scholarly journals Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis

BMC Genetics ◽  
2020 ◽  
Vol 21 (S2) ◽  
Author(s):  
Zhaohui Cai ◽  
Qiongyu Guo ◽  
Zhichao Yao ◽  
Wenping Zheng ◽  
Junfei Xie ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Type Strain ◽  
Bactrocera Dorsalis ◽  
Symbiotic Relationship ◽  
Comparative Genome Analysis ◽  
Circular Chromosome ◽  
Comparative Genome ◽  
Ecological Fitness ◽  
Pan Genome

Abstract Background Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to control insect pests of agricultural, veterinary, and human health importance. Irradiation of pupae in SIT can reduce the ecological fitness of the sterile insects. Our previous study has shown that a gut bacterial strain BD177 that could restore ecological fitness by promoting host food intake and metabolic activities. Results Using long-read sequence technologies, we assembled the complete genome of K. michiganensis BD177 strain. The complete genome of K. michiganensis BD177 comprises one circular chromosome and four plasmids with a GC content of 55.03%. The pan-genome analysis was performed on 119 genomes (strain BD177 genome and 118 out of 128 published Klebsiella sp. genomes since ten were discarded). The pan-genome includes a total of 49305 gene clusters, a small number of 858 core genes, and a high number of accessory (10566) genes. Pan-genome and average nucleotide identity (ANI) analysis showed that BD177 is more similar to the type strain K. michiganensis DSM2544, while away from the type strain K. oxytoca ATCC13182. Comparative genome analysis with 21 K. oxytoca and 12 K. michiganensis strains, identified 213 unique genes, several of them related to amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotics biodegradation and metabolism in BD177 genome. Conclusions Phylogenomics analysis reclassified strain BD177 as a member of the species K. michiganensis. Comparative genome analysis suggested that K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis. The clear classification status of BD177 strain and identification of unique genetic characteristics may contribute to expanding our understanding of the symbiotic relationship of gut microbiota and B. dorsalis.

scholarly journals Comparative Genome Analysis of a Pathogenic Erysipelothrix rhusiopathiae Isolate WH13013 from Pig Reveals Potential Genes Involve in Bacterial Adaptions and Pathogenesis

2020 ◽  
Vol 7 (2) ◽  
pp. 74
Author(s):  
Longsheng Yang ◽  
Yongwei Zhu ◽  
Zhong Peng ◽  
Yi Ding ◽  
Kai Jie ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Erysipelothrix Rhusiopathiae ◽  
Comparative Genome Analysis ◽  
Circular Chromosome ◽  
Comparative Genome ◽  
Virulent Strains ◽  
Core Genes

Erysipelothrix rhusiopathiae is a common pathogen responsible for pig erysipelas. However, the molecular basis for the pathogenesis of E. rhusiopathiae remains to be elucidated. In this study, the complete genome sequence of the E. rhusiopathiae strain WH13013, a pathogenic isolate from a diseased pig, was generated using a combined strategy of PacBio RSII and Illumina sequencing technologies. The strategy finally generated a single circular chromosome of approximately 1.78 Mb in size for the complete genome of WH13013, with an average GC content of 36.49%. The genome of WH13013 encoded 1633 predicted proteins, 55 tRNAs, as well as 15 rRNAs. It contained four genomic islands and several resistance-associated genes were identified within these islands. Phylogenetic analysis revealed that WH13013 was close to many other sequenced E. rhusiopathiae virulent strains. The comprehensive comparative analysis of eight E. rhusiopathiae virulent strains, including WH13013, identified a total of 1184 core genes. A large proportion (approximately 75.31%) of these core genes participated in nutrition and energy uptake and metabolism as well as the other bioactivities that are necessary for bacterial survival and adaption. The core genes also contained those encoding proteins participating in the biosynthesis and/or the components of the proposed virulence factors of E. rhusiopathiae, including the capsule (cpsA, cpsB, cpsC), neuraminidase (nanH), hyaluronidase (hylA, hylB, hylC), and surface proteins (spaA, rspA, rspB). The obtaining of the complete genome sequence of this virulent strain, WH13013, and this comprehensive comparative genome analysis will help in further studies of the genetic basis of the pathogenesis of E. rhusiopathiae.

scholarly journals Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse  KZ-Related Phages

2011 ◽  
Vol 86 (3) ◽  
pp. 1844-1852 ◽  
Author(s):  
A. Cornelissen ◽  
S. C. Hardies ◽  
O. V. Shaburova ◽  
V. N. Krylov ◽  
W. Mattheus ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Giant Virus ◽  
Comparative Genome Analysis ◽  
Comparative Genome

Complete genome sequence and comparative genome analysis of Streptococcus parauberis KCTC11980

2015 ◽  
Vol 37 (11) ◽  
pp. 959-968
Author(s):  
Jung Soo Seo ◽  
Mun Gyeong Kwon ◽  
Jee Youn Hwang ◽  
Sung Hee Jung ◽  
Hyun Ja Han ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Streptococcus Parauberis

scholarly journals Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10185
Author(s):  
Romen Singh Naorem ◽  
Jochen Blom ◽  
Csaba Fekete
Keyword(s):  
Genome Analysis ◽  
Genetic Background ◽  
Multiple Drug Resistance ◽  
Clinical Isolates ◽  
Ecological Niches ◽  
Comparative Genome Analysis ◽  
Pathogenic Potential ◽  
Comparative Genome ◽  
Pan Genome ◽  
Niche Adaptation

Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.

scholarly journals Complete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces

2020 ◽  
Vol 16 ◽  
pp. 117693432094219
Author(s):  
Su Xu ◽  
Jianjun Cheng ◽  
Xiangchen Meng ◽  
Yan Xu ◽  
Ying Mu
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Genetic Basis ◽  
Lactobacillus Reuteri ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Orthologous Group ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Fresh Feces

Lactobacillus reuteri YSJL-12 was isolated from healthy sow fresh feces and used as probiotics additives previously. To investigate the genetic basis on probiotic potential and identify the genes in the strain, the complete genome of YSJL-12 was sequenced. Then comparative genome analysis on 9 strains of Lactobacillus reuteri was performed. The genome of YSJL-12 consisted of a circular 2,084,748 bp chromosome and 2 circular plasmids (51,906 and 15,134 bp). From among the 2065 protein-coding sequences (CDSs), the genes resistant to the environmental stress were identified. The function of COG (Clusters of Orthologous Group) protein genes was predicted, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were analyzed. The comparative genome analysis indicated that the pan-genome contained a core genome of 1257 orthologous gene clusters, an accessory genome of 1064 orthologous gene clusters, and 1148 strain-specific genes, and the antibacterial mechanism among Lactobacillus reuteri strains might be different. The phylogenetic analysis and genomic collinearity revealed that the phylogenetic relationship among 9 strains of Lactobacillus reuteri was connected with host species and showed host specificity. The research could help us to better predict genes function and understand genetic basis on adapting to host gut in Lactobacillus reuteri YSJL-12.

Sign in / Sign up

Export Citation Format

Share Document