scholarly journals Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1504
Author(s):  
Wenwei Lu ◽  
Zhangming Pei ◽  
Mengning Zang ◽  
Yuan-kun Lee ◽  
Jianxin Zhao ◽  
...  
Keyword(s):  
Core Genome ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Bifidobacterium Bifidum ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Chinese Adults ◽  
Related Factors ◽  
Conserved Core ◽  
First Time

The potential probiotic benefits of Bifidobacterium bifidum have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of B. bifidum isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of B. bifidum. The phylogenetic tree results indicated that the phylogeny of B. bifidum may be related to the geographical features of its isolation source. B. bifidum was found to have an open pan-genome and a conserved core genome. The genetic diversity of B. bifidum is mainly reflected in carbohydrate metabolism- and immune/competition-related factors, such as the glycoside hydrolase gene family, bacteriocin operons, antibiotic resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Additionally, the type III A CRISPR-Cas system was discovered in B. bifidum for the first time. B. bifidum strains exhibited niche-specific characteristics, and the results of this study provide an improved understanding of the genetics of this species.

scholarly journals Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Jianchao Ying ◽  
Jun Ye ◽  
Teng Xu ◽  
Qian Wang ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Rhodococcus Equi ◽  
Comparative Genomic Analysis ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Studies ◽  
Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

scholarly journals Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

2015 ◽  
Vol 83 (12) ◽  
pp. 4896-4896
Author(s):  
Benard W. Kulohoma ◽  
Jennifer E. Cornick ◽  
Chrispin Chaguza ◽  
Feyruz Yalcin ◽  
Simon R. Harris ◽  
...  
Keyword(s):  
Common Core ◽  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

scholarly journals Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success ◽  
First Time

Abstract Background Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of these structures is highly energy intensive and as such flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report for the first time on the occurrence of two peritrichous flagellar loci in some enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.

scholarly journals Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 661 ◽  
Author(s):  
Nadezhda Chernysheva ◽  
Evgeniya Bystritskaya ◽  
Anna Stenkova ◽  
Ilya Golovkin ◽  
Olga Nedashkovskaya ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Active Enzyme ◽  
Comparative Genomic ◽  
The Core ◽  
Pan Genome ◽  
Carbohydrate Active Enzyme ◽  
Pharmaceutical Industries

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

scholarly journals Comparative genomic analysis of Mycobacterium tuberculosis reveals evolution and genomic instability within Uganda I sub-lineage

2020 ◽  
Author(s):  
Stephen Kanyerezi ◽  
Patricia Nabisubi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Core Genome ◽  
Variant Calling ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genome Wide Association ◽  
Comparative Genomic ◽  
Pan Genome ◽  
Genome Wide

AbstractIntroductionTuberculosis (TB) is the leading cause of morbidity and mortality globally, responsible for an estimated annual 10.0 million new cases and 1.3 million deaths among infectious diseases with Africa contributing a quarter of these cases in 2019. Classification of Mycobacterium tuberculosis (MTB) strains is important in understanding their geographical predominance and pathogenicity. Different studies have gone ahead to classify MTB using different methods. Some of these include; RFLP, spoligotyping, MIRU-VNTR and SNP set based phylogeny. The SNP set based classification has been found to be in concordance with the region of difference (RD) analysis of MTB complex classification system. In Uganda, the most common cause of pulmonary tuberculosis (PTB) is Uganda genotype of MTB and accounts for up to 70 % of isolates.MethodsSequenced MTB genome samples were retrieved from NCBI and others from local sequencing projects. The genomes were subjected to snippy (a rapid haploid variant calling and core genome alignment) to call variants and annotate them. Outputs from snippy were used to classify the isolates into Uganda genotypes and Non Ugandan genotypes based on 62 SNP set. The Ugandan genotype isolates were later subjected to 413 SNP set and then to a pan genome wide association analysis.Results6 Uganda genotype isolates were found not to classify as either Uganda I or II genotypes based on the 62 SNP set. Using the 413 SNP set, the 6 Uganda genotype isolates were found to have only one SNP out of the 7 SNPs that classify the Uganda I genotypes. They were also found to have both missense and frameshift mutations within the ctpH gene whereas the rest of Uganda I that had a mutation within this gene, was a missense.ConclusionAmong the Uganda genotypes genomes, Uganda I genomes are unstable. We used publicly available datasets to perform analysis like mapping, variant calling, mixed infection, pan-genome analysis to investigate and compare evolution of the Ugandan genotype.

scholarly journals Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

2009 ◽  
Vol 191 (15) ◽  
pp. 4854-4862 ◽  
Author(s):  
Patricia Romero ◽  
Nicholas J. Croucher ◽  
N. Luisa Hiller ◽  
Fen Z. Hu ◽  
Garth D. Ehrlich ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Major Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Bioinformatic Tools ◽  
Dichelobacter Nodosus ◽  
First Time

ABSTRACT Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage φSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.

scholarly journals Genomic Features and Comparative Genomic Analysis of novel Bacillus glycinifermentans strain JRCGR-1

2021 ◽  
Author(s):  
Asad Karim ◽  
poirot olivier ◽  
Ambrina Khatoon ◽  
Matthieu Legendre
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Public Database ◽  
Genome Sequences ◽  
Genomic Features ◽  
The Public ◽  
Comparative Genomics Analysis ◽  
High Level

Abstract To the best of our knowledge, only six B. glycinifermentans sp. genome sequences are available in the public database. Here, we performed genome sequencing and comparative genomics analysis of B. glycinifermentans strain JRCGR-1. Cluster analysis of strain JRCGR-1 genes showed that 92.6% of genes were present in the orthogroups and 7.4% genes were not assigned to any group. The pangenome size was calculated at 8329 genes and presented an open genome characteristic. Phylogeny based on the pan and core genome demonstrated that all the B. glycinifermentans strains belong to the same clade. The strain JRCGR-1, ANI, TETRA and DDH values were in the range of 96.1-99.04%, 0.996-997, 73.5–84.7%, respectively. The strain JRCGR genome exhibits a high level of synteny with multiple locations in B. sonorensis sp. and B. licheniformis sp. The finding of the current study provides knowledge that facilitates a better understanding of this at the genomic level.

scholarly journals Comparative analysis of prophage-like elements inHelicobactersp. genomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2012 ◽  
Author(s):  
Xiangyu Fan ◽  
Yumei Li ◽  
Rong He ◽  
Qiang Li ◽  
Wenxing He
Keyword(s):  
Antibiotic Resistance ◽  
Comparative Analysis ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Bacterial Virulence ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Resistance Proteins ◽  
Cluster A ◽  
First Time

Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information onHelicobactersp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. Phylogenetic relationships of Cluster AHelicobacterprophages were investigated. Furthermore, genomes ofHelicobacterprophages from Clusters B, C, and D were analyzed. Interestingly, some putative antibiotic resistance proteins and virulence factors were associated withHelicobacterprophages.

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