The system services nearly five million people each day commuting from as far as China.
While each subway line hosts a characteristic set of bacteria during morning rush hour, researchers said by evening these unique bacteria joined into one uniform kind populating the entire system.
"In the morning, each line has unique microbial features reflecting the regions it passes, but with more and more people using the subway during the day, the microbial communities of all the lines become more similar," biologist Gianni Panagiotou said.
"The Metro is constantly cleaning every surface that we touch, but the train compartments have little personal space — passengers are squashed there, and we are talking about one of the busiest and densest cities in the world.
"With five million people riding the subway every day, the fingerprint of the whole city had to be there."
While most of the bugs they found were harmless, researchers discovered one line that may serve as a potential source of antibiotic resistance.
The genes giving the antibiotic resistance started out on one line in the morning and spread to become common on every line in the later hours of the day.
They said these results could allow improved detection of potential health risks and limit disease spread on public transport worldwide.
"The idea for this project is not to scare people, because what we observed was that higher traffic Metro lines do not carry higher health risks, neither in terms of pathogens or in terms of antibiotic resistance genes," Panagiotou said.
"Instead, we want to better understand how urban planning can impact the types of bacteria we encounter so that studies like ours investigating the microbial composition of train compartments may guide future public health strategies and public transit designs."
In 2016 an international consortium of scientists and volunteers led by researchers in America were in the process of developing a snapshot of the bacteria found aboard a city's public transport network.
Melbourne and Sydney were among 58 cities to participate in the study.
A staggering 48 per cent of the genetic data collected in New York did not match any known organism showing how little is known about our microbiome.
In 2014 a News Corp study showed one of the city's filthiest buses was also one of the busiest routes.
The 333 to Bondi Beach recorded dirt levels three and a half times above the benchmark for cleanliness used to check non-food-preparation surfaces in public venues.
It came after a report the previous year revealed train seats had not been properly cleaned in a decade.