Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Nam, Nguyen Nhat; Khoa, Hoang Dang; Trinh, Kieu The Loan; Lee, Nae Yoon

doi:10.3390/foods12112140

Cited by 39 publications

(9 citation statements)

References 268 publications

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“…These combined advantages position Alg169 as a promising candidate for industrial applications requiring efficient and environmentally friendly alginate degradation. While our approach does come with inherent limitations, including increased costs, ineffective screening methods for certain enzyme activities, and challenges related to heterologous expression systems [22,51,52], we were able to achieve a significant breakthrough by uncovering Alg169, an alginate lyase with remarkable enzyme activity. Future research will focus on enhancing its stability at varying pH and temperature ranges, exploring immobilization methods, and scaling up the degradation process for brown seaweed for industrial applications.…”

Section: Discussionmentioning

confidence: 99%

Expression and Characterization of an Efficient Alginate Lyase from Psychromonas sp. SP041 through Metagenomics Analysis of Rotten Kelp

Wang,

Cai,

Zhong

et al. 2024

Genes

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Alginate is derived from brown algae, which can be cultivated in large quantities. It can be broken down by alginate lyase into alginate oligosaccharides (AOSs), which exhibit a higher added value and better bioactivity than alginate. In this study, metagenomic technology was used to screen for genes that code for high-efficiency alginate lyases. The candidate alginate lyase gene alg169 was detected from Psychromonas sp. SP041, the most abundant species among alginate lyase bacteria on selected rotten kelps. The alginate lyase Alg169 was heterologously expressed in Escherichia coli BL21 (DE3), Ni-IDA-purified, and characterized. The optimum temperature and pH of Alg169 were 25 °C and 7.0, respectively. Metal ions including Mn2+, Co2+, Ca2+, Mg2+, Ni2+, and Ba2+ led to significantly increased enzyme activity. Alg169 exhibited a pronounced dependence on Na+, and upon treatment with Mn2+, its activity surged by 687.57%, resulting in the highest observed enzyme activity of 117,081 U/mg. Bioinformatic analysis predicted that Alg169 would be a double-domain lyase with a molecular weight of 65.58 kDa. It is a bifunctional enzyme with substrate specificity to polyguluronic acid (polyG) and polymannuronic acid (polyM). These results suggest that Alg169 is a promising candidate for the efficient manufacturing of AOSs from brown seaweed.

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Section: Discussionmentioning

confidence: 99%

Expression and Characterization of an Efficient Alginate Lyase from Psychromonas sp. SP041 through Metagenomics Analysis of Rotten Kelp

Wang,

Cai,

Zhong

et al. 2024

Genes

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“…Mass spectrometry is generally considered the gold standard technique for proteomics analysis and is widely used to analyse bodily fluids, including saliva [ 90 ]. Metagenomics The study of microbial communities and their genomic material within natural living environments, including unculturable microorganisms, is conducted through functional gene screening or sequencing analysis [ 91 ]. Next-generation sequencing (NGS) technology is considered the gold standard in this field, employing two common strategies.…”

Section: Scientific Progress In Dental Omicsmentioning

confidence: 99%

Bridging the gap between omics research and dental practice

Kabbashi,

Roomaney,

Chetty

2024

BDJ Open

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Aim The burgeoning field of omics research has witnessed exponential growth in both medicine and dentistry. However, despite more than a decade of advancements, clinical dentistry, particularly in Low- and Middle-Income Countries (LMICs), has seen limited progress in integrating omics-based approaches into routine practice. This review aims to provide a comprehensive overview of the integration of omics approaches in dentistry, focusing on the challenges and opportunities for translating research findings into clinical practice. Methods we conducted a literature review using key databases to provide a brief overview of the history of genomics in dentistry. Additionally, we summarised recent breakthroughs in omics relevant to oral health practitioners, emphasising the inadequate translation of omics research into clinical practice. Results Despite significant growth in omics research in both medicine and dentistry, its translation into routine clinical practice in dentistry remains limited. We summarise recent breakthroughs in omics and highlight the gap between research advancements and clinical implementation. Discussion and conclusion The integration of omics approaches holds promise for enhancing diagnostics, personalised treatment strategies, and preventive measures in dental practice, ushering in a new era of precision oral healthcare. However, several challenges, including infrastructure limitations, cost-effectiveness, and education gaps, hinder the widespread adoption of omics-based approaches in clinical dentistry. A strong commitment to transforming dentistry is required to embrace this transition. This shift has the potential to revolutionise oral healthcare by advancing precision diagnostics and treatment strategies tailored to individual patient needs.

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“…Human microbiome studies address the comprehensive microorganisms for their role in health and disease 13 . Metagenomics is an approach of microbiome study, with a focus of microbial genetic DNA 14 . Widely used in environmental and biological studies, metagenomic techniques offer comprehensive insights into diverse microbial habitats 15 , 16 , including fish intestines and gills 17 .…”

Section: Introductionmentioning

confidence: 99%

Uncovering the microbiome landscape in sashimi delicacies

Ho,

Chen,

Liao

et al. 2024

Sci Rep

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It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray–Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray–Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.

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Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Cited by 39 publications

References 268 publications

Expression and Characterization of an Efficient Alginate Lyase from Psychromonas sp. SP041 through Metagenomics Analysis of Rotten Kelp

Expression and Characterization of an Efficient Alginate Lyase from Psychromonas sp. SP041 through Metagenomics Analysis of Rotten Kelp

Bridging the gap between omics research and dental practice

Uncovering the microbiome landscape in sashimi delicacies

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