{"id":409470,"date":"2021-09-20T16:17:29","date_gmt":"2021-09-20T19:17:29","guid":{"rendered":"https:\/\/revistapesquisa.fapesp.br\/?p=409470"},"modified":"2021-10-04T13:38:49","modified_gmt":"2021-10-04T16:38:49","slug":"urban-germs","status":"publish","type":"post","link":"https:\/\/revistapesquisa.fapesp.br\/en\/urban-germs\/","title":{"rendered":"Urban germs"},"content":{"rendered":"

In June, researchers from every continent on Earth released the world\u2019s first catalog of the microbial ecosystem in urban areas. Using 4,728 samples collected from streets, shoes, public transport, and hospitals over three years, the group genetically mapped the microbiota\u2014the bacteria, viruses, fungi, and other microorganisms\u2014of 60 cities in 32 countries, three of which were in Brazil. One of the main findings of the study was that there were 31 species of bacteria that appeared in 97% of the samples. They form a central group of microorganisms prevalent in cities all over the world.<\/p>\n

In this group, there are three particularly abundant bacteria: Cutibacterium acnes<\/em>, found in human skin, which causes the appearance of pimples; Bradyrhizobium <\/em>sp. BTAi1<\/em>, a microorganism usually found in the soil, which fixes nitrogen in plants; and Micrococcus luteus<\/em>, a bacterium that lives in soil and on human skin and has been linked to occasional hospital-acquired infections. In total, the study identified 4,246 species of microorganisms. Among the new species not yet cataloged by science, the scientists identified 10,928 viruses, 1,302 bacteria, and two archaea (single-cell beings similar to bacteria). SARS-CoV-2, which causes COVID-19, is an RNA virus and does not appear in the results\u2014the study only looked at microorganisms with DNA genomes\u00a0 and the urban microbiome samples were obtained before the pandemic began.<\/p>\n

With this type of survey, it is possible to observe how microorganisms disperse locally within cities and monitor their spread on a global scale, which is very useful in a pandemic, in addition to detecting genes that promote antibiotic resistance. The study is the result of a collaboration between scientists that specialize in genomics, data analysis, engineering, epidemiology, and public health and together form the MetaSUB consortium, short for Metagenomics and Metadesign of Subways and Urban Biomes.<\/p>\n

The origin of this project dates back to 2013, when geneticist Christopher Mason, from Cornell University in the USA, began collecting microbiological samples in the New York subway. \u201cEvery time you sit down in the subway, you are likely commuting with an entirely new species of microorganism,\u201d said Mason in publicity material for the study. Shortly after the American geneticist published his first article on the subject, researchers from all over the world got in touch wanting to conduct similar analyses in their cities. One of them was Brazilian molecular biologist Emmanuel Dias-Neto.<\/p>\n

\u201cIn the early 2010s I started to investigate the links between bacteria and oral cancer. I often traveled home by subway and wondered what microorganisms were traveling alongside me and how I might be able to study them. A colleague of mine read about a similar project in New York. I got in touch with the authors and they asked me to participate in the first meeting in 2016,\u201d recalls the director of the MetaSUB consortium for South America and head of the Medical Genomics Laboratory of the International Research Center (CIPE) at the A.C.Camargo Cancer Center. Dias-Neto led the effort to collect 199 Brazilian samples that were included in the study from the cities of Ribeir\u00e3o Preto in the state of S\u00e3o Paulo, Rio de Janeiro, and S\u00e3o Paulo itself.<\/p>\n

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CDC \/ Bobby Strong\u2002|\u2002NIAID\u2002|\u2002CDC\u2009\/\u2009Betsy Crane<\/span><\/a> Images of three of the microorganisms most frequently found in urban microbiomes (left to right<\/em>): the bacteria Cutibacterium acnes<\/em>, Staphylococcus epidermidis<\/em>, and Micrococcus luteus <\/em>CDC \/ Bobby Strong\u2002|\u2002NIAID\u2002|\u2002CDC\u2009\/\u2009Betsy Crane<\/span><\/p><\/div>\n

The sample collection protocol involves the use of a swab with a synthetic tip. The swab is dipped in a DNA preservation solution and then wiped over the chosen surface for three minutes. Data such as latitude and longitude, temperature, air humidity, and number of people in the location are also recorded. The material is then placed in a tube that can be kept at room temperature. The samples from all over the world are sent to New York, where they are analyzed by the same equipment, following a single methodology. \u201cAbout 30 samples came from S\u00e3o Paulo, many from benches in plazas and parks such as Trianon Park on Avenida Paulista, as well as from A.C.Camargo premises,\u201d says Dias-Neto. In addition to public places, rental bicycles, and the soles of peoples\u2019 shoes, samples were also collected from the subway and the Oswaldo Cruz Foundation (FIOCRUZ) in Rio de Janeiro, and the University of S\u00e3o Paulo (USP) and bus stops in Riber\u00e3o Preto. Houtan Noushmehr from USP and Milton Oz\u00f3rio Moraes from FIOCRUZ also participated in the study.<\/p>\n

In S\u00e3o Paulo, the Monument to the Flags provided an interesting sample. At some points on the sculpture\u2019s surface, two communities of conflicting microorganisms were identified. On top of a white biofilm composed of bacteria, there was a dark film formed of fungi. \u201cThe fungi produce antibacterial substances so that it can invade the bacteria’s space. The bacteria, in turn, defend themselves by producing an antifungus,\u201d explains Dias-Neto. “We sequenced this point of contact between the biofilms in the hope of finding something that could be used as the basis for a new drug.”<\/p>\n

The information gathered by MetaSUB could prove useful in criminal investigations. Although there is a group of microorganisms found in the microbiomes of urban areas across the globe, each city in the study had its own set of microorganisms that serve as a signature of its microbiome. S\u00e3o Paulo, for example, can be uniquely identified by the presence of the virus Meleagrid alphaherpesvirus 1<\/em> and the bacteria Pandoraea vervacti <\/em>and Paraburkholderia terrae.<\/em> Rio de Janeiro can be identified by a cyanobacterium called Prochlorococcus<\/em> sp. MIT 0604<\/em>, a microorganism that performs photosynthesis and was formerly known as blue algae, and two viruses that infect cyanobacteria (Synechococcus phage S-SSM4<\/em> and Synechococcus phage S-SM1<\/em>). \u201cIn forensics, for example, it would be possible to analyze the biological material on the sole of a person’s shoe and find out which city they have been in,\u201d points out Dias-Neto.<\/p>\n