Background

Antibiotics have achieved major advances in medicine and surgery, saving patients’ lives and extending the expected human lifespan [1]. Following the golden era when natural antibiotics were discovered and prescribed in 1925–1950, the chemistry era followed in the 1970s, with synthetic tweaking to improve activity. However, in 2000, the resistance era, largely due to the overuse and misuse of these medications, began [2, 3]. This coincided with the development of new technologies such as the manipulation of recombinant DNA and the high-throughput synthesis of chemicals that has given rise to hopes of drug discoveries other than antibiotics [4]. Although the high-throughput biochemical screening of large collections of syntheses has provided some interesting leads, the complexity and diversity of these molecules has been insufficient to provide the same level of bioactivity as found in naturally occurring antibiotics. It has been suggested that the coexistence of microbes with other microbes and fungi in the environment leads to selection of the most potent targets so that the best source of new antibiotics are compounds naturally produced by microorganisms [5]. It has therefore been recommended that natural products are revisited as an alternative to synthetic collections following the methods in the “golden age of the discovery of antibiotics” that screened microbial cell extracts from soil to find new antibiotic scaffolds. It has been also recommended that new technologies are embraced to overcome problems of compound discovery. Thus, the exploration of genome sequences of microorganisms and data from metagenomics of the microbial dark matter- microorganisms that have resisted to easy cultivation in the laboratory [6] has revealed a very large spectrum of potential for secondary metabolites with potential antibiotic functions [7].

Microbial secondary metabolites are organic compounds that are not directly involved in primary growth and development, but rather have auxiliary functions including defense and communication [8]. Natural antimicrobial products consist mainly of two groups i) bacteriocins [9] where biosynthesis is carried out conventionally via ribosome, and ii) polyketides (PKS) and non-ribosomal peptides (NRPS) where biosynthesis is ribosome independent. The atypical biosynthesis of NRPS and PKS known as “thiotempling” is supported by a multi-enzymatic, multi-domain synthases NRPSs and PKSs, respectively that add amino-acid monomers for NRPS and acyl Coenzyme A for PKS products. The primary sequence of the peptide product is determined by the sequential arrangement of active sites called modules within NRPSs and modular PKSs. These modules contain multiple functional domains that are necessary for catalyzing each condensation and chain elongation or modification reaction [10,11,12]. Genes encoding biosynthetic enzymes for the synthesis of these secondary metabolites are typically co-localized on the chromosome and are referred to as “biosynthetic gene clusters” (BGCs). Since the first elucidation of the PKS gene cluster for erythromycin in the early 1990s [13, 14], many gene clusters responsible for the biosynthesis of NRPS and PKS have been reported and deposited in International Nucleotide Sequence Database Collection (INSDC) entries (DDBJ/GenBank/EMBL) [15]. In addition, the community-driven website developed many specialized pieces of software such as Antismash [16,17,18] and Streptome DB [19] that enabled the detection of NRPS and PKS [20,21,22,23,24] in a wide range of microorganisms such as Bacteria, Fungi, Archaea and Eukarya. The general principle behind in silico mining consists of using a library of enzymes/protein domains commonly observed in secondary metabolite biosynthetic pathways to identify homologues in the genome sequences of the organisms of interest. For this task, sequence based comparison software, such as BLAST [25] or DIAMOND [42] where NRP-PK are produced at a high rate and which may constitute one of the defensive mechanisms used by microorganisms to survive [43, 44]. Indeed, while most natural products were isolated from environmental microbial strains recently, Staphylococcus lugdunensis, a human commensal, was described to have a protective role against Staphylococcus aureus colonization in the nasal human microbiota. This may be mediated by the antibacterial non-ribosomal peptide, Lugdunin [45]. Thus, human microbiota could be the future source of new antimicrobial discoveries, and further exploration of this ecological niche, coupled with newer technologies such as cell-free assays and high-throughput screening, should be envisaged. Further transcriptomic and gene silencing approaches can confirm the implication of NRPS/PKS clusters in the observed antimicrobial potency. Moreover, our results showed that Bacillus, Paenibacillus and Streptomyces genomes were outlier in the number of NRPS/PKS clusters. While Streptomyces species are known to be prolific producers of antibiotics and other natural products, the high rate of NRPS/PKS in Bacillus spp. is likely to reflect their abundance in the microbiota and their particular ecological role involving multiple interactions with cohabiting microbes. Given that, these species should be vigorously pursued for new antimicrobial product discoveries.

Conclusions

This work is a pioneering study to search for new NRPS-PKS naturally produced by the human digestive microbiota and showing potent antibiotic activity in vitro. The NRPPUR database integrates the latest experimentally verified information and provides standardized domain descriptions related to the gene clusters. Our database serves as a useful reference to facilitate research and development related to secondary metabolite types NRPS and PKS with potential antibiotic activity. A web interface (http://www.mediterranee-infection.com/article.php?laref=955&titre=nrppur-database-) has been developed allowing rpsBlast analyses to be performed to search for NRPS-PKS.