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Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes

Year 2021, Volume 6, Issue 4, 717 - 726, 31.12.2021
https://doi.org/10.35229/jaes.989058

Abstract

In this study, we used shotgun metagenome sequencing to examine the metabolic diversity, microbial community structure and diverse antimicrobial resistance genes of mucilage in the surface waters of the Çanakkale Strait (Dardanelles). Mucilage samples were collected in April 2021 from the three different stations of the Dardanelles. The dominant microbial communities at the phylum level were Bacteroidetes (20.06%), Proteobacteria (13.68%), Verrucomicrobia (6.25%), Planctomycetes (3.02%) and Cyanobacteria (2.5%). Metabolic pathway analysis using KEGG (Kyoto Encyclopedia of Genes and Genomes) revealed that most of the genes of mucilage samples were involved in unclassified (73.86%) followed by metabolism (14.45%), genetic information processing (4.16%), environmental information processing (2.57%), cellular processing (1.88%), human diseases (1.61%), and organismal systems (1.47%). The dfrA3 gene was the most prevalent (20.36%) followed by CRP (18.17%), PmrE (14.92%), rpoB2 (11.17%), SoxR (7.49%), AbeS (6.83%), baeR (5.22%), PmrF (3.70%), dfrA22 (2.20%), dfrA26 (1.76%), dfrA20 (1.63%), golS (1.26%), CAT (1.03%), mtrA (1.01%), TMB-1 (0.64%), novA (0.64%), dfrK (0.59%), vanXB (0.48%), dfrG (0.39%), FosC2 (0.31%), and MexA (0.20%) genes. Antibiotic resistance gene (ARG) types mainly included the resistance genes of multidrug (40.19%), trimethoprim (26.93%), polymyxin (18.62%), rifamycin (11.17%), chloramphenicol (1.03%), aminocoumarin (0.64%), beta-lactamase (0.64%), fosfomycin (0.31%), and vancomycin (0.48%). Antibiotic-resistant bacteria in mucilage can adhere to human skin during swimming, fishing, water sports etc., enter the body through the nose and mouth, and transfer genetic information to the bacteria in contact areas in the human body. Therefore, this situation is risky in public health, and necessary precautions should be taken. In the light of these findings, it has been observed that there is a need for more detailed studies in the future.

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Çanakkale Boğazı Yüzey Sularındaki Müsilaj İçin Shotgun Metagenomik Analizi: Metabolik Çeşitlilik, Mikrobiyal Topluluk Yapısı ve Antibiyotik Direnç Genleri

Year 2021, Volume 6, Issue 4, 717 - 726, 31.12.2021
https://doi.org/10.35229/jaes.989058

Abstract

Bu çalışma da Çanakkale Boğazı yüzey sularındaki müsilajın metabolik çeşitliliğini, mikrobiyal topluluk yapısını ve çeşitli antimikrobiyal direnç genlerini incelemek için shotgun metagenom dizilimi kullandık. Nisan 2021'de Çanakkale Boğazı'nın üç farklı istasyonundan müsilaj örnekleri toplandı. Filum düzeyinde baskın mikrobiyal topluluklar Bacteroidetes (%20.06), Proteobacteria (%13.68), Verrucomicrobia (%6.25), Planctomycetes (%3.02) ve Cyanobacteria (%2.5) olarak belirlendi. KEGG (Kyoto Genler ve Genomlar Ansiklopedisi) kullanılarak yapılan metabolik yol analizi, müsilaj örneklerinin genlerinin çoğunun sınıflandırılmamış (%73.86), ardından sırasıyla metabolizma (%14.45), genetik prosesler (%4.16), çevresel prosesler ( %2.57, hücresel prosesler (%1.88), insan hastalıkları (%1.61) ve organizma sistemleri (%1.47) ile ilişkili olduğunu göstermiştir. dfrA3 geni baskın olup (%20,36), ardından sırasıyla CRP (%18,17), PmrE (%14,92), rpoB2 (%11,17), SoxR (%7,49), AbeS (%6,83), baeR (%5,22), PmrF (%3,70), dfrA22 (%2,20), dfrA26 (%1,76), dfrA20 (%1,63), golS (%1,26), CAT (%1,03), mtrA (%1,01), TMB-1 (%0,64), novA (%0,64), dfrK (%0,59), vanXB (%0,48), dfrG (%0,39), FosC2 (%0,31) ve MexA (%0,20) genleri yer almıştır. Antibiyotik direnç geni (ARG) tipleri, temel olarak çoklu ilaç direnci (%40,19), trimetoprim (%26,93), polimiksin (%18,62), rifamisin (%11,17), kloramfenikol (%1,03), aminokumarin (%0,64), beta-laktamaz (%0,64), fosfomisin (%0,31) ve vankomisin (%0,48) direnç genlerini içeriyordu. Müsilaj yapısında yüksek çoklu antibiyotik direnci ve trimetoprim, polimiksin, rifamisin ve kloramfenikol gibi önemli antibiyotik dirençlerinin bulunması halk sağlığı açısından riskli bir durum olarak değerlendirilebilir. Bu bulgular ışığında gelecekte farklı zamanlarda ve derinliklerden alınacak örneklerle daha detaylı çalışmalara ihtiyaç olduğu gözlemlenmiştir.

