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

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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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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Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽

10.1016/j.ygeno.2020.05.004 ◽

2020 ◽

Vol 112 (5) ◽

pp. 2915-2921 ◽

Cited By ~ 2

Author(s):

Thiago Mafra Batista ◽

Heron Oliveira Hilario ◽

Gabriel Antônio Mendes de Brito ◽

Rennan Garcias Moreira ◽

Carolina Furtado ◽

...

Keyword(s):

Secondary Metabolites ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Binding Protein ◽

Protein A ◽

Gene Clusters ◽

Whole Genome ◽

Ice Binding ◽

Ice Binding Protein

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

Marine Genomics ◽

10.1016/j.margen.2020.100782 ◽

2020 ◽

Vol 54 ◽

pp. 100782 ◽

Cited By ~ 1

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

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Whole-Genome Sequencing of Lentibacillus sp. Strain JNUCC-1, Isolated from Fermented Anchovy Sauce (Myeolchi Aekjeot)

Microbiology Resource Announcements ◽

10.1128/mra.01542-19 ◽

2020 ◽

Vol 9 (15) ◽

Author(s):

Hoo-Dhon Byun ◽

Chang-Gu Hyun

Keyword(s):

16S Rrna ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Novel Species ◽

Whole Genome Sequence ◽

Whole Genome ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Content Type ◽

Anchovy Sauce

Lentibacillus sp. strain JNUCC-1 was isolated from Korean traditionally fermented anchovy sauce. The 16S rRNA sequence of JNUCC-1 showed 95.2% and 95.1% similarity to Lentibacillus populi WD4L-1T and Virgibacillus siamensis MS3-4T, respectively, indicating that it is a novel species. The whole-genome sequence, which contains 3,687,469 bp and 3,833 genes in 3 contigs, is reported.

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Can multidrug-resistant organisms become resistant to ultraviolet (UV) light following serial exposures? Characterization of post-UV genomic changes using whole-genome sequencing

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.51 ◽

2021 ◽

pp. 1-7

Author(s):

Hosoon Choi ◽

Piyali Chatterjee ◽

Munok Hwang ◽

Eileen M. Stock ◽

Janell S. Lukey ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uv Light ◽

Multidrug Resistant ◽

Uv Disinfection ◽

Whole Genome ◽

Uv Resistance ◽

Kill Rate ◽

Uv Lamp

Abstract Objectives: No-touch disinfection systems like xenon- or mercury-based ultraviolet (UV) are now commonly being used for hospital room disinfection. However, serial exposure to UV light can potentially lead to the development of bacterial resistance. We sought to determine whether UV resistance develops due to serial exposure to UV light using 3 epidemiologically important multidrug-resistant microbial strains. Methods: Methicillin-resistant Staphylococcus aureus (MRSA), carbapenemase–producing Klebsiella pneumoniae (KPC) and metallo-β-lactamase–producing Klebsiella pneumoniae (MBL) were serially exposed to 25 growth-irradiation cycles of UV produced by a xenon-based UV (Xe-UV) lamp for 5 minutes or a mercury-based UV (Hg-UV) lamp for 10 minutes. After each UV exposure cycle, the surviving colony-forming units (CFUs) were measured and compared with the initial inoculum of each cycle for each strain, respectively. Results: In each cycle, ˜1–10 million of MRSA, KPC, and MBL were used to test the effect of UV irradiation. Postexposure colony counts remained low (3–100 colonies) throughout the 25 serial exposures to both xenon- and mercury-based UV. The log-kill rate after each exposure showed no changes following UV disinfection by Xe-UV. The MRSA log-kill rate increased after repeated exposure to Hg-UV unlike KPC and MBL K. pneumoniae, which did not change. Whole-genome sequencing (WGS) analyses performed on these 3 strains demonstrated no significant genetic changes after multiple UV irradiation cycles. Conclusions: Exposure of multidrug-resistant bacteria to UV produced from 2 different UV sources did not engender UV resistance after 25 serial exposures, as demonstrated by WGS analysis; thus, UV disinfection is unlikely to generate UV-resistant hospital flora.

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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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