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

2021 ◽  
Author(s):  
Yaqian Xiao ◽  
Ruhan Jiang ◽  
Xiaoxiong Wu ◽  
Qi Zhong ◽  
Yi Li ◽  
...  
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Natural Environments ◽  
Genomic Features ◽  
Content Type ◽  
The Core ◽  
Core Function ◽  
Polycyclic Aromatic

This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable.

scholarly journals AmpDI Is Involved in Expression of the Chromosomal L1 and L2 β-Lactamases of Stenotrophomonas maltophilia

2009 ◽  
Vol 53 (7) ◽  
pp. 2902-2907 ◽  
Author(s):  
Tsuey-Ching Yang ◽  
Yi-Wei Huang ◽  
Rouh-Mei Hu ◽  
Shao-Cheng Huang ◽  
Yu-Tzu Lin
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Stenotrophomonas Maltophilia ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Context ◽  
One Step ◽  
L1 And L2

ABSTRACT Two ampD homologues, ampD I and ampD II, of Stenotrophomonas maltophilia have been cloned and analyzed. Comparative genomic analysis revealed that the genomic context of the ampD II genes is quite different, whereas that of the ampD I genes is more conserved in S. maltophilia strains. The ampD system of S. maltophilia is distinct from that of the Enterobacteriaceae and Pseudomonas aeruginosa in three respects. (i) AmpDI of S. maltophilia is not encoded in an ampDE operon, in contrast to what happens in the Enterobacteriaceae and P. aeruginosa. (ii) The AmpD systems of the Enterobacteriaceae and P. aeruginosa are generally involved in the regulation of ampR-linked ampC gene expression, while AmpDI of S. maltophilia is responsible for the regulation of two intrinsic β-lactamase genes, of which the L2 gene, but not the L1 gene, is linked to ampR. (iii) S. maltophilia exhibits a one-step L1 and L2 gene derepression model involving ampD I, distinct from the two- or three-step derepression of the Enterobacteriaceae and P. aeruginosa. Moreover, the ampD I and ampD II genes are constitutively expressed and not regulated by the inducer and AmpR protein, and the expression of ampD II is weaker than that of ampD I. Finally, AmpDII is not associated with the derepression of β-lactamases, and its role in S. maltophilia remains unclear.

scholarly journals Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates

mSystems ◽  
2021 ◽  
Author(s):  
Wangxiao Zhou ◽  
Ye Jin ◽  
Yanzi Zhou ◽  
Yuan Wang ◽  
Luying Xiong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Health Issues ◽  
Content Type ◽  
Genome Wide Analysis ◽  
Genome Wide

Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage.

scholarly journals Draft Genome Sequence of Listeria monocytogenes CIIMS-NV-3, a Strain Isolated from Vaginal Discharge of a Woman from Central India

2019 ◽  
Vol 8 (6) ◽  
Author(s):  
Pooja M. Kishnani ◽  
Nitin V. Kurkure ◽  
Sukhadeo B. Barbuddhe ◽  
Swapnil P. Doijad ◽  
Trinad Chakraborty ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Central India ◽  
Vaginal Swab ◽  
Comparative Genomic Analysis ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type

We present here the draft genome sequence of Listeria monocytogenes CIIMS-NV-3, a serovar 4b strain isolated from the vaginal swab of a female patient from central India. The availability of this genome may provide useful information on virulence characteristics for comparative genomic analysis.

scholarly journals Draft Genome Sequence of Vibrio vulnificus 86573B, a Bacterium Isolated from Diseased Tilapia in Taiwan

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Shu-Ting Cho ◽  
Yi-Ming Tsai ◽  
Chun-Yao Chen ◽  
Chih-Horng Kuo
Keyword(s):  
Genome Sequence ◽  
Vibrio Vulnificus ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type

Vibrio vulnificus 86573B is a biotype 1 strain isolated from a moribund tilapia collected in Kaohsiung, Taiwan, during an outbreak early in 1997. Here, we report the draft genome sequence of this bacterium to facilitate the investigation of its biology and future comparative genomic analysis.

