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 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 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 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 genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible

2021 ◽  
pp. 100015
Author(s):  
Eamon O. Murchu ◽  
Sinead O'Neill ◽  
Paula Byrne ◽  
Cillian De Gascun ◽  
Michelle O'Neill ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

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