Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances—isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA—a promising result, since it is an important multidrug-resistant human pathogen. 1. Introduction The search for new antimicrobials becomes more important because of the increasing resistance of pathogenic microorganisms. However, the decrease of the development of the antibacterial drugs has been reported, due to the abandonment and reduction of research and difficulty in isolating novel compounds which can cope with resistant pathogens [1–3]. Over two-thirds of clinically used antibiotics consist of natural products or their semisynthetic byproducts [4], and the majority of known natural products with antimicrobial activity are from soil Actinobacteria [5]. This group of bacteria is very varied physiologically and metabolically and forms important substances, such as enzymes and powerful antibiotics [6–8]. In recent years, researchers have turned to untapped natural sources and to places with extreme environmental conditions of temperature, pH, and humidity, believing that organisms obtained from ecosystems that have not yet been exploited are frequently associated with new physiological and metabolic diversity [9]. Although soil has been exploited by the drug industry for some 50 years, only a minuscule fraction of the globe has been sampled, and only a small fraction of Actinobacteria has been discovered [10]. There has been a lot of discussion about the fact that
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