Where environmental microbiome meets its host: Subway and passenger microbiome relationships

Abstract

Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.

Gut and oral microbiota associations with viral mitigation behaviors during the COVID-19 pandemic

“…Overall, if we assume that decreased social contact and increased hygiene measures (e.g., hand washing) can decrease diversity, then our study suggests that other factors (e.g., household pets) and those implied but not directly measured (e.g., diet) may offset these potential losses in diversity. It has also been recognized that humans can share microorganisms through social interactions, cohabitation, and exchanges with both the natural and built environments (Tong et al, 2021;Peimbert and Alcaraz, 2022). Previous reports have also identified microbiota associations with pet ownership were also found in conjunction with stool studies (Kates et al, 2020) and our study suggests that pets may be an important reservoir of microbes in humans, a relationship that may be heightened in periods of decreased social contact.…”

Evolutionary ecology of human‐associated microbes

“…Although they do not find strong patterns, some clustering suggests that different types of protection could lead to vaginal changes that affect the microbiota. Peimbert and Alcaraz (2023) consider human commuter behaviour, reviewing the existing literature on the subway microbiome. They link data describing the built environment and the skin microbiota and emphasise the need for more information about specific human behaviours in the subway (sit/hold/etc., cleaning routine of subways, etc.)…”

Editorial 2024

“…These 21 papers focus on various types of microbial diversity, including domesticates, pathogens, and host‐associated microbiota, using a range of methodologies including population and evolutionary genomics, metagenomics, and field and laboratory experiments. As a whole, the papers address a few main subjects: domesticated microorganisms and microorganisms thriving in anthropogenic environments (Harrouard et al., 2023; Silva et al., 2023; von Gastrow et al., 2023), fungal pathogens (Ali et al., 2023; Louet et al., 2023; Rogério et al., 2023; Saubin et al., 2023; Stalder et al., 2023; Wang et al., 2023; Zewdie et al., 2023), metagenomics and microbiomes of animals and human (Bischofberger & Hall, 2023; Corsi et al., 2023; Mac Alpine et al., 2023; Moeller, 2023; Pedro et al., 2023; Peimbert & Alcaraz, 2023; Tessandier et al., 2023; Yuan et al., 2023), and metagenomics and microbiomes of crops (Gao et al., 2023; Richard et al., 2023). Collectively the articles in this Special Issue ‘underline the huge impact of the anthropogenic environment in microbial evolution, including the emergence and spread of pathogens as well as the benefits provided by domesticated or mutualistic fungi and bacteria’ (Giraud et al., 2023).…”

“…Rogério et al, 2023;Saubin et al, 2023;Stalder et al, 2023;Wang et al, 2023;Zewdie et al, 2023), metagenomics and microbiomes of animals and human(Bischofberger & Hall, 2023;Corsi et al, 2023;Mac Alpine et al, 2023;Moeller, 2023;Pedro et al, 2023;Peimbert & Alcaraz, 2023;Tessandier et al, 2023;Yuan et al, 2023), and metagenomics and microbiomes of crops(Gao et al, 2023;Richard et al, 2023). Collectively the articles in this Special Issue 'underline the huge impact of the anthropogenic environment in microbial evolution, including the emergence and spread of pathogens as well as the benefits provided by domesticated or mutualistic fungi and bacteria'(Giraud et al, 2023).Finally, our third Special Issue, Insights into Ecological & Evolutionary Processes via Community Metabarcoding includes 'papers that highlight the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary -omics data types and/or models/theory to infer overall ecosystem processes'(Gillespie et al, 2023).…”