With antibiotic resistance on the rise, the earth's rivers and water sources suffering from chronic levels of pollution, and industrialized farming damaging ecosystems crucial to the health of humans and the planet, scientists are searching for innovative solutions to the global emergency we are confronted with.

Even if many of us are aware that certain types of bacteria are important for human health, it's not so widely known that carefully balanced communities of microorganisms, called microbiomes, are crucial for environmental health and thriving ecosystems.

Researchers are only just beginning to grasp the full significance of the microbiome and how it affects humans and the environment. With the right tools, researchers can start to understand these connections to help us make better choices about the products we produce and use and the environmental standards we employ, so that we can create a healthier and more sustainable planet.

What Is a Microbiome?

All of us have microbiome populations, made up of a unique combination of bacteria, viruses and fungi. Our gut, mouth and skin each host their own unique microbiome community vital for maintaining a robust immune system, a healthy gut, a resilient skin barrier and overall good health.

And microbiomes aren't just limited to humans and other animals. Oceans, soils and rivers all host microbiome communities that impact entire ecosystems. A healthy soil microbiome is crucial for the growth of crops and wildlife, and water microbiomes in oceans and rivers help feed and support a vast range of species. This combination of microbiomes upholds the fabric of life.  

Yet human activities are creating ever more tears in this fabric: antibiotics and pollution from household chemicals are infiltrating these sensitive ecosystems and causing critical imbalances in microbiome populations. As we produce refuse carrying antibiotics and other products, wastewater filters through to our rivers and wetlands and kills microorganisms that are vital to these ecosystems. Significantly, wastewater contamination not only damages ecosystems but also plays a pivotal role in the rise of antimicrobial resistance (AMR).

A Global Crisis

AMR happens when microbes acquire resistance, mutate or are exposed to an environment where they can develop without the balance provided by nonresistant strains, resulting in their spread. This process can cause infections that are resistant to otherwise life-saving drug treatments.

In April the United Nations declared AMR a global crisis, releasing a report stating drug-resistant diseases could cause 10 million deaths a year by 2050 if decisive action is not taken.

The application of pesticides to crops also causes damage to native microbiome populations, as these chemicals penetrate ecosystems and contaminate our soils and rivers. Insect and wildlife populations, as well as soil and water microbiomes, are then negatively impacted by exposure to antimicrobials and toxic chemicals.

Research co-led by the University of York in England revealed that antibiotic contamination in rivers was present in 65 percent of 711 sites tested across 72 countries, with antibiotic presence exceeding the safe level at 111 of the sites. Lower-income countries were most impacted, because of high consumption of antibiotics in those regions coupled with a lack of adequate wastewater treatment technologies and sanitation facilities.

An Uncertain Future

Another recent study highlighted the fact that as global water scarcity is further exacerbated by climate change, governments are backing policies to radically increase the reuse of reclaimed wastewater.The introduction of pharmaceutical products to agricultural environments, however, is expected to rise in line with the reuse of wastewater as polluted water resources are applied to crop irrigation.

The European Union (EU) has recognized a need for minimum standards to manage the risks of using reclaimed wastewater in agriculture, but other regions have yet to make this move. In Mexico, around 260,000 hectares of agricultural land, the equivalent of approximately 360,000 professional soccer fields, are irrigated with wastewater, the majority of which is untreated.

Although the long-term impact of untreated wastewater irrigation remains unknown, it is clear that the introduction of chemically polluted water to agricultural systems is a contributing factor to the rapid rise of AMR, as native soil and water microbiomes become critically depleted.

A Warming Planet

The microbiome also plays a vital role in protecting our planet from global warming. Carbon sequestration, where carbon dioxide (and other forms of carbon) is removed from the atmosphere and captured in storage, is a natural process that regulates the temperature of the earth and helps sustain life. The plethora of microbiomes present in the environment make a significant contribution to this process, with plants, trees and soil absorbing more carbon than they release. Oceans are also paramount to carbon sequestration, providing the largest carbon store on the planet.

The disruption and depletion of the native microbiomes in these environments is reducing their capacity to store carbon. Degraded soil results in carbon dioxide being released back into the atmosphere and a reduced ability to support plant growth. Increased carbon dioxide emissions have already led to rising temperatures and acidification of the oceans, in turn reducing their capacity for carbon sequestration.

Damage to these unique microbiomes is ultimately contributing to a rise in global temperatures that threatens to cause deep damage to the planet.

Changing Attitudes

What can be done to protect these microbial communities, which are vital to the health of the earth? Agricultural, healthcare and consumer goods industries need to adapt on a policy level to prevent the unfolding crisis.

Scientists, researchers and policy makers are working together to protect vital microbiome communities and address AMR. To do so successfully, however, a clearer understanding of these complex microbial communities is required as there are still many unanswered questions about the specific roles they play within human health and the environment.

For example, gut microbiome composition has been associated with a number of diseases, most famously with inflammatory bowel disease, as well as other conditions such as skin disease, autoimmune diseases, asthma, arthritis, obesity and neurological diseases, including depression and autism,.

Algorithms Unlock Answers

The microbiome still has many secrets to reveal. As well as posing great challenges, these unknowns offer great opportunities to science and industry. What we can be sure of is that the secret to unlocking these capabilities can be found in data. And there are a lot of microbiome data out there, easily exceeding other biological data types (genomic, metabolomic, transcriptomic and epigenomic) in volume, complexity and scale.

Today the challenge is no longer generating data, the bottleneck lies in connecting, navigating and analyzing these complex data, with challenges that include high dimensionality and compositionality.

Bespoke computational tools, including artificial intelligence and machine learning, are now being applied to scientific data as these methods are capable of spotting connections that humans can't. By using and training computer algorithms, researchers are able to analyse microbiome data and garner new insights at unprecedented speed and scale.

The next step is for researchers and organizations to use and share these insights to generate real-world solutions that can be used to treat disease, understand human health and produce sustainable solutions designed to protect native microbiomes and nurture the ecosystems crucial to the future of our planet.