scholarly journals Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siham Fatani ◽  
Yoshimoto Saito ◽  
Mohammed Alarawi ◽  
Takashi Gojobori ◽  
Katsuhiko Mineta
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Plant Biomass ◽  
Seawater Temperature ◽  
Cellulase Activity ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Isolation And Characterization ◽  
Bacillus Paralicheniformis

Abstract Background Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. Results Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. Conclusions Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.

First isolation and characterization of Brucella suis from yak

Genome ◽  
2020 ◽  
Vol 63 (8) ◽  
pp. 397-405
Author(s):  
Xiaowen Yang ◽  
Ning Wang ◽  
Xiaofang Cao ◽  
Pengfei Bie ◽  
Zhifeng Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health And Safety ◽  
Host Cells ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Qinghai Province ◽  
Isolation And Characterization ◽  
Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

scholarly journals Isolation and Whole-Genome Sequencing of 12 Mushroom-Associated Bacterial Strains: an Inquiry-Based Laboratory Exercise in a Genomics Course at the Rochester Institute of Technology

2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Narayan H. Wong ◽  
Andrew J. Rosato ◽  
Yara M. Rose ◽  
Trevor S. Penix ◽  
Janice B. Fung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Life Sciences ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Mushroom Species ◽  
Laboratory Exercise ◽  
Rochester Institute Of Technology ◽  
Institute Of Technology

Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology.

Isolation and characterisation of an ISKNV-genotype megalocytivirus from imported angelfish Pterophyllum scalare

2020 ◽  
Vol 140 ◽  
pp. 129-141
Author(s):  
Y Kawato ◽  
PG Mohr ◽  
MStJ Crane ◽  
LM Williams ◽  
MJ Neave ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Sea Bream ◽  
Whole Genome ◽  
Red Sea Bream ◽  
Capsid Protein Gene ◽  
Infected Cells ◽  
Clade 1 ◽  
Pterophyllum Scalare

Using cultures of the SKF-9 cell line, megalocytivirus AFIV-16 was isolated from imported angelfish Pterophyllum scalare held in quarantine at the Australian border. The cytopathic effect caused by isolate AFIV-16 presented as cell rounding and enlargement, but complete destruction of the infected cell cultures did not occur. The infected cells demonstrated immunocytochemical reactivity with monoclonal antibody M10, which is used for diagnosis of OIE-listed red sea bream iridoviral disease. Using electron microscopy, the virus particles, consisting of hexagonal nucleocapsids, were observed in the cytoplasm of SKF-9 cells. The replication of AFIV-16 in cultured SKF-9 cells was significantly greater at 28°C incubation than at 22 and 25°C incubation, whereas no difference in growth characteristics was observed for red sea bream iridovirus (RSIV) isolate KagYT-96 across this temperature range. Whole genome sequencing demonstrated that AFIV-16 has a 99.96% similarity to infectious spleen and kidney necrosis virus (ISKNV), the type species in the genus Megalocytivirus. AFIV-16 was classified into ISKNV genotype Clade 1 by phylogenetic analysis of the major capsid protein gene nucleotide sequence. This is the first report of whole genome sequencing of an ISKNV genotype megalocytivirus isolated from ornamental fish.

scholarly journals Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

2020 ◽  
Vol 54 ◽  
pp. 100782 ◽  
Author(s):  
Wael M. Abdel-Mageed ◽  
Burhan Lehri ◽  
Scott A. Jarmusch ◽  
Kevin Miranda ◽  
Lamya H. Al-Wahaibi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gene Clusters ◽  
Environmental Adaptation ◽  
Whole Genome ◽  
Bacterial Strains ◽  
South Shetland Trench

scholarly journals Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo-Hye Nam ◽  
DongAhn Yoo ◽  
Young-Ok Kim ◽  
Jung Youn Park ◽  
Younhee Shin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Artificial Selection ◽  
Sea Bream ◽  
Whole Genome ◽  
Red Sea Bream ◽  
Fish Farms ◽  
The Impact

scholarly journals Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

3 Biotech ◽  
2021 ◽  
Vol 11 (8) ◽  
Author(s):  
Soufiane Maski ◽  
Serigne Inssa Ngom ◽  
Bahia Rached ◽  
Taha Chouati ◽  
Mohamed Benabdelkhalek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Plant Cell Wall ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Draft Genome ◽  
Glycoside Hydrolases ◽  
Whole Genome ◽  
A Genome ◽  
Bacillus Paralicheniformis

AbstractThermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.

scholarly journals Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

2020 ◽  
Vol 5 (11) ◽  
pp. e002244
Author(s):  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Low Income ◽  
The Philippines ◽  
Surveillance Systems ◽  
Whole Genome ◽  
Global Public Health ◽  
Bacterial Strains

The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.

scholarly journals Campylobacter Phage Isolation and Characterization: What We Have Learned So Far

2019 ◽  
Vol 2 (1) ◽  
pp. 18 ◽  
Author(s):  
Claudia Jäckel ◽  
Jens Hammerl ◽  
Stefan Hertwig
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Molecular Analysis ◽  
Scientific Literature ◽  
Food Products ◽  
Research Field ◽  
Whole Genome ◽  
Isolation And Characterization ◽  
Long Time ◽  
Phage Isolation

Lytic Campylobacter phages, which can be used to combat this pathogen in animals and on food products, have been studied for more than 30 years. Though, due to some peculiarities of the phages, which hampered their isolation and particularly their molecular analysis for a long time, progress in this research field was rather slow. Meanwhile, the situation has changed and much more is known about the biology and genetics of those phages. In this article, we address specific issues that should be considered when Campylobacter phages are studied, starting with the isolation and propagation of the phages and ending with a thorough characterization including whole-genome sequencing. The basis for advice and recommendations given here is a careful review of the scientific literature and experiences that we have had ourselves with Campylobacter phages.

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