scholarly journals Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus

2021 ◽  
Vol 9 (9) ◽  
pp. 1992
Author(s):  
Zheng Huang ◽  
Xingya Zhou ◽  
Catherine Stanton ◽  
Reynolds Paul Ross ◽  
Jianxin Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Lactobacillus Acidophilus ◽  
Genome Comparison ◽  
Fermented Foods ◽  
Whole Genome ◽  
Human Gastrointestinal Tract ◽  
Characteristics Analysis ◽  
Whole Genome Comparison ◽  
The Difference

Lactobacillus acidophilus is a common kind of lactic acid bacteria usually found in the human gastrointestinal tract, oral cavity, vagina, and various fermented foods. At present, many studies have focused on the probiotic function and industrial application of L. acidophilus. Additionally, dozens of L. acidophilus strains have been genome sequenced, but there has been no research to compare them at the genomic level. In this study, 46 strains of L. acidophilus were performed comparative analyses to explore their genetic diversity. The results showed that all the L. acidophilus strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition of bacteriocin operon, CRISPR-Cas systems and prophages mainly. Additionally, L. acidophilus was a pan-genome open species with a difference in carbohydrates utilization, antibiotic resistance, EPS operon, surface layer protein operon and other functional gene composition. This work provides a better understanding of L. acidophilus from a genetic perspective, and offers a frame for the biotechnological potentiality of this species.

scholarly journals Whole genome comparison of donor and cloned dogs

2013 ◽  
Vol 3 (1) ◽  
Author(s):  
Hak-Min Kim ◽  
Yun Sung Cho ◽  
Hyunmin Kim ◽  
Sungwoong Jho ◽  
Bongjun Son ◽  
...  
Keyword(s):  
Genome Comparison ◽  
Whole Genome ◽  
Whole Genome Comparison

scholarly journals Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

2021 ◽  
Author(s):  
Qian Yang ◽  
Dongmei Yan ◽  
Yang Song ◽  
Shuangli Zhu ◽  
Yun He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Foot And Mouth Disease ◽  
Coxsackievirus B3 ◽  
Whole Genome ◽  
Nucleotide Substitution Rate ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Heavy Burden ◽  
Group D

Abstract Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

scholarly journals Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy

2011 ◽  
Vol 66 (7) ◽  
pp. 1499-1503 ◽  
Author(s):  
Michael Hornsey ◽  
Nick Loman ◽  
David W. Wareham ◽  
Matthew J. Ellington ◽  
Mark J. Pallen ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Genome Comparison ◽  
Whole Genome ◽  
Single Patient ◽  
Whole Genome Comparison
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