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 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):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

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 flagella is highly energy intensive and therefore 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 predicted 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 the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of 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 Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A. Coutinho
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

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 flagella is highly energy intensive and therefore 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 predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~ 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 the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of 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 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):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

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 flagella is highly energy intensive and therefore 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 predicted 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 the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of 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 Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-Lactamases in Klebsiella pneumoniae

2007 ◽  
Vol 51 (8) ◽  
pp. 3004-3007 ◽  
Author(s):  
Ying-Tsong Chen ◽  
Tsai-Ling Lauderdale ◽  
Tsai-Lien Liao ◽  
Yih-Ru Shiau ◽  
Hung-Yu Shu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses ◽  
The Common

ABSTRACT A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3 extended-spectrum β-lactamases in the common backbone of IncHI2 plasmids. Mechanisms for dissemination of the resistance genes are highlighted in comparative genomic analyses.

scholarly journals A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:-

2018 ◽  
Vol 9 ◽  
Author(s):  
Eleonora Mastrorilli ◽  
Daniele Pietrucci ◽  
Lisa Barco ◽  
Serena Ammendola ◽  
Sara Petrin ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Ecological Success

scholarly journals Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Seung Woo Ahn ◽  
Se Hee Lee ◽  
Hong-Seok Son ◽  
Seong Woon Roh ◽  
Yoon-E Choi
Keyword(s):  
Phylogenetic Analysis ◽  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Antibiotic Resistance Gene ◽  
Genomic Analysis ◽  
Halophilic Bacterium ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Analyses

Abstract Background Lentibacillus species are gram variable aerobic bacteria that live primarily in halophilic environments. Previous reports have shown that bacteria belonging to this species are primarily isolated from salty environments or food. We isolated a bacterial strain CBA3610, identified as a novel species of the genus Lentibacillus, from a human fecal sample. In this report, the whole genome sequence of Lentibacillus sp. CBA3610 is presented, and genomic analyses are performed. Results Complete genome sequence of strain CBA3610 was obtained through PacBio RSII and Illumina HiSeq platforms. The size of genome is 4,035,571 bp and genes estimated to be 4714 coding DNA sequences and 64 tRNA and 17 rRNA were identified. The phylogenetic analysis confirmed that it belongs to the genus Lentibacillus. In addition, there were genes related to antibiotic resistance and virulence, and genes predicted as CRISPR and prophage were also identified. Genes related to osmotic stress were found according to the characteristics of halophilic bacterium. Genomic differences from other Lentibacillus species were also confirmed through comparative genomic analysis. Conclusions Strain CBA3610 is predicted to be a novel candidate species of Lentibacillus through phylogenetic analysis and comparative genomic analysis with other species in the same genus. This strain has antibiotic resistance gene and pathogenic genes. In future, the information derived from the results of several genomic analyses of this strain is thought to be helpful in identifying the relationship between halophilic bacteria and human gut microbiota.

scholarly journals Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

2021 ◽  
Author(s):  
Claudio Montenegro ◽  
Livia Martins ◽  
Fernanda de Oliveira Bustamante ◽  
Ana Christina Brasileiro-Vidal ◽  
Andrea Pedrosa-Harand
Keyword(s):  
Genomic Analysis ◽  
In Silico Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Orthologous Genes ◽  
Genomic Analyses ◽  
Genomic Studies ◽  
Macroptilium Atropurpureum ◽  
Evolutionary New Centromeres ◽  
Silico Analysis

The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicated the preservation of large genomic blocks in legumes. However, the chromosome dynamics along its evolution was not investigated in the tribe. We conducted a comparative genomic analysis using CoGe Synmap platform to define a useful genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes (n = 11), then searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus, n = 11) and Glycininae (Amphicarpaea edgeworthii, n = 11 and Spatholobus suberectus, n = 9) subtribes, and in the outgroup (Medicago truncaluta, n = 8). To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of the non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureusi, n = 11). We inferred the APK with n = 11, 22 GBs (A to V) and 60 sub-GBs. We hypothesized that the main rearrangements within Phaseolinae involved nine APK chromosomes, with extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. We demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstructed the main events responsible for the chromosome number reduction. The development of the GB system and the proposed APK provide useful tools for future comparative genomic analyses of legume species.

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 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 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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