Microbial "fingerprint": the new coordinate of the city

New York’s "anti-radiation", South Africa’s Cape Town’s "sea salty taste".

An international consortium collected samples from public transportation systems and hospitals in 60 cities around the world, sequenced and analyzed them, and at the same time fully annotated all identified microbial species, including thousands of viruses, bacteria, and two undocumented species.

"Each city has its own microbial'molecular fingerprint'.

Start in New York and go to the world

The project started in 2013 and has gradually developed into the largest global urban microbial metagenomics research to date.

But Mason didn't expect at the time that one of his "little ideas" would go to the world.

After the first discovery was published in Cell-System, researchers from all over the world began to contact him, and they all wanted to do similar research in their own cities.

As a result, Mason developed a sample collection plan and posted an instructional video on YouTube.

In 2015, Mason created the MetaSUB (Metrogenomics and Metadesign of Metro and Urban Biome) Consortium.

"We collect samples from multiple cities in Japan (the cities where the Tokyo Olympic venues are located) at different times, and continue to collect samples in longitudinally comparable locations this year.

Researchers participating in this project collected samples with cotton swabs that did not contain DNA and RNA, and sent the samples and positive and negative control groups to the laboratory for analysis.

Find the city "fingerprint"

In the end, researchers from six continents collected 4728 samples in 3 years.

Sampling was conducted at 3 main time points, the pilot study from 2015 to 2016 and the two global city sampling days in 2016 and 2017 (June 21).

In order to analyze very large data sets, the researchers generated an open source analysis path, including a complete, advanced and peer-reviewed metagenomic tools for classification and identification, gene prediction, AMR detection, functional analysis, de novo assembly, and taxonomies Annotation and geospatial mapping, etc.

"As far as we know, this study is the world's first extensive metagenomic study of urban microbiota.

The data shows that the microbiota of the core city is the center of global diversity, and the microbial characteristics reveal the characteristics of the city.

In addition to the different microbial characteristics of different cities, the analysis also revealed 31 core microbes in all cities-these species were found in 97% of the samples, as well as unique geographic variations that may reflect epidemiological changes.

Researchers have identified 4246 known urban microorganisms, but any subsequent sampling may continue to find species that have never been seen before.
This highlights the original potential of discovering microbial diversity and biological functions in urban environments.

"Our data shows that although 1,000 samples are sufficient to find about 80% of the observed taxa and AMR markers, there is still a considerable part of the urban microbiota to be identified.
Moreover, considering that genetic variation is affected by environmental factors, samples near the equator show More diversity.
” Mason said.

Uncover the "truth" behind

Back in 2013, Mason's idea at the time was simple, to use sampling to find new microorganisms.

"There are countless species on the earth, but we only had 100,000 to 200,000 complete and solid genome reference data.
" Mason said that the discovery of new species will help establish microbial genealogy, understand the relationship between different species, and obtain microbes.
A new discovery in the evolution of life.

As data accumulates, these studies have begun to have implications for detecting outbreaks of known and unknown microbial infections and studying the prevalence of antibiotic-resistant microbes in different urban environments.
Moreover, these findings also have many potential practical applications.
"Based on the sequence data collected so far, we have discovered more than 800,000 new CRISPR sequences," Mason said.
These findings indicate that new antibiotics and small molecules annotated by the Biosynthetic Gene Cluster (BGC) are expected to promote drug development.

However, the researchers said that this study has three main limitations.
First, it only measures DNA, which means RNA viruses are excluded, and evidence of transcriptional activity from bacteria and archaea is also excluded.
Second, it was unable to identify most of the DNA collected.
This is at least partly due to the highly novel characteristics of urban microbial communities, which may improve as more data are generated.
Third, AMR genes are usually difficult to distinguish from similar genes that do not produce resistance, so the result may have a certain degree of "noise".

Swiss researchers Andre Kahles and Gunnar Ratsch of the MetaSUB Consortium released a global DNA sequence portal MetaGraph, which indexes all known gene sequences (including MetaSUB data) and maps known or newly discovered gene elements to them.
The location on the earth, which will help discover new microbial interactions and functions.

"The next step is to synthesize and verify some of these molecules, and predict BGC, and then see what role they have in medicine or treatment.
" Mason said, "We are now sampling, sequencing, and comparing the microorganisms in these urban sewage Link public health work to track new viruses and bacteria.
We will use this data to predict drugs and antibiotics and verify them in culture.
"

People often think that tropical rain forests contain rich biodiversity and various new molecules.
In fact, the same is true on subway railings or benches.
(Source: Tang Feng, China Science News)

Related paper information:

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