scholarly journals Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Shuilin Liao ◽  
Yayu Wang ◽  
Huan Liu ◽  
Guangyi Fan ◽  
Sunil Kumar Sahu ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
De Novo ◽  
Southern China ◽  
Sulfur Metabolism ◽  
Gene Clusters ◽  
Metagenomic Sequencing ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Mangrove Ecosystems ◽  
Unique Genes

ABSTRACT Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially the variations between pristine and anthropogenic mangroves. To elucidate this, we investigated the microbial taxonomic and functional shifts of the mangrove microbiomes and their potential for bioactive compounds in two different coastal mangrove ecosystems in southern China. A gene catalogue, including 87 million unique genes, was constructed, based on deep shotgun metagenomic sequencing. Differentially enriched bacterial and archaeal taxa between pristine mangroves (Guangxi) and anthropogenic mangroves (Shenzhen) were found. The Nitrospira and ammonia-oxidizing archaea, specifically, were more abundant in Shenzhen mangroves, while sulfate-reducing bacteria and methanogens were more abundant in Guangxi mangroves. The results of functional analysis were consistent with the taxonomic results, indicating that the Shenzhen mangrove microbiome has a higher abundance of genes involved in nitrogen metabolism while the Guangxi mangrove microbiome has a higher capacity for sulfur metabolism and methanogenesis. Biosynthetic gene clusters were identified in the metagenome data and in hundreds of de novo reconstructed nonredundant microbial genomes, respectively. Notably, we found different biosynthetic potential in different taxa, and we identified three high quality and novel Acidobacteria genomes with a large number of BGCs. In total, 67,278 unique genes were annotated with antibiotic resistance, indicating the prevalence and persistence in multidrug-resistant genes in the mangrove microbiome. IMPORTANCE This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.

scholarly journals Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi

2019 ◽  
Vol 103 (8) ◽  
pp. 3277-3287 ◽  
Author(s):  
Phuong Nguyen Tran ◽  
Ming-Ren Yen ◽  
Chen-Yu Chiang ◽  
Hsiao-Ching Lin ◽  
Pao-Yang Chen
Keyword(s):  
Bioactive Compounds ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Bacteria And Fungi

scholarly journals Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex

2017 ◽  
Vol 199 (13) ◽  
Author(s):  
E. Joel Loveridge ◽  
Cerith Jones ◽  
Matthew J. Bull ◽  
Suzy C. Moody ◽  
Małgorzata W. Kahl ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bioactive Compounds ◽  
Single Molecule ◽  
Complete Genome ◽  
Burkholderia Cepacia ◽  
Gene Clusters ◽  
Burkholderia Cepacia Complex ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type

ABSTRACT Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis. The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization. IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis. Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.

scholarly journals Biosynthetic gene clusters and the evolution of fungal chemodiversity

2020 ◽  
Vol 37 (7) ◽  
pp. 868-878 ◽  
Author(s):  
Antonis Rokas ◽  
Matthew E. Mead ◽  
Jacob L. Steenwyk ◽  
Huzefa A. Raja ◽  
Nicholas H. Oberlies
Keyword(s):  
Gene Cluster ◽  
Horizontal Transfer ◽  
De Novo ◽  
Functional Divergence ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Evolutionary Processes

This highlight synthesizes knowledge of the molecular evolutionary processes – functional divergence, horizontal transfer, and de novo assembly – that govern biosynthetic gene cluster diversification and the generation of chemodiversity in fungi.

scholarly journals Dual Role of GdmH in Producer Immunity and Secretion of the Staphylococcal Lantibiotics Gallidermin and Epidermin

2001 ◽  
Vol 67 (3) ◽  
pp. 1380-1383 ◽  
Author(s):  
Matthias Hille ◽  
Stefanie Kies ◽  
Friedrich Götz ◽  
Andreas Peschel
Keyword(s):  
Antimicrobial Peptides ◽  
Gene Clusters ◽  
Synergistic Activity ◽  
Biosynthetic Gene ◽  
Cellular Functions ◽  
Biosynthetic Gene Clusters ◽  
Atp Binding Cassette Transporters ◽  
Immunity Genes ◽  
Unique Genes

ABSTRACT The biosynthetic gene clusters of the staphylococcal lantibiotics epidermin and gallidermin are distinguished by the presence of the unique genes epiH and gdmH, respectively. They encode accessory factors for the ATP-binding cassette transporters that mediate secretion of the antimicrobial peptides. Here, we show thatgdmH also contributes to immunity to gallidermin but not to nisin. gdmH alone affected susceptibility to gallidermin only moderately, but it led to a multiplication of the immunity level mediated by the FEG immunity genes when cloned together with the gdmT gene, suggesting a synergistic activity of the H and FEG systems. gdmH-related genes were identified in the genomes of several bacteria, indicating an involvement in further cellular functions.

