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BioBe research finds that individuals can be identified based on their microbiomes


The Biology and the Built Environment Center (BioBE) at the University of Oregon has published a new report in the journal PeerJ which finds that each microbiome emited by people contains a unique signature that can be used to identify the person it stemmed from, according to a report by Healthline.

The researchers created an experimental chamber at BioBE which featured advanced controls that allowed them to configure the room’s airflow, temperature, and humidity levels.

Lined with anti-static plastic sheeting, the sterilized chamber contained sterile air filters at the intakes and exhaust outputs.

The study involved 11 participants, all of whom were free of infectious disease and had not taken any antibiotics in the previous four months.

The participants, which were given tank tops and shorts to wear, each took turns sitting alone in the room for 90 to 240 minutes at a time.

The sparse room contained a chair for the participant, a laptop for entertainment purposes, and a range of petri collection dishes lining the floor to gather any bacteria that settled out of the air.

At the end of each test, the researchers collected the bacterial samples from the air filters and petri dishes, then immediately resterilized the room.

They were able to successfully extract from the samples a specific gene called 16S ribosomal RNA, which can be found in all bacteria and can indicate species and strain.

Of the 11 participants, the researchers collected more than 14 million genetic sequences to help identify the thousands of different types of bacteria among them, including Staphylococcus, Propionibacterium, and Corynebacterium.

Despite the fact that all of these bacteria types are common among humans, they often appeared in different ratios or were from a specific strain.

After analyzing the dataset, the researchers found that they could identify five of the 11 participants based on their unique microbiome fingerprints.

For example, one individual carried a specific type of Staphylococcus epidermidis at higher levels than the other participants, while another person showed a strong Lactobacillus crispatus signature.

The air within the testing chamber was enough to be able to differentiate among four different participants, however, the exhaust air itself did not contain enough bacteria to confirm. The final two participants could not be detected by any airborne source.

“As collection and sequencing methods improve, so will these results,” said James Meadow, former postdoctoral research associate for BioME and now lead data scientist at Phylagen, and lead author on the paper. “DNA sequencing is in the midst of a revolution. Things are changing very quickly. What the human genome project did over a decade can now be done in weeks for a tiny fraction of the cost.”

Meadow said that while the study has certain limitations, its findings should be able to pave the way for future applications.

“A single person sitting in an experimental chamber is not all that realistic,” he said. “So we would love to expand this study to see, for instance, if we can pick a person out of a crowd. I can think of lots of reasons we would want to know if some nefarious character has been in a certain room in the last few hours, and maybe there is a way to use microbes for that.”

Since DNA is a stable molecule that can live long after its host organism has died, the study measured the combined counts of both living and dead bacteria, said Meadow.

“The presence of a microbe’s DNA does not mean it is alive or active, simply that its DNA was present,” said Lita Proctor, coordinator of the NIH Human Microbiome Project. “We must be very careful to conduct follow-up studies to verify if these microbial cloud microbes are in fact alive or active.”

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