Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons

Xiao, Yaqian; Jiang, Ruhan; Xin, Wu; Zhong, Qi; Li, Yi; Wang, Hongqi

doi:10.1128/spectrum.01420-21

Cited by 13 publications

(11 citation statements)

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“…Combined with previous analyses of the evolutionary relationships of related S. maltobacteria, it could be inferred that isolates from the semblable environmental resources were clustered together, while this conclusion did not apply to clinical isolates due to the differences in the hosts themselves. Our result was consistent with the investigation of S. maltophilia by Yaqian Xiao et al and the genomic analysis of Aeromonas veronii by Hai-chao Song et al (Song et al 2021;Xiao et al 2021), suggesting that there was no evolutionary correlation between the genome and its ecological niche adaptation.…”

Section: Evolutionary Analysis Of S Maltophiliasupporting

confidence: 93%

“…Some S. maltophilia isolates were reported to being capable of degrading alkanes, aromatics, and heavy metals, which play an important role in the degradation of pollutants and environmental remediation (Xiong et al 2020) (Venkidusamy and Megharaj 2016) (Jauhari et al 2014). For example, S. maltophilia strain W18 was isolated from crude oil-contaminated soil as a typical PAH-degrading strain of this species (Xiao et al 2021). As for isolates from clinical sources, the transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) has been reported to occur frequently in recent literatures (Cruz-Cordova et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait

Cheng

Rao

et al. 2023

J Appl Genetics

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Stenotrophomonas maltophilia is a species with immensely broad phenotypic and genotypic diversity that could widely distribute in natural and clinical environments. However, little attention has been paid to reveal their genome plasticity to diverse environments. In the present study, a comparative genomic analysis of S. maltophilia isolated from clinical and natural sources was systematically explored its genetic diversity of 42 sequenced genomes. The results showed that S. maltophilia owned an open pangenome and had strong adaptability to different environments. A total of 1612 core genes were existed with an average of 39.43% of each genome, and the shared core genes might be necessary to maintain the basic characteristics of those S. maltophilia strains. Based on the results of the phylogenetic tree, ANI value and the distribution of accessory genes, genes associated with the fundamental process of those strains from the same habitat were found to be mostly conserved in evolution. Isolates from the same habitat had a high degree of similarity in COG category, and the most signi cant KEGG pathways were mainly involved in carbohydrate and amino acid metabolism, indicating that genes related to essential processes were mostly conserved in evolution for the clinical and environmental settings. Meanwhile, the number of resistance and e ux pump gene was signi cantly higher in the clinical setting than that of in the environmental setting. Collectively, this study highlights the evolutionary relationships of S. maltophilia isolated from clinical and environmental sources, shedding new light on its genomic diversity.

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Section: Evolutionary Analysis Of S Maltophiliasupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait

Cheng

Rao

et al. 2023

J Appl Genetics

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“…Our phylogenetic tree was also able to recapitulate most of the established genetic clusters, despite the fact that previous work relied primarily on in silico MLST [17]. Other papers have previously established core genomes of S. maltophilia either by individual gene or by orthogroup [43][44][45][46]. Xu et al established a core genome of 1612 genes at a stricter cutoff of 100 % with only 42 strains, as opposed to the more lenient 80 % cutoff that we used to achieve a similarly sized core genome with 372 strains.…”

Section: Discussionmentioning

confidence: 73%

“…Other papers have previously established core genomes of S. maltophilia either by individual gene or by orthogroup [43–46]. Xu et al .…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals genetic diversity which correlates with colonization and persistence in vivo

McDaniel,

Sumpter,

Lindgren

et al. 2023

Microbiology

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Stenotrophomonas maltophilia is a Gram-negative emerging opportunistic pathogen often present in people with respiratory diseases such as cystic fibrosis (CF). People with CF (pwCF) experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that Pseudomonas aeruginosa promotes persistence of S. maltophilia in mouse respiratory infections. As is typical for environmental opportunistic pathogens, S. maltophilia has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of S. maltophilia, combining short and long read sequencing to construct nearly complete genomes of 10 clinical isolates. The genomes of these isolates were then compared with all publicly available S. maltophilia genome assemblies, and each isolate was then evaluated for colonization/persistence in vivo, both alone and in coinfection with P. aeruginosa . We found that while the overall genome size and GC content were fairly consistent between strains, there was considerable variability in both genome structure and gene content. Similarly, there was significant variability in S. maltophilia colonization and persistence in experimental mouse respiratory infections in the presence or absence of P. aeruginosa . Ultimately, this study gives us a greater understanding of the genomic diversity of clinical S. maltophilia isolates, and how this genomic diversity relates to both interactions with other pulmonary pathogens and to host disease progression. Identifying the molecular determinants of infection with S. maltophilia can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.

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“…An analysis of the principal components of the entire study area without dividing it into zones showed that the frequency of the detection of strains capable of only aerobic degradation of hydrocarbons and the presence of the gene for the anaerobic destruction of linear hydrocarbons, masD , are most closely related to the area where gas hydrates were found ( Figure 8 ). In addition, this analysis made revealed a strong relationship between the detection of pmoA and alkBB genes, which can be explained by the fact that in areas of fluid discharge in gas fields, methane is often accompanied by heavier linear hydrocarbons [ 17 , 41 ]. In addition, the detection of the bssA gene was correlated with an increase in the intensity of the anaerobic oxidation of hydrocarbons ( Figure 9 ).…”

Section: Discussionmentioning

confidence: 99%

Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan

Пономарева

Eskova

Shakirov

et al. 2022

Biology

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The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total DNA. However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions. In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons. When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (masD) make it possible to separate areas with traditional and gas-hydrate types of deposits. Using cultured methods, we found that representatives of the Nocardiaceae family of the phylum Actinomycetota were tied to the areas where gas hydrates were found. The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods. For the first time, this ability was revealed for the genera Stenotrophomonas, Psychrobacter, Micrococcus and Peribacillus. The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.

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Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons

Cited by 13 publications

References 50 publications

Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait

Comparative genomic analysis of Stenotrophomonas maltophilia unravels their genetic variations and versatility trait

Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals genetic diversity which correlates with colonization and persistence in vivo

Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan

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