**2.1. The medical field**

The applications of these NGS technologies in medicine have allowed expansion in the fields of diagnosis, treatment and prevention, especially concerning bacterial diseases. One of their major applications has been the quantification of expression levels of each transcript under different conditions that simulate the intracellular environment. Such work has been done by Pinto et al. (2014) to understand the host–pathogen relationship [5]. Westermann et al. (2012) demonstrated the validity of this technique, with the transcriptome of the pathogenic bacteria as their host, using the dual RNA-seq that simultaneously analyzed the gene expressions of the pathogen and host [6]. This gives us better understanding of the systems biology involving bacteria and their hosts, helping scientists to develop drugs and vaccines.

Another field that has been explored extensively involves metatranscriptome, as scientists have sought to comprehend the composition and regulation of microbial ecosystems [7, 8]. To pursue this, they have used the RNA-seq technique to generate, and allow the interpretation of, a large volume of very reliable data. Leimena et al. (2013) also validated the RNA-seq technique using the microbiota of a human small intestine with ileostomy. Their aim was to understand the interactions involved in this microbial ecosystem and how these relationships can be associated with disease [8]. Transcriptome analysis pipelines (see Section 5) can be used with different experimental designs and applied to many bacteria in addition to those in the medical field.

#### **2.2. The industrial field**

Industrial applications have been developed in recent years, mainly in the probiotic industry, since it benefits the world economy. Bisanz et al. (2014) used the RNA-seq technique [9] to show the metatranscriptome of probiotic yogurt, seeking to understand the metabolic activities that allow the survival of this organism in the products. Their results show the adaptive capacity of this bacterium, as well as the variation in differential gene expression, yielding the taste or storage life of the product [9]. Studies such as these are important because they enrich the knowledge of the industrial field and open new possibilities for an attractive area in the marketplace, which results in improvement in the quality of the product that is ultimately delivered to the consumer.

In addition to the probiotic market, another important area is the bacterial production and synthesis of biomolecules. Wiegand et al. (2013) used the RNA-seq technique to under‐ stand the regulatory RNAs in the fermentation of *Bacillus licheniformis*. Their study identified active genomic regions which, in turn, contribute to the efficiency and optimization of the fermentation process, which can promote the industrial production of exoenzymes and antibiotics [10].

Microorganisms produce antioxidant molecules that can be used in the pharmaceutical and cosmetic industries. They also produce other compounds, such as propionate, that are applicable in the production of chemical aids and are produced by *Propionibacterium freuden‐ reichii ssp. shermanii*, which one is considered valuable in the food industry [11]. In this area, the RNA-seq technology is very promising and its application can bring advances in these studies.
