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  1. Artikel ; 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

    Scientific data

    2023  Band 10, Heft 1, Seite(n) 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-Begriff(e) Humans ; Africa ; Genomics ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Tuberculosis/genetics ; Tuberculosis/drug therapy ; Genome, Bacterial
    Sprache Englisch
    Erscheinungsdatum 2023-04-14
    Erscheinungsland England
    Dokumenttyp 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
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; 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  Band 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.
    Schlagwörter Science ; Q
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2023-04-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; 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  , Seite(n) 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.
    Sprache Englisch
    Erscheinungsdatum 2023-11-25
    Erscheinungsland England
    Dokumenttyp 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
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; 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  Band 12, Heft 2, Seite(n) e0108722

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

    Abstract We report the draft genome sequences of Enterobacter hormaechei subsp.
    Sprache Englisch
    Erscheinungsdatum 2023-01-12
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01087-22
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; 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

    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, ... ...

    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.
    Schlagwörter Bacillus safensis ; desert soils ; genome ; genomics ; nutrient deficiencies ; phylogeny ; soil salinity ; ultraviolet radiation ; Morocco
    Sprache Englisch
    Erscheinungsverlauf 2022-12
    Umfang p. 1173-1187.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel ; 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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  6. Artikel ; 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  Band 22, Heft 6, Seite(n) 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-Begriff(e) Phylogeny ; Genomics ; Bacillus/genetics ; Soil
    Chemische Substanzen Soil
    Sprache Englisch
    Erscheinungsdatum 2022-09-29
    Erscheinungsland Germany
    Dokumenttyp 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
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; 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.
    Schlagwörter 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
    Sprache Englisch
    Erscheinungsverlauf 2023-01
    Umfang p. 21-38.
    Erscheinungsort Springer International Publishing
    Dokumenttyp Artikel ; Online
    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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  8. Artikel ; 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

    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 ... ...

    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.
    Sprache Englisch
    Erscheinungsdatum 2022-11-16
    Erscheinungsland Netherlands
    Dokumenttyp 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
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; 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  Band 9, Heft 32

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

    Abstract Here, we report the draft genome sequence of
    Sprache Englisch
    Erscheinungsdatum 2020-08-06
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00634-20
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology.

    Laamarti, Meriem / Chemao-Elfihri, M W / Kartti, Souad / Laamarti, Rokia / Allam, Loubna / Ouadghiri, Mouna / Smyej, Imane / Rahoui, Jalila / Benrahma, Houda / Diawara, Idrissa / Alouane, Tarek / Essabbar, Abdelomunim / Siah, Samir / Karra, Mohammed / El Hafidi, Naima / El Jaoudi, Rachid / Sbabou, Laila / Nejjari, Chakib / Amzazi, Saaid /
    Mentag, Rachid / Belyamani, Lahcen / Ibrahimi, Azeddine

    Microbiology resource announcements

    2020  Band 9, Heft 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.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-08-06
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00767-20
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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