Co-occurrence patterns of bacteria within microbiome of Moscow subway

Klimenko, Natalia; Tyakht, Alexander V.; Toshchakov, Stepan V.; Shevchenko, Margarita; Korzhenkov, Aleksei A.; Afshinnekoo, Ebrahim; Mason, Christopher E.; Alexeev, Dmitry

doi:10.1016/j.csbj.2020.01.007

Cited by 28 publications

(35 citation statements)

References 48 publications

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“…The study of the taxonomic diversity of our samples demonstrated the aerosol and surface profiles at the stations, which corresponded with the data from other world subway systems. The majority of the identified genera ( Acinetobacter , Streptococcus , Streptococcus , and Corynebacterium ) are commensals of human skin and mucous membranes [ 6 , 17 , 18 , 19 ], which are widespread in the subways of different cities all around the world (New York, Oslo, Mexico City, Athens, and Boston) [ 17 , 18 , 20 , 21 ]. Some genera ( Cutibacterium , Ralstonia , and Psychrobacter ) were predominant either at the station as a whole or were mostly found in the aerosol or on the surfaces.…”

Section: Discussionmentioning

confidence: 99%

“…For a comparative analysis of the microbiome, the variable region V4 of the 16S rRNA gene sequencing data was obtained from a previously conducted study (hereinafter referred to as Knomics [ 6 ]). The samples mentioned in this article were swabs from various surfaces of four stations.…”

Section: Methodsmentioning

confidence: 99%

“…Various surfaces in four stations of the Moscow subway were characterized in an earlier study [ 6 ]. However, this study was a pilot and did not include an assessment of viability or pathogenicity, according to the authors.…”

Section: Introductionmentioning

confidence: 99%

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Microbiological Characteristics of Some Stations of Moscow Subway

Pochtovyi

Vasina

Verdiev

et al. 2022

Biology

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The subway is one of the most actively used means of transport in the traffic infrastructure of large metropolitan areas. More than seven million passengers use the Moscow subway every day, which promotes the exchange of microorganisms between people and the surrounding subway environment. In this research, a study of the bacterial communities of two Moscow subway stations was conducted and the common subway microbiome was determined. However, there were differences in microbiological and antibiotic-resistance profiles, depending on the station. The station’s operational period since opening correlated with the taxonomic diversity and resistance of the identified bacteria. Moreover, differences between aerosol and surface bacterial communities were found at the two subway stations, indicating the importance of diversified sampling during the microbiome profiling of public areas. In this study, we also compared our data with previously published results obtained for the Moscow subway. Despite sample collection at different stations and seasons, we showed the presence of 15 common genera forming the core microbiome of the Moscow subway, which represents human commensal species, as well as widespread microorganisms from the surrounding environment.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Microbiological Characteristics of Some Stations of Moscow Subway

Pochtovyi

Vasina

Verdiev

et al. 2022

Biology

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“…Despite this limitation, a general-level profile of the gut microbiome composition provided by the proposed platform can be useful for assessing the general degree of dysbiosis. It can help in more advanced tasks like predicting response to drug therapy (as suggested by the discovered link between cancer immunotherapy response and Bacteroides levels [57]) or diet (for example, high-fiber diet [1]), measuring contribution of gut microbes to microbiome of built environments [58] as well as rapidly assessing the gut microbiome dysbiosis in patients with viral infections like COVID- Table 1 List of the 12 target taxa in the platform.…”

Section: Discussionmentioning

confidence: 99%

Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

Kurina

Popenko

Klimenko

et al. 2020

Molecular and Cellular Probes

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A B S T R A C TNowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods -the platform and high-throughput 16S rRNA sequencing -across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.

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“…Co-occurrence patterns within and between microbial communities, however, have to-date been relatively sparsely studied ( Williams et al, 2014 ; Klimenko et al, 2020 ). In addition, the research on critical transitions in the gut microbiome is still in its early stages and primarily related to the gut microbiome within individuals ( Tytgat et al, 2019 ; Malard et al, 2020 ).…”

Section: A Wider Perspective: Co-occurrence Patterns In a Planetary Health Contextmentioning

confidence: 99%

On the Verge of a Catastrophic Collapse? The Need for a Multi-Ecosystem Approach to Microbiome Studies

Larsen

Burgwal

2021

Front. Microbiol.

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While the COVID-19 pandemic has led to increased focus on pathogenic microbes that cross the animal-human species barrier, calls to include non-pathogenic interactions in our perspective on public health are gaining traction in the academic community. Over generations, the diversity of the human gut microbiota is being challenged by external perturbations and reduced acquisition of symbiotic species throughout life. When such reduced diversity concerns not only the microbial species, but also the higher taxonomic levels and even the guild level, adequate compensation for possible losses may be lacking. Shifts from a high-abundance to a low-abundance state, known as a tipping point, may result in simultaneous shifts in covarying taxa and ultimately to a catastrophic collapse in which the ecosystem abruptly and possibly irreversibly shifts to an alternative state. Here, we propose that co-occurrence patterns within and between microbial communities across human, animal, soil, water, and other environmental domains should be studied in light of such critical transitions. Improved mechanistic understanding of factors that shape structure and function is needed to understand whether interventions can sustainably remodel disease-prone microbiota compositions to robust and resilient healthy microbiota. Prerequisites for a rational approach are a better understanding of the microbial interaction network, both within and inter-domain, as well as the identification of early warning signs for a catastrophic collapse, warranting a timely response for intervention. We should not forget that mutualism and pathogenicity are two sides of the same coin. Building upon the planetary health concept, we argue that microbiome research should include system level approaches to conserve ecosystem resilience.HIGHLIGHTS1. Non-pathogenic interactions between ecosystems play a key role in maintaining health.2. The human gut microbiome may be on the verge of a catastrophic collapse.3. Research should identify keystone taxa and guilds that interconnect different domains.4. We should not forget that mutualism and pathogenicity are two sides of the same coin.

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Co-occurrence patterns of bacteria within microbiome of Moscow subway

Cited by 28 publications

References 48 publications

Microbiological Characteristics of Some Stations of Moscow Subway

Microbiological Characteristics of Some Stations of Moscow Subway

Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

On the Verge of a Catastrophic Collapse? The Need for a Multi-Ecosystem Approach to Microbiome Studies

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