scholarly journals Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

2018 ◽  
Author(s):  
Sarbashis Das ◽  
B. M. Fredrik Pettersson ◽  
Phani Rama Krishna Behra ◽  
Amrita Mallick ◽  
Martin Cheramie ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Skin Lesions ◽  
Comparative Genomic Analysis ◽  
Mycobacterium Marinum ◽  
Genomic Diversity ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Separate Species ◽  
Mutational Hotspots

AbstractMycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the “M”- and the “Aronson”-type. We suggest that these two clusters should be considered, if not two separate species, at least two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to that M. marinum occupy different ecological niches.

scholarly journals Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production

2019 ◽  
Vol 19 (4) ◽  
Author(s):  
Débora Trichez ◽  
Andrei S Steindorff ◽  
Carlos E V F Soares ◽  
Eduardo F Formighieri ◽  
João R M Almeida
Keyword(s):  
Renewable Resources ◽  
Xylose Reductase ◽  
Genomic Analysis ◽  
Product Yield ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Brazilian Cerrado ◽  
Genome Sequences ◽  
Yeast Strains ◽  
Spathaspora Passalidarum

ABSTRACT Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.

scholarly journals The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

2008 ◽  
Vol 190 (20) ◽  
pp. 6881-6893 ◽  
Author(s):  
David A. Rasko ◽  
M. J. Rosovitz ◽  
Garry S. A. Myers ◽  
Emmanuel F. Mongodin ◽  
W. Florian Fricke ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Whole Genome ◽  
E Coli ◽  
Important Group ◽  
Commensal Species

ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

scholarly journals Comparative Genomic Analysis ofLactococcus garvieaeStrains Isolated from Different Sources Reveals Candidate Virulence Genes

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Eiji Miyauchi ◽  
Hidehiro Toh ◽  
Akiyo Nakano ◽  
Soichi Tanabe ◽  
Hidetoshi Morita
Keyword(s):  
Gene Cluster ◽  
Host Specificity ◽  
Virulence Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Pathogenic Strain ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Lactococcus Garvieae ◽  
Different Sources

Lactococcus garvieaeis a major pathogen for fish. Two complete (ATCC 49156 and Lg2) and three draft (UNIUD074, 8831, and 21881) genome sequences ofL. garvieaehave recently been released. We here present the results of a comparative genomic analysis of these fish and human isolates ofL. garvieae. The pangenome comprised 1,542 core and 1,378 dispensable genes. The sequencedL. garvieaestrains shared most of the possible virulence genes, but the capsule gene cluster was found only in fish-pathogenic strain Lg2. The absence of the capsule gene cluster in other nonpathogenic strains isolated from mastitis and vegetable was also confirmed by PCR. The fish and human isolates ofL. garvieaecontained the specific two and four adhesin genes, respectively, indicating that these adhesion proteins may be involved in the host specificity differences ofL. garvieae. The discoveries revealed by the pangenomic analysis may provide significant insights into the biology ofL. garvieae.

scholarly journals Unexpected and widespread connections between bacterial glycogen and trehalose metabolism

Microbiology ◽  
2011 ◽  
Vol 157 (6) ◽  
pp. 1565-1572 ◽  
Author(s):  
Govind Chandra ◽  
Keith F. Chater ◽  
Stephen Bornemann
Keyword(s):  
Drug Target ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Classical Pathway ◽  
Outer Capsule ◽  
Trehalose Metabolism ◽  
Glucan Synthesis

Glycogen, a large α-glucan, is a ubiquitous energy storage molecule among bacteria, and its biosynthesis by the classical GlgC-GlgA pathway and its degradation have long been well understood – or so we thought. A second pathway of α-glucan synthesis, the four-step GlgE pathway, was recently discovered in mycobacteria. It requires trehalose as a precursor, and has been genetically validated as a novel anti-tuberculosis drug target. The ability to convert glycogen into trehalose was already known, so the GlgE pathway provides a complementary way of cycling these two metabolites. As well as containing cytosolic storage glycogen, mycobacteria possess an outer capsule containing a glycogen-like α-glucan that is implicated in immune system evasion, so the GlgE pathway might be linked to capsular α-glucan biosynthesis. Another pathway (the Rv3032 pathway) for α-glucan biosynthesis in mycobacteria generates a methylglucose lipopolysaccharide thought to be associated with fatty acid metabolism. A comparative genomic analysis was carried out to evaluate the occurrence and role of the classical pathway, the new GlgE pathway and the Rv3032 pathway across bacteria occupying very different ecological niches. The GlgE pathway is represented in 14 % of sequenced genomes from diverse bacteria (about half as common as the classical pathway), while the Rv3032 pathway is restricted with few exceptions to mycobacteria, and the GlgB branching enzyme, usually presumed to be associated with the classical pathway, correlates more strongly with the new GlgE pathway. The microbiological implications of recent discoveries in the light of the comparative genomic analysis are discussed.

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 Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yoshitaka Tateishi ◽  
Yuriko Ozeki ◽  
Akihito Nishiyama ◽  
Mari Miki ◽  
Ryoji Maekura ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Mycobacterium Intracellulare ◽  
Clinical Strains ◽  
Genetic Components ◽  
Genomic Regions ◽  
Insight Into

Abstract Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

scholarly journals Genomic Analysis of Prophages Recovered from Listeria monocytogenes Lysogens Found in Seafood and Seafood-Related Environment

2021 ◽  
Vol 9 (7) ◽  
pp. 1354
Author(s):  
Hue Thi Kim Vu ◽  
Matthew J. Stasiewicz ◽  
Soottawat Benjakul ◽  
Kitiya Vongkamjan
Keyword(s):  
Mitomycin C ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Sequence Comparisons ◽  
Related Sequence ◽  
Geographical Regions ◽  
Insertion Sites ◽  
The Impact

A prophage is a phage-related sequence that is integrated into a bacterial chromosome. Prophages play an important role in bacterial evolution, survival, and persistence. To understand the impact of Listeria prophages on their host genome organizations, this work sequenced two L. monocytogenes strains (134LM and 036LM), previously identified as lysogens by mitomycin C induction. Draft genomes were generated with assembly sizes of 2,953,877 bp and 3,000,399 bp. One intact prophage (39,532 bp) was inserted into the comK gene of the 134LM genome. Two intact prophages (48,684 bp and 39,488 bp) were inserted in tRNA-Lys and elongation-factor genes of the 036LM genome. The findings confirmed the presence of three corresponding induced phages previously obtained by mitomycin C induction. Comparative genomic analysis of three prophages obtained in the newly sequenced lysogens with 61 prophages found in L. monocytogenes genomes, available in public databases, identified six major clusters using whole genome-based phylogenetic analysis. The results of the comparative genomic analysis of the prophage sequences provides knowledge about the diversity of Listeria prophages and their distribution among Listeria genomes in diverse environments, including different sources or geographical regions. In addition, the prophage sequences and their insertion sites contribute to the genomic diversity of L. monocytogenes genomes. These data of prophage sequences, prophage insertion sites, and prophage sequence comparisons, together with ANIb confirmation, could be useful for L. monocytogenes classification by prophages. One potential development could be refinement of prophage typing tools for monitoring or surveillance of L. monocytogenes contamination and transmission.

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.

Sign in / Sign up

Export Citation Format

Share Document