**7. Challenges and trends in the discovery and development of microbial natural products**

Even though the plethora of natural products of microbial origin mainly isolated from marine and extreme environments is a large field of research, developments in technological aspects such as the increase in natural product production for industrial scale-up or overcoming the difficulty in isolating microorganisms are needed [112].

Genome mining focused on the activation of silent genes, to search gene clusters serving as molecular markers, with complementary informatic tools has been a solution [113, 114]. This technique can be used in metabolic engineering, producing an heterologous host through genetic engineering, using plasmids or recombinant systems using interspaced palindromic repeat, one of the most recent techniques applied in genetic engineering [115].

Another trend also used on unculturable microorganisms is the discovery of environmental DNA coupled to cosmids for gene expression, which have also been used for the selective isolation of biologically active natural products [116].

Search of ideal media and culture conditions have also been a major challenge in optimizing the amount of metabolite present on the microorganism, which have been developed by either trial and error or statistical design [116]; an example is the presence of metallic salts to activate enzymes involved in the biosynthetic route or by manipulating temperature, light, aeration and pH [117] as we saw in the obtention throughout the chapter [117].

*Microorganisms as Alternative Sources of New Natural Products DOI: http://dx.doi.org/10.5772/intechopen.92697*

Another technique widely observed along the chapter was co-cultivation technique between bacteria, fungi or in combination to improve metabolite production.

Conventionally organic solvents are often used for natural product extraction, which is an important step for industrial scale-up [118, 119]. However, due to the health and environmental hazards, alternative extraction techniques have been searched for with the purpose of reducing residues and thus environmental impact [119, 120]. Among the alternative extraction techniques are ultrasound, microwave, enzyme and pulse electric field. The latter techniques have been widely explored on plants; nevertheless, on microorganisms, they have been poorly explored, thus representing a critical challenge in natural product research [121, 122].

The possibility to expand the research in this regard, is also the search of alternative solvents such as supercritical fluids, [119, 120], ionic liquids, gas-expanded liquids and vegetable oils [121–123].
