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

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.

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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

Microbiology Resource Announcements ◽

10.1128/mra.01457-19 ◽

2020 ◽

Vol 9 (6) ◽

Cited By ~ 1

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.

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Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

Frontiers in Microbiology ◽

10.3389/fmicb.2020.01273 ◽

2020 ◽

Vol 11 ◽

Author(s):

Misti D. Finton ◽

Roger Meisal ◽

Davide Porcellato ◽

Lin T. Brandal ◽

Bjørn-Arne Lindstedt

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome ◽

University Campus ◽

Bacterial Strains

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Whole-genome Sequencing of Two Streptomyces Strains Isolated From Sand Dunes of Sahara

10.21203/rs.3.rs-96085/v1 ◽

2020 ◽

Author(s):

Chahira Zerouki ◽

Farid Bensalah ◽

Suvi Kuittinen ◽

Ari Pappinen ◽

Ossi Turunen

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uv Light ◽

Sand Dunes ◽

Gene Clusters ◽

Extreme Environment ◽

Whole Genome ◽

16S Rrna Sequence ◽

Algerian Sahara ◽

Genome Duplications

Abstract Background. Sahara is one of the largest deserts in the world. The hard conditions especially high temperature and aridity lead to unique adaptation of organisms that could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening the antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study the desert Streptomyces microbiology and ecology from genomic perspective. Results. The strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequence as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed by using Pacific Biosciences Sequel II technology (PacBio) and it showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified proteins is 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17 and no genome duplications were detected in the two strains. Although the strains have different phenotypes and are from different regions, they are slightly different from each other in protein sequence level but, differ more from their earlier published relatives. 29 biosynthetic gene clusters (BGCs) coding for secondary metabolites were predicted in each strain indicating antifungal, antibiotic, and other activities of Babs14 and Osf17. Moreover, many other BGCs were related to biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. Conclusion. The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information gives tools to study the ecological adaptation in desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first ones for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to explore more profoundly the desert microbiome.

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Bacillus velezensis UTB96 Is an Antifungal Soil Isolate with a Reduced Genome Size Compared to That of Bacillus velezensis FZB42

Microbiology Resource Announcements ◽

10.1128/mra.00667-19 ◽

2019 ◽

Vol 8 (38) ◽

Author(s):

Maliheh Vahidinasab ◽

Masoud Ahmadzadeh ◽

Marius Henkel ◽

Rudolf Hausmann ◽

Kambiz Morabbi Heravi

Keyword(s):

Antifungal Activity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Gene Clusters ◽

Type I ◽

Whole Genome ◽

Bacillus Velezensis ◽

Content Type ◽

Reduced Genome ◽

Soil Isolate

Bacillus velezensis UTB96 was isolated from soil based on its antifungal activity. Whole-genome sequencing of strain UTB96 provided further information about its secondary metabolite gene clusters. Compared to the well-known strain FZB42, UTB96 lacks an IS3 element and a type I restriction endonuclease.

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

BMJ Global Health ◽

10.1136/bmjgh-2019-002244 ◽

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.

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Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome

Natural Product Reports ◽

10.1039/d0np00007h ◽

2020 ◽

Vol 37 (9) ◽

pp. 1164-1180 ◽

Cited By ~ 3

Author(s):

Liwen Zhang ◽

Qun Yue ◽

Chen Wang ◽

Yuquan Xu ◽

István Molnár

Keyword(s):

Secondary Metabolites ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bioactive Compounds ◽

Entomopathogenic Fungi ◽

Gene Clusters ◽

Whole Genome ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters

Whole genome sequencing allows the cataloguing of the parvome (secondary metabolome) of hypocrealean entomopathogenic fungi, uncovering biosynthetic gene clusters for known and novel bioactive compounds with ecological and pharmaceutical significance.

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Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

Microbiology Spectrum ◽

10.1128/spectrum.00533-21 ◽

2021 ◽

Author(s):

Mostafa Y. Abdel-Glil ◽

Prasad Thomas ◽

Jörg Linde ◽

Keith A. Jolley ◽

Dag Harmsen ◽

...

Keyword(s):

High Resolution ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clostridium Perfringens ◽

Multilocus Sequence Typing ◽

Core Genome ◽

Epidemiological Surveillance ◽

Whole Genome ◽

Bacterial Strains

Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels.

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Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara

BMC Genomics ◽

10.1186/s12864-021-07866-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Chahira Zerouki ◽

Farid Bensalah ◽

Suvi Kuittinen ◽

Ari Pappinen ◽

Ossi Turunen

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uv Light ◽

Sand Dunes ◽

Gene Clusters ◽

Extreme Environment ◽

Climatic Conditions ◽

Whole Genome ◽

Protein Coding ◽

Algerian Sahara

Abstract Background Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective. Results Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. Conclusion The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.

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