Current and future resources for functional metagenomics

Abstract

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries—physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

“…However, knowledge regarding the aciduric features of so far uncultivable microorganisms remains scarce. As a crucial technology used to access and explore the genomes and functional information of microorganisms including uncultivable ones, functional metagenomics [16] exhibit high application value. To the best of our knowledge, this is the first work that applied functional metagenomics to explore the acid-resistant genes of dental plaque microbiomes.…”

“…(ii) Some genetic information could be lost during the library construction process. Alternatively, it is known that the process of ligation of the various inserts into a vector is accompanied by a certain amount of randomness and uncontrollability [16], which can diminish or completely lose the genetic information of S. mutans and some other strains.…”

“…To explore this field, we utilized function-based metagenomics [16], which can identify both novel and previously known genes involved in target functions, even with unknown genetic information. Currently, function-based screening of metagenomic libraries has been widely deployed in different fields, including the screening of environmental libraries [17], the investigation of mouse gut colonization [18], of human faecal samples [19] and others.…”

Next-generation approaches to understand and combat the antibiotic resistome

“…Functional metagenomics is a powerful culture-unbiased and sequence-unbiased tool 134 . A metagenomic library is created by extracting total metagenomic DNA from a microbial community, shearing the DNA to a target size distribution and cloning these fragments en masse into a screening vector (see the figure).…”

Antimicrobial Resistance Genes and Wastewater Treatment

“…In this respect, function-based metagenomics are more valuable approaches as they have the potential to identify novel ARGs and MGEs and to correlate resistance genes with the community structure. A functional metagenomics approach involves construction of metagenomic libraries through extraction of DNA, cloning DNA fragments, heterologous expression in surrogate hosts, and screening for specific activities (Lam et al, 2015).…”