Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

Abstract

Background Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes. Results We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26T (= CCTCC M2020899T) as the type strain. The complete genome of P. jilinensis YPG26T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested. Conclusions This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents.

Culturing the Chicken Intestinal Microbiota and Potential Application as Probiotics Development

“…Based on the recommended 16S rRNA sequence 98.65% similarity thresholds for identifying novel bacterial species [11], these uncultured bacteria could be assigned four potential novel species, including Paenibacillus jilinensis sp. nov., validated in our previous studies [12], which fully demonstrate the diversity of chicken intestinal microbiota. In addition, these isolates were dominated by Lactobacillus (62.3% of strains).…”

“…In addition, a total of 89 strains were characterized as previous uncultured bacteria (Figure 1B), and based on the recommended 16S rRNA sequence 98.65% similarity thresholds for identifying bacterial species [11], it could be assigned potential for four novel species, among them, Paenibacillus jilinensis sp. nov. YPG26 has been validated in our previous studies [12], but we are also working to validate three additional novel species by whole genome sequencing-based phylogenomic analysis. To further investigate the effect of mediums on bacterial isolates, we analyzed and summarized the number of isolates from each medium; the results showed that the species of bacterial isolates increased significantly in the M2 and M3 medium supplemented with FBS or blood, respectively (Table 1).…”