How Do We Know What Bacteria is in Our Bodies?

Metagenomics, from Metagenomics

Throughout healthcare, it’s been a struggle to see what’s exactly in our bodies when sick. There are symptoms, of course, but there is not always a precise diagnosis despite advances in diagnostic technology. As a result, it’s harder to fight the disease if the pathogen is rare or even undiscovered. Luckily, there’s been a rising field to combat this: metagenomics.

Fighting disease, down to its roots

In simple terms, metagenomics is the study of all genetic material, like DNA, from microbes in an area. Scientists take this data and try to find gene sequences within the organisms that give them more information to work with, such as  key sequences that help to identify bacteria or sources of antibiotic resistance. It’s much less time consuming than growing a culture (growing your own microbes to study), and made easier with a tool often used by researchers and bioengineers: binning. 

Binning is separating different gene sequences based on their microbe species of origin, using machine and deep learning. It makes it much easier to handle all the sheer data and easily find what you’re looking for, whether it’s genes for pharmaceutical purposes or genes for species identification. However, it can be hard to do this without the proper tools. Let’s take a look at the more commonly used ones.

How we sort our diseases

There are three main tools commonly used: COMEBin, SemiBin2, and MetaBAT2. All of these tools have their own strengths and weaknesses, but one of the most important is whether they can sequence microbes in our body. 

COMEBin is most definitely the best in this specific metric, with it being able to sequence genes 1,137 times, the highest out of all tools tested. Furthermore, it also does rather well in other environments (which is important, since disease doesn’t come from within us!), like sea, soil, and plant-associated microbes.

SemiBin2 also has a great performance, specifically with different types of the same species (This can help us to find data on and fight against microbes resistant to antibiotics!). Like COMEBin, it also bins well on microbes from other environments, proving to be useful for bacteria foreign to our bodies. 

MetaBAT2 does very well with genes sequenced from sea and botanical environments, beating out the other two in these instances. Conversely, it doesn’t do particularly good with environments related to humans, like the human gut. Any of these tools can be used to sort and find useful genes, but different ones should be used for differing circumstances.

So, why do we use this?

Metagenomic binning may seem small in the grand scheme of things, but it’s very important to finding antibiotic resistance and identifying or discovering rare or unknown pathogens. Data handling is critical when dealing with lifesaving technology or deadly disease, and metagenomics is no different. 

Binning is a key part of metagenomics in general, which can help humanity fight against diseases like meningitis, pneumonia, tuberculosis, and other respiratory and pulmonary infections. In conclusion, metagenomic binning, and metagenomics in general, is key to helping us fight bacteria, with the help of gene sequencing!

References

Han, H., Wang, Z., & Zhu, S. (2025). Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57957-6

‌Yazhini, A., Morice, É., Jochheim, A., Lieser, B., & Söding, J. (2025). Evaluation of metagenome binning: advances and challenges. Briefings in Bioinformatics, 26(6). https://doi.org/10.1093/bib/bbaf617

‌Maliha Batool, & Galloway-Peña, J. (2023). Clinical metagenomics—challenges and future prospects. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1186424

‌Metagenomics. (2025). Ucf.edu. https://hulab.ucf.edu/research/projects/metagenomics/Metagenomics.html

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