Music of metagenomics—a review of its applications, analysis pipeline, and associated tools

Wajid, Bilal; Anwar, Faria; Wajid, Imran; Nisar, Haseeb; Meraj, Sharoze; Zafar, Ali; Alshawaqfeh, Mustafa; Ekti, Ali Rıza; Khatoon, Asia; Suchodolski, Jan S.

doi:10.1007/s10142-021-00810-y

Cited by 6 publications

(4 citation statements)

References 351 publications

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“…ASV-based methods have been found to provide better resolution than OTU-based methods [ 111 ]. A detailed discussion of 16S analysis pipelines is beyond the scope of this review, and for more information we refer to some excellent reviews [ 112 , 113 ].…”

Section: Sequencing Methodsmentioning

confidence: 99%

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Srinivas

O’Sullivan

Cotter

et al. 2022

Foods

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The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

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Section: Sequencing Methodsmentioning

confidence: 99%

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Srinivas

O’Sullivan

Cotter

et al. 2022

Foods

View full text Add to dashboard Cite

show abstract

“…Metagenomics allows for a comprehensive evaluation of the bacterial community in diverse habitats, as the whole collection of genomes in a sample is sequenced, instead of the conventional culture‐based approach in which particular strains/species are isolated and cultured in a laboratory setting (Bodor et al, 2020; Wajid et al, 2021).…”

Section: Variable Treatment P‐value Heterotrophic Maturementioning

confidence: 99%

Predictive functional profiling of water bacterial community in the integrated culture of Pacific white shrimp and Nile tilapia under heterotrophic and mature biofloc systems

Martins

Mouriño

Seiffert

et al. 2022

Aquaculture Research

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“…Metagenomics is a technique used for the culture-independent analysis of metagenome, a collective genome representing a whole community (virus, bacteria, or eukaryotic organisms) associated with a particular niche in an ecosystem ( Handelsman, 2004 ; Wajid et al, 2022 ). The term was first coined by Handelsman (2004) .…”

Section: Introductionmentioning

confidence: 99%

Decoding the microbial universe with metagenomics: a brief insight

et al. 2023

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A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.

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Music of metagenomics—a review of its applications, analysis pipeline, and associated tools

Cited by 6 publications

References 351 publications

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Predictive functional profiling of water bacterial community in the integrated culture of Pacific white shrimp and Nile tilapia under heterotrophic and mature biofloc systems

Decoding the microbial universe with metagenomics: a brief insight

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