Endophytic fungi colonize the inter- and/or intracellular regions of healthy plant tissues and have a close symbiotic relationship with their hosts. These microorganisms produce antibiotics, enzymes, and other bioactive compounds that enable them to survive in competitive habitats with other microorganisms. In addition, secondary metabolites confer protection to their host plant against other bacterial and fungal pathogens and/or can promote plant growth. Endophytic fungi are viewed as a promising source of bioactive natural products, which can be optimized through changes in growing conditions. The exploration of novel bioactive molecules produced by these microorganisms has been attracting attention from researchers. The chemical and functional diversity of natural products from endophytic fungi exhibits a broad spectrum of applications in medicine, agriculture, industry and the environment. Fungal endophytes can also enhance the photoprotective effects and photochemical efficiency in the host plants. Modern omic approaches have facilitated research investigating symbiotic plant-endophytic fungi interactions. Therefore, research on endophytic fungi can help discovery novel biomolecules for various biotechnological applications and develop a sustainable agriculture.

In this study, we report the isolation and identification of an endophytic strain of Burkholderia cepacia (COPS strain) associated with Polygala paniculata roots. Polygala plants are rich sources of promising microbiomes, of which the literature reports several pharmacological effects, such as trypanocidal, antinociceptive, anesthetic, anxiolytics, and anticonvulsant activities. B. cepacia COPS belongs to a new sequence type (ST 1870) and harbors a genome estimated in 8.3Mbp which exhibits the aminoglycosides and beta-lactams resistance genes aph(3)-IIa and bla_TEM-116, respectively. Analysis performed using MLST, average nucleotide identity, and digital DNA-DNA hybridization support its species-level identification and reveals its novel housekeeping genes alleles gyrB, lepA, and phaC. The root endophyte B. cepacia COPS drew our attention from a group of 14 bacterial isolates during the primary screening for being potentially active against Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 29212, Micrococcus luteus ATCC 9341, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 and exhibited the broad-spectrum activity against phytopathogenic fungi. In addition, COPS strain showed production of protease, lipase, and esterase in solid media, and its natural product extract showed potent inhibition against fungal plant pathogens, such as Moniliophthora perniciosa, whose antagonism index (89.32) exceeded the positive control (74.17), whereas Sclerotinia sclerotiorum and Ceratocystis paradoxa showed high percentages of inhibition (85.53 and 82.69, respectively). COPS crude extract also significantly inhibited S. epidermidis ATCC 35984, E. faecium ATCC 700221 (MIC values of 32μg/mL for both), E. faecalis ATCC 29212 (64μg/mL), and S. aureus ATCC 25923 (128μg/mL). We observed moderate antagonistic activity against A. baumannii ATCC 19606 and E. coli ATCC 25922 (both at 512μg/mL), as well as potent cytotoxic effects on Leishmania infantum and Leishmania major promastigote forms with 78.25 and 57.30 inhibition. In conclusion, this study presents for the first time the isolation of an endophytic B. cepacia strain associated with P. paniculata and enough evidence that these plants may be considered a rich source of microbes for the fight against neglected diseases.

Polyalthic acid (PA) is a diterpene found in copaiba oil. As a continuation of our work with PA, we synthesized PA analogs and investigated their antibacterial effects on preformed biofilms of Staphylococcus epidermidis and determined the minimal inhibitory concentration (MIC) of the best analogs against planktonic bacterial cells. There was no difference in activity between the amides 2a and 2b and their corresponding amines 3a and 3b regarding their ability to eradicate biofilm. PA analogs 2a and 3a were able to significantly eradicate the preformed biofilm of S. epidermidis and were active against all the Gram-positive bacteria tested (Enterococcus faecalis, Enterococcus faecium, S. epidermidis, Staphylococcus aureus), with different MIC depending on the microorganism. Therefore, PA analogs 2a and 3a are of interest for further in vitro and in vivo testing to develop formulations for antibiotic drugs against Gram-positive bacteria.

Antibiotic-resistant pathogens are a public health threat that has rapidly spread over decades due to continuous and uncontrolled administration of antimicrobial medicines, becoming an ever-increasing worldwide concern. Since the past decade, no significant innovations have been made, so the search for new compounds that face multidrug-resistant pathogens is critically important. Plant-symbiont microorganisms are capable of producing a variety of bioactive natural products, making it possible to treat several infectious diseases. Biotechnological processes using microorganisms have been increasing in recent years since the discovery of Paclitaxel, an important antimitotic produced by the endophyte Taxomyces andreanae. It was isolated for the first time from the native tree of Pacific Taxus brevifolia. Several studies have demonstrated the isolation and characterization of promising and potent substances capable of inhibiting these pathogens. In addition, both rhizospheric and endophytic communities represent an unexplored reserve of unique chemical structures for drug development. This chapter focuses on the potential of plant-derived microorganisms as a source of bioactive substances and the perspectives for further studies and their application.

There has been an important increase in the emergence of resistance in microbial population worldwide. This trajectory needs, necessarily new approaches to treat infectious diseases. The ability to detect and prevent the evolutionary trajectories of microbial resistance would be of value. Photodynamic inactivation (PDI) represents an efficient alternative treatment for diseases caused by viruses, which can cause infections well documented in various mammals. PDI can kill cells after exposure with the appropriate photosensitizer (PS), light of adequate wavelength combined with the presence of oxygen, without inducing resistance. Cytotoxic reactive species formed interaction with vital biomolecules leading to irreversible microbial inactivation. Bacteriophages can act on delivering antimicrobial agents into bacteria, which consist in a likely instrument for the treatment of infectious diseases. Non-enveloped bacteriophages are more difficult to tolerate photoinactivation than enveloped phages, which makes them an important model tool to evaluate the efficiency of PDI therapy against viruses that cause diseases in humans. Combination of photosensitizers and bacteriophage therapy can be employed to eradicate biofilms, contributing to control of infections also caused by drug-resistant bacteria.

Polygala paniculata is a medicinal plant that harbors a remaining unknown microbiome. Those plants are known for their analgesic and anti-inflammatory properties and are widely found in the Brazilian Atlantic Forest. Herein, we report the isolation of the endophyte Bacillus velezensis GPP30 with a draft genome estimated at 4.0 Mpb.