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Article ; Online: Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa.

Laamarti, Meriem / El Fathi Lalaoui, Yasmine / Elfermi, Rachid / Daoud, Rachid / El Allali, Achraf

2023 Volume 10, Issue 1, Page(s) 212

Abstract: Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this ... ...

Abstract	Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this bacterium causes disease, how the immune system responds to it, how it has evolved over time, and how it is distributed geographically. However, despite extensive research efforts, the evolution and transmission of MTB in Africa remain poorly understood. In this study, we used 17,641 strains from 26 countries to create the first curated African Mycobacterium tuberculosis (MTB) classification and resistance dataset, containing 13,753 strains. We identified 157 mutations in 12 genes associated with resistance and additional new mutations potentially associated with resistance. The resistance profile was used to classify strains. We also performed a phylogenetic classification of each isolate and prepared the data in a format that can be used for phylogenetic and comparative analysis of tuberculosis worldwide. These genomic data will extend current information for comparative genomic studies to understand the mechanisms and evolution of MTB drug resistance.
MeSH term(s)	Humans ; Africa ; Genomics ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Tuberculosis/genetics ; Tuberculosis/drug therapy ; Genome, Bacterial
Language	English
Publishing date	2023-04-14
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02112-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa

Meriem Laamarti / Yasmine El Fathi Lalaoui / Rachid Elfermi / Rachid Daoud / Achraf El Allali

Scientific Data, Vol 10, Iss 1, Pp 1-

2023 Volume 7

Abstract: Abstract Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this ...

Abstract	Abstract Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this bacterium causes disease, how the immune system responds to it, how it has evolved over time, and how it is distributed geographically. However, despite extensive research efforts, the evolution and transmission of MTB in Africa remain poorly understood. In this study, we used 17,641 strains from 26 countries to create the first curated African Mycobacterium tuberculosis (MTB) classification and resistance dataset, containing 13,753 strains. We identified 157 mutations in 12 genes associated with resistance and additional new mutations potentially associated with resistance. The resistance profile was used to classify strains. We also performed a phylogenetic classification of each isolate and prepared the data in a format that can be used for phylogenetic and comparative analysis of tuberculosis worldwide. These genomic data will extend current information for comparative genomic studies to understand the mechanisms and evolution of MTB drug resistance.
Keywords	Science ; Q
Subject code	572
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.

Aminu, Suleiman / Ascandari, AbdulAziz / Laamarti, Meriem / Safdi, Nour El Houda / El Allali, Achraf / Daoud, Rachid

Critical reviews in microbiology

2023 , Page(s) 1–25

Abstract: The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables ... ...

Abstract	The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
Language	English
Publishing date	2023-11-25
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1053620-6
ISSN	1549-7828 ; 1040-841X
ISSN (online)	1549-7828
ISSN	1040-841X
DOI	10.1080/1040841X.2023.2282447
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Article ; Online: Draft Genome Sequences of Two Enterobacter hormaechei subsp.

Zouagui, Houda / Manni, Amina / Laamarti, Meriem / Kartti, Souad / Alouane, Tarek / Lahlou, Lamiaa / Benhrif, Oussama / Temsamani, Loubna / Eljamali, Jamal-Eddine / Filali-Maltouf, Abdelkarim / Ibrahimi, Azeddine / Sbabou, Laila

Microbiology resource announcements

2023 Volume 12, Issue 2, Page(s) e0108722

Abstract: We report the draft genome sequences of Enterobacter hormaechei subsp. ...

Abstract	We report the draft genome sequences of Enterobacter hormaechei subsp.
Language	English
Publishing date	2023-01-12
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.01087-22
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Article ; Online: Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits.

Laamarti, Meriem / Chemao-Elfihri, Mohammed Walid / Essabbar, Abdelmounim / Manni, Amina / Kartti, Souad / Alouane, Tarek / Temsamani, Loubna / Eljamali, Jamal-Eddine / Sbabou, Laila / Ouadghiri, Mouna / Filali-Maltouf, Abdelkarim / Belyamani, Lahcen / Ibrahimi, Azeddine

Functional & integrative genomics

2022 Volume 22, Issue 6, Page(s) 1173–1187

Abstract: Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, ... ...

Abstract	Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
MeSH term(s)	Phylogeny ; Genomics ; Bacillus/genetics ; Soil
Chemical Substances	Soil
Language	English
Publishing date	2022-09-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2014670-X
ISSN	1438-7948 ; 1438-793X
ISSN (online)	1438-7948
ISSN	1438-793X
DOI	10.1007/s10142-022-00905-0
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Article ; Online: Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits

Funct Integr Genomics. 2022 Dec., v. 22, no. 6 p.1173-1187

2022

Abstract	Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
Keywords	Bacillus safensis ; desert soils ; genome ; genomics ; nutrient deficiencies ; phylogeny ; soil salinity ; ultraviolet radiation ; Morocco
Language	English
Dates of publication	2022-12
Size	p. 1173-1187.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	2014670-X
ISSN	1438-7948 ; 1438-793X
ISSN (online)	1438-7948
ISSN	1438-793X
DOI	10.1007/s10142-022-00905-0
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Article ; Online: Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase

Chemao-Elfihri, Mohammed Walid / Hakmi, Mohammed / Essabbar, Abdelmounim / Manni, Amina / Laamarti, Meriem / Kartti, Souad / Alouane, Tarek / Temsamani, Loubna / Eljamali, Jamal-Eddine / Sbabou, Laila / Aanniz, Tarik / Ouadghiri, Mouna / Belyamani, Lahcen / Ibrahimi, Azeddine / Filali-Maltouf, Abdelkarim

Antonie van Leeuwenhoek. 2023 Jan., v. 116, no. 1 p.21-38

2023

Abstract: Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in ... ...

