The great screen anomaly—a new frontier in product discovery through functional metagenomics

Abstract

Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product.

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

“…T he massive influx of novel sequence data derived from nextgeneration sequencing (NGS) technologies, in the context of both individual genomes (1) and metagenomes (2,3), has far outstripped efforts to link those sequences to specific organisms and biological functions (4). Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation.…”

Uncovering Plant Growth-Mediating Allelochemicals Produced by Soil Microorganisms

“…The overall set of techniques we describe in this article have several concerns that should be noted and possibly alleviated in future research. Building the metagenomic library has caveats covered in previous reviews (Ekkers et al 2012;Kao-Kniffin et al 2013). Also, the initial screen might not be the best method for narrowing clones for further studies on allelopathic activity.…”

Explorando produtos naturais microbianos nas fronteiras da Química e da Biologia

“…As (29), piericidina B 1 (30), glucopiericidina A (31) piericidina A 5 (32), piericidina C 1 (33), 9'-desmetil-piericidina A 1 (34), piericidina B 5 (35) e piericidina IT-143-B (36) (Figura 3), sugerindo que essa relação favorece a sobrevivência das vespas através da proteção das larvas no casulo contra patógenos. 52 Streptomyces sp., simbionte do besouro Dendroctonus frontalis, é responsável pela produção da micangimicina (37) (Figura 3), que inibe o crescimento do fungo Ophiostoma minus, competidor natural do fungo Entomocorticium sp.…”

“…Limitações relacionadas à baixa expressão em E. coli podem ser contornadas pela expressão em outros sistemas como Streptomyces, Pseudomonas e Bacillus, mas diferenças relacionadas a "códon usage", ausência de elementos regulatórios e enovelamento ainda caracterizam uma dificuldade a ser ultrapassada. 30 Pederina (14), onamida (15), briostatina (16) e apratoxina (17) (Figura 2) são exemplos de compostos com atividade antitumoral cuja descoberta foi direcionada por metagenoma. Pederina é um policetídeo produzido por uma bactéria simbionte do besouro Paederus fuscipes.…”