Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge

Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies

This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.

N-Succinyltransferase Encoded by a Cryptic Siderophore Biosynthesis Gene Cluster in Streptomyces Modifies Structurally Distinct Antibiotics

The antibiotic desertomycin A and its previously undescribed inactive N-succinylated analogue, desertomycin X, were isolated from Streptomyces sp. strain YIM 121038. Genome sequencing and analysis readily identified the desertomycin biosynthetic gene cluster (BGC), which lacked genes encoding acyltransferases that would account for desertomycin X formation. Scouting the genome for putative N-acyltransferase genes led to the identification of a candidate within a cryptic siderophore BGC (csb) encoding a putative homologue of the N6'-hydroxylysine acetyltransferase IucB. Expression of the codon-optimized gene designated csbC in Escherichia coli yielded the recombinant protein that was able to N-succinylate desertomycin A as well as several other structurally distinct antibiotics harboring amino groups. Some antibiotics were rendered antibiotically inactive due to the CsbC-catalyzed succinylation in vitro. Unlike many known N-acyltransferases involved in antibiotic resistance, CsbC could not efficiently acetylate the same antibiotics. When expressed in E. coli, CsbC provided low-level resistance to kanamycin and ampicillin, suggesting that it may play a role in antibiotic resistance in natural habitats, where the concentration of antibiotics is usually low. IMPORTANCE In their natural habitats, bacteria encounter a plethora of organic compounds, some of which may be represented by antibiotics produced by certain members of the microbial community. A number of antibiotic resistance mechanisms have been described, including those specified by distinct genes encoding proteins that degrade, modify, or expel antibiotics. In this study, we report identification and characterization of an enzyme apparently involved in the biosynthesis of a siderophore, but also having the ability of modify and thereby inactivate a wide variety of structurally diverse antibiotics. This discovery sheds light on additional capabilities of bacteria to withstand antibiotic treatment and suggests that enzymes involved in secondary metabolism may have an additional function in the natural environment.

Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis

A key step in the biosynthesis of numerous polyketides is the stereospecific formation of a spiroacetal (spiroketal). We report here that spiroacetal formation in the biosynthesis of the macrocyclic polyketides ossamycin and oligomycin involves catalysis by a novel spiroacetal cyclase. OssO from the ossamycin biosynthetic gene cluster (BGC) is homologous to OlmO, the product of an unannotated gene from the oligomycin BGC. The deletion of olmO abolished oligomycin production and led to the isolation of oligomycin-like metabolites lacking the spiroacetal structure. Purified OlmO catalyzed complete conversion of the major metabolite into oligomycin C. Crystal structures of OssO and OlmO reveal an unusual 10-strand β-barrel. Three conserved polar residues are clustered together in the β-barrel cavity, and site-specific mutation of any of these residues either abolished or substantially diminished OlmO activity, supporting a role for general acid/general base catalysis in spiroacetal formation.

Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products

Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.

Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic

Streptomyces bacteria are recognized as an important source for antibiotics with broad applications in human medicine and animal health. Here, we report the isolation of a new lichen-associating Streptomyces sp. YIM 130001 from the tropical rainforest in Xishuangbanna (Yunnan, China), which displayed antibacterial activity against Bacillus subtilis. The draft genome sequence of this isolate strain revealed 18 putative biosynthetic gene clusters (BGCs) for secondary metabolites, which is an unusually low number compared to a typical streptomycete. Inactivation of a lantibiotic dehydrogenase-encoding gene from the BGC presumed to govern biosynthesis of a thiopeptide resulted in the loss of bioactivity. Using comparative HPLC analysis, two peaks in the chromatogram were identified in the extract from the wild-type strain, which were missing in the extract from the mutant. The compounds corresponding to the identified peaks were purified, and structure of one compound was elucidated using NMR. The compound, designated geninthiocin B, showed high similarity to several 35-membered macrocyclic thiopeptides geninthiocin, Val-geninthiocin and berninamycin A. Bioinformatics analysis of the geninthiocin B BGC revealed its close homology to that of berninamycins.

Genomics-Based Insights Into the Biosynthesis and Unusually High Accumulation of Free Fatty Acids by Streptomyces sp. NP10

Streptomyces sp. NP10 was previously shown to synthesize large amounts of free fatty acids (FFAs). In this work, we report the first insights into the biosynthesis of these fatty acids (FAs) gained after genome sequencing and identification of the genes involved. Analysis of the Streptomyces sp. NP10 draft genome revealed that it is closely related to several strains of Streptomyces griseus. Comparative analyses of secondary metabolite biosynthetic gene clusters, as well as those presumably involved in FA biosynthesis, allowed identification of an unusual cluster C12-2, which could be identified in only one other S. griseus-related streptomycete. To prove the involvement of identified cluster in FFA biosynthesis, one of its three ketosynthase genes was insertionally inactivated to generate mutant strain mNP10. Accumulation of FFAs in mNP10 was almost completely abolished, reaching less than 0.01% compared to the wild-type strain. Cloning and transfer of the C12-2 cluster to the mNP10 mutant partially restored FFA production, albeit to a low level. The discovery of this rare FFA biosynthesis cluster opens possibilities for detailed characterization of the roles of individual genes and their products in the biosynthesis of FFAs in NP10.

Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation

Two actinobacterial strains, ADI 127-17^T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17^T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17^T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17^T (= DSM 46855^T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17^T = DSM 46855^T = CECT 9355^T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092^T and A. hoggarensis DSM 45943^T to unravel unique genome features and biosynthetic potential of the new isolates.