Single-cell technologies in environmental omics

Kodzius, Rimantas; Gojobori, Takashi

doi:10.1016/j.gene.2015.10.031

Cited by 24 publications

(18 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The throughput of microtiter plates has been enhanced through the incorporation of robotic technologies [104]. Also, fluorescence-activated cell sorting (FACS) has been used to distribute single cells into microtiter plates [105]. However, these kind of experiments require a strong prior knowledge on the best convenient substrates and also the chemistry on how it works.…”

Section: Microtiter Plate Screeningmentioning

confidence: 99%

“…FACS enables the selection of cells based on cell size, shape, and fluorescence [12], [59], [106], [107], [108]. FACS have many advantages: (1) it deposits single events into a variety of vessels quickly and accurately; (2) the laminar flow fluidics of FACS prevents disruption of cells during sorting; and (3) the contamination is limited because of the small volume of each droplet [105], [109], [110]. Due to its powerful sorting abilities, FACS is easily coupled to a number of different high-throughput screening methods such as droplet sorting and reporter-based screening.…”

Section: Facs-based Screeningmentioning

confidence: 99%

See 1 more Smart Citation

Recent Advances in Function-Based Metagenomic Screening

Ngara

Zhang

2018

Genomics, Proteomics &Amp; Bioinformatics

126

View full text Add to dashboard Cite

Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.

show abstract

Section: Microtiter Plate Screeningmentioning

confidence: 99%

Section: Facs-based Screeningmentioning

confidence: 99%

Recent Advances in Function-Based Metagenomic Screening

Ngara

Zhang

2018

Genomics, Proteomics &Amp; Bioinformatics

126

View full text Add to dashboard Cite

show abstract

“…The future progress should obviously focus on extensive marine bioprospecting based on metagenomics approaches (Kodzius and Gojobori 2015). Sample heterogeneity is a major issue when dealing with environmental omics, and single cell techniques for reducing sample heterogeneity are arguably the best way forward (Kodzius and Gojobori 2016). These experimental approaches should be followed by comprehensive in silico comparison of metabolic features of local species compared to their counterparts from other environments.…”

Section: Discussionmentioning

confidence: 99%

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

Nielsen

Archer

Essack

et al. 2017

Appl Microbiol Biotechnol

Self Cite

View full text Add to dashboard Cite

The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger “catalog” of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.

show abstract

“…It is suggested that if metagenomics and SCGA methodologies are coupled with other "omics" technologies, such as transcriptomics, proteomics and metabolomics (i.e. study and quantification of mRNA transcript levels, proteins and cellular metabolites respectively), it could lead to further development of scientific capabilities for harnessing the genetic and metabolic potential of the extremophilic microbial diversity [30,31].…”

Section: Introductionmentioning

confidence: 99%

Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms through the Integration of Metagenomics and Single-Cell Genomics

Goyal¹,

Swaroop²,

Pandey³

2021

Extremophilic Microbes and Metabolites - Diversity, Bioprospecting and Biotechnological Applications

View full text Add to dashboard Cite

Microorganisms thriving under extreme environments have proven to be an invaluable resource for metabolic products and processes. While studies carried out on microbial characterization of extremophilic environments during golden era of microbiology adapted a ‘reductionist approach’ and focused on isolation, purification and characterization of individual microbial isolates; the recent studies have implemented a holistic approach using both culture-dependent and culture-independent approaches for characterization of total microbial diversity of the extreme environments. Findings from these studies have unmistakably indicated that microbial diversity within extreme environments is much higher than anticipated. Consequently, unraveling the taxonomic and metabolic characteristics of microbial diversity in extreme environments has emerged as an imposing challenge in the field of microbiology and microbial biotechnology. To a great extent, this challenge has been addressed with inception and advancement of next-generation sequencing and computing methods for NGS data analyses. However, further it has been realized that in order to maximize the exploitation of genetic and metabolic diversity of extremophilic microbial diversity, the metagenomic approaches must be combined synergistically with single-cell genomics. A synergistic approach is expected to provide comprehensions into the biology of extremophilic microorganism, including their metabolic potential, molecular mechanisms of adaptations, unique genomic features including codon reassignments etc.

show abstract

Single-cell technologies in environmental omics

Cited by 24 publications

References 70 publications

Recent Advances in Function-Based Metagenomic Screening

Recent Advances in Function-Based Metagenomic Screening

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms through the Integration of Metagenomics and Single-Cell Genomics

Contact Info

Product

Resources

About