scholarly journals Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Delong Meng ◽  
Xueduan Liu ◽  
Xing Li ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Resistance Genes ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Metal Resistance ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
History Of

ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

scholarly journals Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Minenosuke Matsutani ◽  
Nami Matsumoto ◽  
Hideki Hirakawa ◽  
Yuh Shiwa ◽  
Hirofumi Yoshikawa ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Content Type ◽  
Acetobacter Pasteurianus ◽  
Respiratory Chains

ABSTRACT Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na+/H+ antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na+/H+ antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains. IMPORTANCE Acetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains. The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na+/H+ antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.

scholarly journals Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India

2019 ◽  
Vol 8 (27) ◽  
Author(s):  
Amrita Salim ◽  
Pradeesh Babu ◽  
Keerthi Mohan ◽  
Manju Moorthy ◽  
Devika Raj ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type ◽  
E Coli

ABSTRACT We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.

scholarly journals Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

2016 ◽  
Vol 54 (12) ◽  
pp. 3010-3017 ◽  
Author(s):  
Fang Hu ◽  
Lavanya Rishishwar ◽  
Ambily Sivadas ◽  
Gabriel J. Mitchell ◽  
I. King Jordan ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Limit Of Detection ◽  
Genomic Analysis ◽  
Invasive Disease ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Nontypeable Haemophilus Influenzae ◽  
Content Type ◽  
Testing Scheme ◽  
Pcr Targeting

Haemophilushaemolyticushas been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeableHaemophilus influenzae(NTH. influenzae). NTH. influenzaeandH. haemolyticusare often misidentified because none of the existing tests targeting the known phenotypes ofH. haemolyticusare able to specifically identifyH. haemolyticus. Through comparative genomic analysis ofH. haemolyticusand NTH. influenzae, we identified genes unique toH. haemolyticusthat can be used as targets for the identification ofH. haemolyticus. A real-time PCR targetingpurT(encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detectingH. haemolyticuswere 98.9% and 97%, respectively. To improve the discrimination ofH. haemolyticusand NTH. influenzae, a testing scheme combining two targets (H. haemolyticuspurTandH. influenzaehpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification ofH. haemolyticusand 92.8% sensitivity and 100% specificity for the identification ofH. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused byH. haemolyticusand NTH. influenzae.

scholarly journals Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificity

2011 ◽  
Vol 193 (22) ◽  
pp. 6342-6357 ◽  
Author(s):  
Neha Jalan ◽  
Valente Aritua ◽  
Dibyendu Kumar ◽  
Fahong Yu ◽  
Jeffrey B. Jones ◽  
...  
Keyword(s):  
Host Range ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Bacterial Spot ◽  
Content Type ◽  
Xanthomonas Axonopodis ◽  
Bacterial Spot Disease

Xanthomonas axonopodispv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence ofX. axonopodispv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrusXanthomonaspathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogenX. campestrispv. vesicatoria 85-10, with a completely different host range. We also comparedX. axonopodispv. citrumelo to the genome of citrus canker pathogenX. axonopodispv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition topthA, effectors such asxopE3, xopAI, andhrpWwere absent fromX. axonopodispv. citrumelo while present inX. axonopodispv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that ofX. axonopodispv. citri. We also identified unique effectors inX. axonopodispv. citrumelo that may be related to the different host range as compared to that ofX. axonopodispv. citri.X. axonopodispv. citrumelo also lacks various genes, such assyrE1, syrE2, and RTX toxin family genes, which were present inX. axonopodispv. citri. These may be associated with the distinct virulences ofX. axonopodispv. citrumelo andX. axonopodispv. citri. Comparison of the complete genome sequence ofX. axonopodispv. citrumelo to those ofX. axonopodispv. citri andX. campestrispv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.

Sign in / Sign up

Export Citation Format

Share Document