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Microorganisms
Special Issues
The Urban Microbiome
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The Urban Microbiome

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (15 April 2025) | Viewed by 12707

Special Issue Editors

Dr. Haruo Suzuki

E-Mail Website
Guest Editor
Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
Interests: microbial diversity; urban microbiome; microbiome of built environment (MoBE); antimicrobial resistance; metagenomics; comparative genomics; plasmid host range; reproducible bioinformatics
Dr. Soojin Jang

E-Mail Website
Guest Editor
Antibacterial Resistance Laboratory, Institut Pasteur Korea, Seongnam-si 13488, Republic of Korea
Interests: bacterial antibiotic resistance; reactive oxygen species; molecular bacteriology; applied microbiology; antimicrobials; bacteriology; bacterial genetics; microbial culture; bacterial drug resistance; microbial molecular biology

Special Issue Information

Dear Colleagues,

Microorganisms is now inviting manuscripts for a Special Issue entitled "The Urban Microbiome". The Issue is dedicated to researching microbial communities in all urban environments, including building surfaces and in air, water/sewage, soil, plants, etc. Research on the urban microbiome has greatly advanced our understanding of the factors determining microbial community structure in these environments. A better understanding of the role of the urban microbiome in the functioning of cities and the health of city dwellers may facilitate urban design that takes microbial diversity into account.

Original articles, (meta)genome reports, perspectives/opinions/commentaries, systematic reviews, and meta-analyses are all eligible for publication. Topics of interest include environmental microbiology, evolutionary microbiology, microbial ecology, microbial genetics and genomics, bioinformatics tools and databases, and others related to the urban microbiome. All manuscripts will be peer-reviewed.

For “(meta)genome reports”, while submissions from studies of any scale are welcome (no restriction on sample size), the following points are recommended to promote detailed metadata and foster data sharing and open science for reproducibility:

  • Detailed Metadata Descriptions

Comprehensive metadata is essential for future meta-analysis research. Examples include links to publicly accessible administrative information pages summarizing data on urban characteristics, climate, population density, gender ratio, age distribution, waves of infections caused by microorganisms (e.g., COVID-19), antibiotic usage, and more.

  • Facilitating Data Reusability

Making input, intermediate, and output files publicly available ensures that researchers worldwide can verify and reuse datasets. For instance, in previous microbiome studies based on 16S rRNA gene sequences, critical data files—such as multiple sequence alignments and phylogenetic trees for microbial diversity metrics (e.g., UniFrac)—have rarely been shared. Addressing this gap can significantly advance the field and ensure reproducibility.

Dr. Haruo Suzuki
Dr. Soojin Jang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • urban microbiome
  • shotgun metagenomic sequencing, targeted amplicon sequencing (16S/18S/ITS), metatranscriptome, metaproteome, metametabolome
  • metagenome-assembled genomes (MAGs)
  • microbiome of built environment (MoBE)
  • MetaSUB international consortium
  • biosynthetic gene clusters (BGCs)
  • antimicrobial resistance (AMR)
  • mobile genetic elements (MGEs) such as phages and plasmids
  • pathogenic microbes including SARS-CoV-2

