# 3 Reflecting on some limitations of metagenomics

In the previous sections you witnessed how scientist harness the power of metagenomics in a variety of research questions and practical applications. However, it is also important to mention some limitations of this approach, to also reinforce the fact that metagenomics is constantly improving.

Metagenomics sequences all DNA in a sample and is very sensitive, meaning that contaminating DNA from the laboratory equipment, chemicals, or the scientists themselves can accidentally be added to a sample. As a result, it can be difficult to know whether all DNA sequences truly come from the environment being studied, leading to incorrect conclusions about which organisms are actually there rather than a fluke.

Another challenge is that the amount of DNA found does not always match the number of organisms in the environment. Some species have larger genomes or more copies of certain genes, while other organisms break down more slowly in the environment releasing less DNA and over a longer period of time. Scientists are studying the problem in great detail to improve the interpretation of metagenomic data.

As you learned in the section on airborne DNA, metagenomics can also raise ethical concerns, especially when used on human-related samples such as gut microbiomes or wastewater. Environmental samples (including water contaminated with human faeces) may contain human DNA, which could reveal sensitive information about health or identity. Protecting privacy and obtaining informed consent when using metagenomics are important areas that need improvement.

- Metagenomics from a soil sample reveals two species of worm with very different DNA levels. However, field surveys suggest their populations have similar size. Which limitation is being demonstrated?

- This is an example of the difficulty of linking DNA abundance to actual organism numbers, because DNA quantity does not directly reflect population size.

- Scientists analysing sewage samples to study pathogenic microbes and antimicrobial resistance also detected human genetic information. Which metagenomics issue does this raise?

- This raises ethical concerns about privacy and the handling of human genetic information in metagenomics studies. In this case, human DNA is shed in the faeces and can be sequenced by metagenomics in sewage.

- A scientist finds unexpected human DNA in a water sample from a subglacial Antarctic lake. Which limitation does this illustrate?

- This illustrates the risk of contamination, where DNA not belonging to the original sample is accidentally introduced (probably during sample collection or manipulation in the laboratory).

OpenLearn - The metagenomics revolution: an introduction
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