Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods

Serrano-Silva, Nancy; Calderón-Ezquerro, María del Carmen

doi:10.1016/j.envpol.2017.12.035

“…S2a-b. These genera can be also found within the most abundant taxa in other studies on very different urban areas[41,[69][70][71].…”

supporting

confidence: 66%

Seasonal Changes of the Airborne Microbiome in a Large Urban Area

Núñez¹,

Moreno²,

García³

et al. 2020

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0

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Background Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. Besides its ecological importance, the spatial and temporal characterization of aerosolized microorganisms is relevant for understanding allergy and disease outbreaks, especially in highly populated cities. Results In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km 2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both kingdoms characteristic of seasonal periods, but not of specific sampling sites or plant coverage. Conclusions The present study suggests that the near surface atmosphere of urban environments constitutes a stable ecosystem, with a relatively homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.

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“…415 Actinobacteria and Proteobacteria, which are the most common phyla found in 416 soil(Delgado-Baquerizo et al, 2018), such as Sphingomonas, Kocuria, Pseudomonas 417 and Paracoccus Figure 1c-d and Figure S4a-b. These genera can be also found within 418the most abundant taxa in other studies on very different urban areas(Li et al, 2019; 419 Polymenakou et al, 2020;Serrano-Silva and Calderon-Ezquerro, 2018; Yan et al, 420 2018a).…”

supporting

confidence: 53%

Seasonal changes dominate long term variability of the urban air microbiome across space and time.

Núñez

¹

,

Moreno

²

,

García

³

et al. 2021

Preprint

0

View full text Add to dashboard Cite

Background Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. Besides its ecological importance, the spatial and temporal characterization of aerosolized microorganisms is relevant for understanding allergy and disease outbreaks, especially in highly populated cities. Results In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km 2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both kingdoms characteristic of seasonal periods, but not of specific sampling sites or plant coverage. Conclusions The present study suggests that the near surface atmosphere of urban environments constitutes a stable ecosystem, with a relatively homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.

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“…In this study, alpha diversity analysis also included unidentified OTUs by 97% sequence identity because unidentified OTU should be counted for diversity. OTUs with less than 10 sequences were discarded due to the possibility of error like many previous studies [29, 30]. Chao1 values could be changed whether low-abundance read is included in analysis.…”

Section: Discussionmentioning

confidence: 99%

Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load

Han¹,

Yi

²

,

Kim³

et al. 2019

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Data concerning the human microbiota composition during Clostridioides (Clostridium) difficile infection (CDI) using next-generation sequencing are still limited. We aimed to confirm key features indicating tcdB positive patients and compare the microbiota composition between subgroups based on toxin gene load ( tcdB gene) and presence of significant diarrhea. Ninety-nine fecal samples from 79 tcdB positive patients and 20 controls were analyzed using 16S rRNA gene sequencing. Chao1 index for alpha diversity were calculated and principal coordinate analysis was performed for beta diversity using Quantitative Insights into Microbial Ecology (QIIME) pipeline. The mean relative abundance in each group was compared at phylum, family, and genus levels. There were significant alterations in alpha and beta diversity in tcdB positive patients (both colonizer and CDI) compared with those in the control. The mean Chao1 index of tcdB positive patients was significantly lower than the control group ( P <0.001), whereas there was no significant difference between tcdB groups and between colonizer and CDI. There were significant differences in microbiota compositions between tcdB positive patients and the control at phylum, family, and genus levels. Several genera such as Phascolarctobacterium , Lachnospira , Butyricimonas , Catenibacterium , Paraprevotella , Odoribacter , and Anaerostipes were not detected in most CDI cases. We identified several changes in the microbiota of CDI that could be further evaluated as predictive markers. Microbiota differences between clinical subgroups of CDI need to be further studied in larger controlled studies.

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Metagenomic survey of bacterial diversity in the atmosphere of Mexico City using different sampling methods

Cited by 39 publications

References 26 publications

Seasonal Changes of the Airborne Microbiome in a Large Urban Area

Seasonal Changes of the Airborne Microbiome in a Large Urban Area

Seasonal changes dominate long term variability of the urban air microbiome across space and time.

Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load

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