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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14 pages, 5046 KiB  
Article
Diversity and Composition of the Airborne Fungal Community in Mexico City with a Metagenomic Approach
by Carolina Brunner-Mendoza, María del Carmen Calderón-Ezquerro, César Guerrero-Guerra, Alejandro Sanchez-Flores, Ilse Salinas-Peralta and Conchita Toriello
Microorganisms 2024, 12(12), 2632; https://doi.org/10.3390/microorganisms12122632 - 19 Dec 2024
Viewed by 838
Abstract
Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly [...] Read more.
Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry and rainy seasons, with the genera Cladosporium and Penicillium presenting the highest relative abundances across seasons. The Agaromycetes showed an increase during the rainy season. Regarding the areas, the north and center sites showed similar meteorological conditions and fungal community composition patterns. According to the Shannon and Simpson indices, the south area showed a greater species diversity during the dry season. These insights into the interactions between urbanization, seasonality, and airborne microbial communities could contribute to more effective urban management, reduced health risks, and the promotion of sustainable development. Full article
(This article belongs to the Special Issue The Urban Microbiome)
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14 pages, 2668 KiB  
Article
Green Roof Substrate Microbes Compose a Core Community of Stress-Tolerant Taxa
by Thomas Van Dijck, Vincent Stevens, Laure Steenaerts, Sofie Thijs, Carmen Van Mechelen, Tom Artois and François Rineau
Microorganisms 2024, 12(7), 1261; https://doi.org/10.3390/microorganisms12071261 - 21 Jun 2024
Viewed by 1414
Abstract
Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof [...] Read more.
Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. No study included a spatiotemporal aspect to investigate the core microbiota residing in the substrates of extensive green roofs, although these key taxa are hypothesized to be amongst the most ecologically important taxa. Here, we identified the core microbiota residing in extensive green roof substrates and investigated whether microbial community composition is affected by the vegetation that is planted on extensive green roofs. Eleven green roofs from three different cities in Flanders (Belgium), planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.; Sedum–herbs–grasses roofs) or solely species of Sedum (Sedum–moss roofs), were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Identifying the key microbial taxa revealed that most taxa are dominant phylotypes in soils worldwide. Many bacterial core taxa are capable of nitrogen fixation, and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Considering that soil microbes adapted to the local edaphic conditions have been found to improve plant fitness, further investigation of the core microbiome is warranted to determine the extent to which these stress-tolerant microbes are beneficial for the vegetational layer. Although Sedum–herbs–grasses roofs contained more plant species than Sedum–moss roofs, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Future studies are recommended to comprehensively characterize the vegetational layer and composition to examine the primary drivers of microbial community assembly processes. Full article
(This article belongs to the Special Issue The Urban Microbiome)
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12 pages, 918 KiB  
Article
Mold Odor from Wood Treated with Chlorophenols despite Mold Growth That Can Only Be Seen Using a Microscope
by Johnny C. Lorentzen, Olle Ekberg, Maria Alm, Folke Björk, Lars-Erik Harderup and Gunnar Johanson
Microorganisms 2024, 12(2), 395; https://doi.org/10.3390/microorganisms12020395 - 16 Feb 2024
Cited by 1 | Viewed by 2282
Abstract
We previously reported that indoor odorous chloroanisoles (CAs) are still being emitted due to microbial methylation of hazardous chlorophenols (CPs) present in legacy wood preservatives. Meanwhile, Swedish researchers reported that this malodor, described since the early 1970s, is caused by hazardous mold. Here, [...] Read more.
We previously reported that indoor odorous chloroanisoles (CAs) are still being emitted due to microbial methylation of hazardous chlorophenols (CPs) present in legacy wood preservatives. Meanwhile, Swedish researchers reported that this malodor, described since the early 1970s, is caused by hazardous mold. Here, we examined to what extent CP-treated wood contains mold and if mold correlates with perceived odor. We found no studies in PubMed or Web of Science addressing this question. Further, we investigated two schools built in the 1960s with odor originating from crawlspaces. No visible mold was evident in the crawlspaces or on the surfaces of treated wood samples. Using a microscope, varying amounts of mold growth were detected on the samples, all containing both CP(s) and CA(s). Some samples smelled, and the odor correlated with the amount of mold growth. We conclude that superficial microscopic mold on treated wood suffices produced the odor. Further, we argue that CPs rather than mold could explain the health effects reported in epidemiological studies that use mold odor as an indicator of hazardous exposure. Full article
(This article belongs to the Special Issue The Urban Microbiome)
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17 pages, 1268 KiB  
Perspective
The Microbiome of the Built Environment: The Nexus for Urban Regeneration for the Cities of Tomorrow
by Antonia Bruno, Sara Fumagalli, Giulia Ghisleni and Massimo Labra
Microorganisms 2022, 10(12), 2311; https://doi.org/10.3390/microorganisms10122311 - 22 Nov 2022
Cited by 15 | Viewed by 6366
Abstract
Built environments are, for most of us, our natural habitat. In the last 50 years, the built-up area has more than doubled, with a massive biodiversity loss. The undeniable benefits of a city providing all the basic needs to a growing population showed [...] Read more.
Built environments are, for most of us, our natural habitat. In the last 50 years, the built-up area has more than doubled, with a massive biodiversity loss. The undeniable benefits of a city providing all the basic needs to a growing population showed longer-term and less obvious costs to human health: autoimmune and non-communicable diseases, as well as antimicrobial resistance, have reached unprecedented and alarming levels. Humans coevolved with microbes, and this long-lasting alliance is affected by the loss of connection with natural environments, misuse of antibiotics, and highly sanitized environments. Our aim is to direct the focus onto the microbial communities harbored by the built environments we live in. They represent the nexus for urban regeneration, which starts from a healthy environment. Planning a city means considering, in a two-fold way, the ecosystem health and the multidimensional aspects of wellbeing, including social, cultural, and aesthetic values. The significance of this perspective is inspiring guidelines and strategies for the urban regeneration of the cities of tomorrow, exploiting the invaluable role of microbial biodiversity and the ecosystem services that it could provide to create the robust scientific knowledge that is necessary for a bioinformed design of buildings and cities for healthy and sustainable living. Full article
(This article belongs to the Special Issue The Urban Microbiome)
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