Abstract	Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in their habitat, which can be exploited in biotechnology. In this work, the genome of Paenibacillus sp. MDMC362 isolated from the Merzouga desert in Morocco was sequenced to understand its survival strategy's genetic basis; and to evaluate the thermostability of a catalase extracted from genomic annotation files using molecular dynamics. Paenibacillus sp. MDMC362 genome was rich in genetic elements involved in the fight against different stresses, notably temperature stress, UV radiations, osmotic stress, carbon starvation, and oxidative stress. Indeed, we could identify genes of the operons groES-groEL and hrcA-grpE-dnaK and those involved in the different stages of sporulation, which can help the bacteria to survive the high temperatures imposed by a desertic environment. We also observed the genetic components of the UvrABC system and additional mechanisms involved in DNA repair, which help overcome UV radiation damage. Other genes have been identified in the genome, like those coding for ectoine and proline, that aids fight osmotic stress and desiccation. Catalase thermostability investigation using molecular dynamics showed that the protein reached stability and conserved its compactness at temperatures up to 373.15 K. These results suggest a potential thermostability of the enzyme. Since the studied protein is a core protein, thermostability could be conserved among Paenibacillus sp. MDMC362 closely related strains; however, bacteria from harsh environments may have a slight advantage regarding protein stability.
Keywords	DNA repair ; Paenibacillus ; biotechnology ; carbon ; catalase ; face ; genomics ; habitats ; heat ; molecular dynamics ; nutrient availability ; operon ; osmotic stress ; oxidative stress ; proline ; sporulation ; starvation ; temperature ; thermal stability ; ultraviolet radiation ; Morocco
Language	English
Dates of publication	2023-01
Size	p. 21-38.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-022-01793-x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase.

Antonie van Leeuwenhoek

2022

Abstract	Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in their habitat, which can be exploited in biotechnology. In this work, the genome of Paenibacillus sp. MDMC362 isolated from the Merzouga desert in Morocco was sequenced to understand its survival strategy's genetic basis; and to evaluate the thermostability of a catalase extracted from genomic annotation files using molecular dynamics. Paenibacillus sp. MDMC362 genome was rich in genetic elements involved in the fight against different stresses, notably temperature stress, UV radiations, osmotic stress, carbon starvation, and oxidative stress. Indeed, we could identify genes of the operons groES-groEL and hrcA-grpE-dnaK and those involved in the different stages of sporulation, which can help the bacteria to survive the high temperatures imposed by a desertic environment. We also observed the genetic components of the UvrABC system and additional mechanisms involved in DNA repair, which help overcome UV radiation damage. Other genes have been identified in the genome, like those coding for ectoine and proline, that aids fight osmotic stress and desiccation. Catalase thermostability investigation using molecular dynamics showed that the protein reached stability and conserved its compactness at temperatures up to 373.15 K. These results suggest a potential thermostability of the enzyme. Since the studied protein is a core protein, thermostability could be conserved among Paenibacillus sp. MDMC362 closely related strains; however, bacteria from harsh environments may have a slight advantage regarding protein stability.
Language	English
Publishing date	2022-11-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-022-01793-x
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Article ; Online: Draft Genome Sequence of Stenotrophomonas maltophilia MDMC339, Isolated from Soil of Merzouga Desert in Morocco.

Chemao-Elfihri, M W / Manni, Amina / Laamarti, Meriem / Kartti, Souad / Essabbar, Abdelmounim / Alouane, Tarek / Temsamani, Loubna / Eljamali, Jamal-Eddine / Ouadghiri, Mouna / El Hajjami, Nargisse / Sbabou, Laila / Belyamani, Lahcen / Ibrahimi, Azeddine / Filali-Maltouf, Abdelkarim

Microbiology resource announcements

2020 Volume 9, Issue 32

Abstract: Here, we report the draft genome sequence ... ...

Abstract	Here, we report the draft genome sequence of
Language	English
Publishing date	2020-08-06
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00634-20
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Article ; Online: Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology.

Microbiology resource announcements

2020 Volume 9, Issue 32

Abstract: Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end of 2019 in Wuhan, China. The isolates were obtained from ...

Abstract	Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end of 2019 in Wuhan, China. The isolates were obtained from nasopharyngeal swabs from Moroccan patients with COVID-19. Mutation analysis revealed the presence of the spike D614G mutation in all six genomes, which is widely present in several genomes around the world.
Keywords	covid19
Language	English
Publishing date	2020-08-06
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00767-20
Database	MEDical Literature Analysis and Retrieval System OnLINE

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