Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin.

A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated strain NJES-13 from its close relatives within the family Dermatophilaceae. Hence, it clearly indicated that strain NJES-13 represented a putative new actinobacterial species isolated from the gut microbiota of mammals inhabiting the Antarctic. The obtained complete genome of strain NJES-13 consisted of a circular 3.45 Mb chromosome with a DNA G+C content of 67.0 mol%. Furthering genome mining of strain NJES-13 showed the presence of five biosynthetic gene clusters (BGCs) including one type III PKS responsible for the biosynthesis of the core of gephyromycins, and a series of genes encoding for bacterial EPS biosynthesis. Thus, based on the combined phylogenetic and active metabolites characterization presented in this study, we confidently conclude that strain NJES-13 is a novel, fresh actinobacterial candidate to produce active gephyromycins and microbial bioflocculanting EPS, with potential pharmaceutical, environmental and biotechnological implications.

一株被命名为NJES - 13的新型多功能放线菌从南极帝企鹅的粪便中分离出来。发现这株新分离菌能产生两种活性的地霉素类似物以及生物絮凝胞外多糖（EPS）代谢产物。基于16S rRNA基因序列成对比较的系统发育分析表明，NJES - 13菌株与远洋动球菌Aji5 - 31T密切相关，基因相似度为95.9%，低于新物种界定的阈值（98.65%）。对平均核苷酸一致性（ANI，75.9 - 79.1%）、平均氨基酸一致性（AAI，52.4 - 66.9%）和数字DNA - DNA杂交（dDDH，18.6 - 21.9%）进行的额外系统基因组计算，以及基于细菌基因组中最新细菌核心基因（UBCG）集构建的系统基因组树，明确地将NJES - 13菌株与其在嗜皮菌科内的近亲区分开来。因此，这清楚地表明NJES - 13菌株代表了一种从栖息在南极的哺乳动物肠道微生物群中分离出来的潜在的新型放线菌物种。NJES - 13菌株获得的完整基因组由一个3.45 Mb的环形染色体组成，DNA G + C含量为67.0 mol%。对NJES - 13菌株进一步的基因组挖掘显示存在五个生物合成基因簇（BGCs），包括一个负责地霉素核心生物合成的III型聚酮合酶，以及一系列编码细菌EPS生物合成的基因。因此，基于本研究中呈现的系统发育和活性代谢产物特征的综合分析，我们有把握地得出结论：NJES - 13菌株是一种新型的、有潜力产生活性地霉素和微生物生物絮凝EPS的放线菌候选菌株，具有潜在的药学、环境和生物技术方面的意义。