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Details

Primary Language English
Subjects Science
Journal Section Articles
Authors

Sevdan YILMAZ> (Primary Author)
ÇANAKKALE ONSEKİZ MART ÜNİVERSİTESİ, DENİZ BİLİMLERİ VE TEKNOLOJİSİ FAKÜLTESİ, SU ÜRÜNLERİ YETİŞTİRİCİLİĞİ BÖLÜMÜ
0000-0002-4809-5809
Türkiye


Dilek KAHRAMAN YILMAZ>
ÇANAKKALE ONSEKİZ MART ÜNİVERSİTESİ, DENİZ BİLİMLERİ VE TEKNOLOJİSİ FAKÜLTESİ
0000-0002-9626-5446
Türkiye


Ekrem Şanver ÇELİK>
ÇANAKKALE ONSEKİZ MART ÜNİVERSİTESİ, DENİZ BİLİMLERİ VE TEKNOLOJİSİ FAKÜLTESİ
0000-0003-4514-457X
Türkiye


Mehmet Ali KÜÇÜKER>
İZMİR YÜKSEK TEKNOLOJİ ENSTİTÜSÜ
0000-0001-9648-8925
Türkiye

Early Pub Date December 30, 2021
Publication Date December 31, 2021
Application Date August 31, 2021
Acceptance Date December 27, 2021
Published in Issue Year 2021, Volume 6, Issue 4

Cite

Bibtex @research article { jaes989058, journal = {Journal of Anatolian Environmental and Animal Sciences}, eissn = {2548-0006}, address = {}, publisher = {Bülent VEREP}, year = {2021}, volume = {6}, number = {4}, pages = {717 - 726}, doi = {10.35229/jaes.989058}, title = {Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes}, key = {cite}, author = {Yılmaz, Sevdan and Kahraman Yılmaz, Dilek and Çelik, Ekrem Şanver and Küçüker, Mehmet Ali} }
APA Yılmaz, S. , Kahraman Yılmaz, D. , Çelik, E. Ş. & Küçüker, M. A. (2021). Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes . Journal of Anatolian Environmental and Animal Sciences , 6 (4) , 717-726 . DOI: 10.35229/jaes.989058
MLA Yılmaz, S. , Kahraman Yılmaz, D. , Çelik, E. Ş. , Küçüker, M. A. "Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes" . Journal of Anatolian Environmental and Animal Sciences 6 (2021 ): 717-726 <https://dergipark.org.tr/en/pub/jaes/issue/66598/989058>
Chicago Yılmaz, S. , Kahraman Yılmaz, D. , Çelik, E. Ş. , Küçüker, M. A. "Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes". Journal of Anatolian Environmental and Animal Sciences 6 (2021 ): 717-726
RIS TY - JOUR T1 - Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes AU - SevdanYılmaz, DilekKahraman Yılmaz, Ekrem ŞanverÇelik, Mehmet AliKüçüker Y1 - 2021 PY - 2021 N1 - doi: 10.35229/jaes.989058 DO - 10.35229/jaes.989058 T2 - Journal of Anatolian Environmental and Animal Sciences JF - Journal JO - JOR SP - 717 EP - 726 VL - 6 IS - 4 SN - -2548-0006 M3 - doi: 10.35229/jaes.989058 UR - https://doi.org/10.35229/jaes.989058 Y2 - 2021 ER -
EndNote %0 Journal of Anatolian Environmental and Animal Sciences Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes %A Sevdan Yılmaz , Dilek Kahraman Yılmaz , Ekrem Şanver Çelik , Mehmet Ali Küçüker %T Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes %D 2021 %J Journal of Anatolian Environmental and Animal Sciences %P -2548-0006 %V 6 %N 4 %R doi: 10.35229/jaes.989058 %U 10.35229/jaes.989058
ISNAD Yılmaz, Sevdan , Kahraman Yılmaz, Dilek , Çelik, Ekrem Şanver , Küçüker, Mehmet Ali . "Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes". Journal of Anatolian Environmental and Animal Sciences 6 / 4 (December 2021): 717-726 . https://doi.org/10.35229/jaes.989058
AMA Yılmaz S. , Kahraman Yılmaz D. , Çelik E. Ş. , Küçüker M. A. Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes. JAES. 2021; 6(4): 717-726.
Vancouver Yılmaz S. , Kahraman Yılmaz D. , Çelik E. Ş. , Küçüker M. A. Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes. Journal of Anatolian Environmental and Animal Sciences. 2021; 6(4): 717-726.
IEEE S. Yılmaz , D. Kahraman Yılmaz , E. Ş. Çelik and M. A. Küçüker , "Shotgun Metagenomic Analysis for Mucilage in the Surface Waters of The Çanakkale Strait (Dardanelles): Metabolic Diversity, Microbial Community Structure and Antibiotic Resistance Genes", Journal of Anatolian Environmental and Animal Sciences, vol. 6, no. 4, pp. 717-726, Dec. 2021, doi:10.35229/jaes.989058


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