دورية أكاديمية
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Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.

التفاصيل البيبلوغرافية
العنوان: Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.
المؤلفون: Liew KJ; Codon Genomics, 42300 Seri Kembangan, Selangor, Malaysia., Shahar S; Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia., Shamsir MS; Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia., Shaharuddin NB; School of Professional and Continuing Education, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia., Liang CH; Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia., Chan KG; Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia., Pointing SB; Department of Biological Sciences, National University of Singapore, Singapore, Singapore., Sani RK; Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA. rajesh.sani@sdsmt.edu., Goh KM; Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia. gohkianmau@utm.my.
المصدر: Environmental microbiome [Environ Microbiome] 2024 May 06; Vol. 19 (1), pp. 29. Date of Electronic Publication: 2024 May 06.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BMC Country of Publication: England NLM ID: 101768168 Publication Model: Electronic Cited Medium: Internet ISSN: 2524-6372 (Electronic) Linking ISSN: 25246372 NLM ISO Abbreviation: Environ Microbiome Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [London] : BMC, [2019]-
مستخلص: Background: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.
Results: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.
Conclusions: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.
(© 2024. The Author(s).)
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معلومات مُعتمدة: FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS); FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS); FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS); FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS); FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS); 4J549 UTM QuickWin grant; 4J549 UTM QuickWin grant; T2EP30123-0028 Singapore Ministry of Education ARC Tier 2 fund; 1736255, 1849206, and 1920954 National Science Foundation
فهرسة مساهمة: Keywords: Hybrid assembly; Lignocellulose degradation; Metagenome-assembled genomes; Microbial mat; Thermophile
تواريخ الأحداث: Date Created: 20240505 Latest Revision: 20240508
رمز التحديث: 20240508
مُعرف محوري في PubMed: PMC11071339
DOI: 10.1186/s40793-024-00572-7
PMID: 38706006
قاعدة البيانات: MEDLINE
الوصف
تدمد:2524-6372
DOI:10.1186/s40793-024-00572-7