Metagenomic analysis of fungal taxa inhabiting Mecca region, Saudi Arabia.
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ABSTRACT:
SUBMITTER: Moussa TA
PROVIDER: S-EPMC4971153 | biostudies-literature | 2016 Sep
REPOSITORIES: biostudies-literature
Publications
Metagenomic analysis of fungal taxa inhabiting Mecca region, Saudi Arabia.
Moussa Tarek A A TA Al-Zahrani Hassan S HS Almaghrabi Omar A OA Sabry Nevien M NM Fuller Michael P MP
Genomics data 20160721
The data presented contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of the Mecca region, Saudi Arabia. Sequences were amplified using fungal specific primers, which amplified the amplicon aligned between the 18S and 28S rRNA genes. A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla were identified in four contrasting locations. The raw sequencing data used to perform this analysis along with ...[more]
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Project description:A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota-99.31%, Basidiomycota-0.59%, Chytridiomycota-0.04%, Glomeromycota-0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota-74.26%, Basidiomycota-25.71%, Chytridiomycota-0.01%) and Thuwal (Ascomycota-99.59%, Basidiomycota-0.40%, Chytridiomycota-0.002%); while only Ascomycota-90.98% and Basidiomycota-9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road-59.88%, Khulais-68.26% and Thuwal-94.84%; while Pezizomycetes was dominant at Mecca old road-56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road-25.73%; while Tremellomycetes-5.77%, Malasseizomycetes-2.13% and Microbotryomycetes-1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.
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Project description:COVID-19 vaccine acceptance and refusal vary across countries and among different socio-demographic groups. This study investigates hesitancy related to the COVID-19 vaccine and the associated factors in the rural-community-dominated Jazan Province, Saudi Arabia. A cross-sectional study through an online questionnaire was conducted from February to April 2021 to investigate the extent of vaccine hesitancy related to the COVID-19 vaccine and the associated factors in the Jazan region. A Chi-squared test and post hoc analysis were conducted to analyze the statistical significance of the association between variables. Of the 569 participants who completed the online questionnaire, the majority were males (81.5%) and had a university education (72.6%). Of the participants, more than one-third (36.9%) were hesitant to vaccinate. Concern about adverse side effects following vaccination was the most reported reason for vaccine hesitancy (42.6%), followed by beliefs that the vaccine was unsafe or ineffective (15.5%). The data analysis revealed that people who lived in cities in Jazan Province or those who did not have a family history of COVID-19 infection were more likely to be vaccine hesitant. It is more important than ever to develop and implement community-based strategies to address vaccine hesitancy, especially in rural areas.
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Project description:Background:Many factors influence hematological values such as sex, age, ethnic origin, geographic location, season, and genetic disease. The aim of this study was to detect the hematological reference value profile for healthy adults from the Aljouf region of Saudi Arabia. Methods:The project was carried out on 2,040 healthy individuals, 1,152 males and 888 females, with ages ranging from 17 to 28 years. A group of participants were recruited from the higher secondary schools, university students and premarital centers of Aljouf cities. Hematological reference value profile, hemoglobin (Hb) concentration, red blood cell (RBC) count, RBC indices, white blood cell (WBC) count, differential WBC and platelet (Plt) count were measured. Moreover, a peripheral blood film was prepared in order to detect abnormalities of RBC and all samples were examined for liver function tests (LFTs) and renal function test (RFT) performed, along with a lipid profile. Results:Hb concentration, hematocrit (Hct) and RBCs were found to be significantly higher in males than in females (P < 0.01). On the contrary, Plt ranges were significantly lower in male as compared to female (P < 0.01). No significant differences in the study population were determined in the other hematological parameters (P > 0.05). Conclusion:Our findings reflect that healthy adults from the Aljouf region have some hematological parameters differing quantitatively from Caucasians. The hematological reference value profile reported here can be used as normal reference values for Saudi people of the Aljouf region to help in diagnosis and consequently treatment of individuals with hematological disorders.
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Project description:BACKGROUND:Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. METHODS:One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). RESULTS:This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) '11.8%' in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). CONCLUSIONS:Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.
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