compared to the typical biochemical differences within a person over time (Gilbert et al., 2018).

Microbiomes establish themselves within their environment very early on (ScienceDaily, 2019). Studies found mice fetuses have their own microbial communities, and in infant humans, bacteria can be detected just four days after birth (Rackaityte and Lynch, 2020).

Infant gut microbial composition is so important to infants. Dysfunction can lead to a higher risk of developing chronic issues down the road, such as asthma in childhood.

Other studies report increased concentration of trimethylamine N-oxide (TMAO) associated with arthrosclerosis is dependent on gut bacterial metabolism (specifically phosphatiylcholine). The latter study provides evidence where gut microbial influenced by diet governs cardiovascular disease.

Factors influencing the human microbiome include location (gut, skin, etc.), diet, antibiotic use, and lifestyle.

Interestingly, lifestyle is not one we often think about. Aside from activities, lifestyle can include your home environment and the pets within, which ultimately influences microbial makeup and diversity.

Novel clinical interventions based on the human microbiome are being developed. These therapies are known as rebiosis, meaning re-establishing a healthy, microbiome after dysbiosis.

Rebiosis has prompted a revolution in personalized medicine, in which precise treatment leads to a positive outcome for individual patients.

One of the most common rebiosis applications is the fecal transplant. As it sounds, the microbes living in the stool of a healthy human can recuperate another individual's impaired health.

For instance, fecal transplants are being used to treat Clostridium difficile infections.

After transplantation, healing is rapid and visible. One of the biggest reasons we can attribute healing to the transplant is that afterward, the microbiota within the patient matches the healthy donor’s.

Due to the success of fecal transplants, it is becoming a more standard alternative to antibiotic treatments for C. diff infections.

4 factors influencing the microbiome are location, environment, lifestyle and antibiotic use

Commonalities between plant and human microbiomes

Interesting insights stemming from researching the relationship between plant and human microbiomes shows the rhizospheres and a mammals' gut have the same four dominant bacterial phyla.

4 common bacterial phyla in both people and plants

To clarify, a rhizosphere is an area of soil around the plant root that is regularly affected by rhizo-deposits (root exudates or substances secreted by plants).

The four dominant bacterial phyla are Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria (Mendes et al. 2015).

Though mammals and plants have these four in common, their relative abundances differ.

Some microbial imbalances also have similar patterns in both animals and plants.

For example, changes in the ratio of Firmicutes to Bacteroidetes in the gut of mammals affect the capacity for energy harvest and lead to obesity.

In the case of the rhizosphere, the abundances of Proteobacteria and Actinobacteria are correlated with defense against fungal pathogens (Mendes et al., 2015).

Plant-human microbiome interactions Diet

Healthy microbiomes lead to higher microbial diversity in plants and humans and, consequently, better agricultural performance and health.

When humans eat fresh plants (fruit, root vegetables, salad, beans, etc.), microbes are transferred from plant tissues and established within the human gut system.

Interestingly, this transfer has shown to be so prominent that there is a hierarchy of primary consumer type and bacterial diversity. A higher bacterial diversity is found in herbivores, followed by omnivores, and finally for carnivores.

Primary consumer hierarchy of microbial diversity

Therefore, individuals consuming more plant products rather than meat or processed food will likely have a higher microbial diversity and therefore potentially better health (Giron et al. 2021).

plant and gut microbial diversity

Indoor environments

We spend most of our lives in closed places. In your office, in your car, in your house, and on average, eight hours a day in your bedroom.

Therefore, indoor microbial communities are critical in shaping the human microbiome. Indoor microbiomes originate primarily from human skin, pets, outside air that comes in, and houseplants.

For instance, places like hospitals are more easily colonized to a large extent by patient-associated microbes. This condition causes many patients in intensive care units develop nosocomial infections or hospital-acquired infections.

These infections are mainly caused by human pathogens like Burkholderia cepacia, Pseudomonas aeruginosa or Stenotrophomonas maltophilia.

Hospitals are an interesting example when it comes to microbial diversity. There is a lot going for it - the number of people coming in and out.

But there is a lot negatively impacting diversity - the fact that hospitals only service one species, that many of the people coming in are suffering a health issue and that the hospital environment itself is highly sterile.

What this means is that hospitals become easily colonized by patient-associated microbes as opposed to healthy microbes.

This environmental condition causes many patients in intensive care units to develop nosocomial infections, or hospital-acquired infections (Berg et al. 2014).

Although it is not so evident, plants have a pivotal role in shaping indoor microbial diversity.

Even if you do not have a houseplant in your office, the incoming air from your window or the rain over your house can have a plant-associated microbiome. Some cloud and hailstone studies support plant-surface bacteria as being the dominant source in rainfall (Šantl-Temkiv et al., 2013).

Furthermore, plants provide beneficial bacteria for indoor rooms and can positively influence human health.

For instance, houseplants have a remarkable capacity to improve indoor air quality. We highlight some of the benefits as well as how to choose house plants in our GoldBio article Indoor plants: Characteristics to Look for & Types to Choose.

There are many ways for plant microbes to enter an indoor environment, such as pollen, the soil on shoes, a wet coat, flowers, fruits, vegetables, animals coming from outside, and the incoming air.

In contrast, enclosed environments such as private/public buildings, clean rooms, and hospitals have a reduced microbial diversity compared to the outdoor environment.

This reduced microbial diversity can facilitate the dominant proliferation of certain strains, which might bear the risk of harming our health. Therefore, we have some tips to increase the microbial diversity in your indoor environment.

Tips to increase microbial diversity in an indoor environment

  • Open your windows whenever possible.
  • Add live houseplants because they are a source of higher microbial biodiversity and health benefits.
  • Play with pets, especially if they’re indoor/outdoor pets.
  • Hang your sheets out to dry.


Plant microbiome, human microbiome, microbiota, microbial diversity, microbiome.


Berg, G., Grube, M., Schloter, M., & Smalla, K. (2014). The plant microbiome and its importance for plant and human health. Frontiers in Microbiology, 5(SEP), 1–2.

Berg, G., Mahnert, A., & Moissl-Eichinger, C. (2014). Beneficial effects of plant-associated microbes on indoor microbiomes and human health? Frontiers in Microbiology, 5(JAN), 1–5.

Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M. C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., Kazou, M., Kinkel, L., Lange, L., Lima, N., Loy, A., Macklin, J. A., Maguin, E., Mauchline, T., McClure, R., … Schloter, M. (2020). Microbiome definition re-visited: old concepts and new challenges. Microbiome, 8(1), 1–22.

Compant, S., Samad, A., Faist, H., & Sessitsch, A. (2019). A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. Journal of Advanced Research, 19(March), 29–37.

Gilbert, J., Blaser, M., Caporaso, G., Jansson, J., Lynch, S., & Knight, R. (2018). Current understanding of the human microbiome. Nature Methods, 24(4), 392–400.

Gupta, R., Anand, G., Gaur, R., & Yadav, D. (2021). Plant–microbiome interactions for sustainable agriculture: a review. Physiology and Molecular Biology of Plants, 27(1), 165–179.

Malla, M. A., Dubey, A., Kumar, A., Yadav, S., Hashem, A., & Allah, E. F. A. (2019). Exploring the human microbiome: The potential future role of next-generation sequencing in disease diagnosis and treatment. Frontiers in Immunology, 10(JAN), 1–23.

Ogunrinola, G. A., Oyewale, J. O., Oshamika, O. O., & Olasehinde, G. I. (2020). The Human Microbiome and Its Impacts on Health. International Journal of Microbiology, 2020.

Rackaityte, E., & Lynch, S. V. (2020). The human microbiome in the 21st century. Nature Communications, 11(1), 19–21.

Sciencedaily. (2019). Even the fetus has gut bacteria. In Sciencedaily.

Soto-Giron, M. J., Kim, J. N., Schott, E., Tahmin, C., Ishoey, T., Mincer, T. J., DeWalt, J., & Toledo, G. (2021). The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Scientific Reports, 11(1), 1–14.