scholarly journals Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome

2020 ◽  
Vol 37 (9) ◽  
pp. 1164-1180 ◽  
Author(s):  
Liwen Zhang ◽  
Qun Yue ◽  
Chen Wang ◽  
Yuquan Xu ◽  
István Molnár
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Entomopathogenic Fungi ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Whole genome sequencing allows the cataloguing of the parvome (secondary metabolome) of hypocrealean entomopathogenic fungi, uncovering biosynthetic gene clusters for known and novel bioactive compounds with ecological and pharmaceutical significance.

scholarly journals Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Snorre Sulheim ◽  
Fredrik A. Fossheim ◽  
Alexander Wentzel ◽  
Eivind Almaas
Keyword(s):  
Heterologous Expression ◽  
Bioactive Compounds ◽  
Metabolic Pathways ◽  
Gene Clusters ◽  
Strain Engineering ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Wide Range ◽  
Metabolic Models ◽  
Genome Scale

Abstract Background A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA sequence. Candidates for further research and development may be prioritized based on properties such as their functional annotation, (dis)similarity to known BGCs, and bioactivity assays. Production of the target compound in the native strain is often not achievable, rendering heterologous expression in an optimized host strain as a promising alternative. Genome-scale metabolic models are frequently used to guide strain development, but large-scale incorporation and testing of heterologous production of complex natural products in this framework is hampered by the amount of manual work required to translate annotated BGCs to metabolic pathways. To this end, we have developed a pipeline for an automated reconstruction of BGC associated metabolic pathways responsible for the synthesis of non-ribosomal peptides and polyketides, two of the dominant classes of bioactive compounds. Results The developed pipeline correctly predicts 72.8% of the metabolic reactions in a detailed evaluation of 8 different BGCs comprising 228 functional domains. By introducing the reconstructed pathways into a genome-scale metabolic model we demonstrate that this level of accuracy is sufficient to make reliable in silico predictions with respect to production rate and gene knockout targets. Furthermore, we apply the pipeline to a large BGC database and reconstruct 943 metabolic pathways. We identify 17 enzymatic reactions using high-throughput assessment of potential knockout targets for increasing the production of any of the associated compounds. However, the targets only provide a relative increase of up to 6% compared to wild-type production rates. Conclusion With this pipeline we pave the way for an extended use of genome-scale metabolic models in strain design of heterologous expression hosts. In this context, we identified generic knockout targets for the increased production of heterologous compounds. However, as the predicted increase is minor for any of the single-reaction knockout targets, these results indicate that more sophisticated strain-engineering strategies are necessary for the development of efficient BGC expression hosts.

scholarly journals De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Opeyemi K. Awolope ◽  
Noelle H. O’Driscoll ◽  
Alberto Di Salvo ◽  
Andrew J. Lamb
Keyword(s):  
Plant Growth ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Gc Content ◽  
Gene Clusters ◽  
Genomic Islands ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Pseudomonas Fragi ◽  
Single Chromosome

Abstract Objectives The role of rhizosphere microbiome in supporting plant growth under biotic stress is well documented. Rhizobacteria ward off phytopathogens through various mechanisms including antibiosis. We sought to recover novel antibiotic-producing bacterial strains from soil samples collected from the rhizosphere. Pseudomonas fragi A13BB was recovered as part of this effort, and the whole genome was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters. Data description Here, we report the complete genome sequence of P. fragi A13BB obtained from de novo assembly of Illumina MiSeq and GridION reads. The 4.94 Mb genome consists of a single chromosome with a GC content of 59.40%. Genomic features include 4410 CDSs, 102 RNAs, 3 CRISPR arrays, 3 prophage regions, and 37 predicted genomic islands. Two β-lactone biosynthetic gene clusters were identified; besides, metabolic products of these are known to show antibiotic and/or anticancer properties. A siderophore biosynthetic gene cluster was also identified even though P. fragi is considered a non-siderophore producing pseudomonad. Other gene clusters of broad interest identified include those associated with bioremediation, biocontrol, plant growth promotion, or environmental adaptation. This dataset unveils various un−/underexplored metabolic or biosynthetic potential of P. fragi and provides insight into molecular mechanisms underpinning these attributes.

scholarly journals CoronaSPAdes: from biosynthetic gene clusters to coronaviral assemblies

2020 ◽  
Author(s):  
Dmitry Meleshko ◽  
Anton Korobeynikov
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Structure ◽  
Gene Clusters ◽  
Full Length ◽  
Biosynthetic Gene ◽  
Scientific Interest ◽  
Biosynthetic Gene Clusters ◽  
Short Read ◽  
Species Recovery

AbstractCOVID-19 pandemy has ignited a broad scientific interest in coronavirus research. The identification of coronaviridae species in natural reservoirs often requires de novo assembly. However, existing transcriptome assemblers often are not able to assemble coronaviruses into a single contig. We developed coronaSPAdes, a new module for SPAdes assembler for coronavirus species recovery. coronaSPAdes uses the knowledge about coronaviridae genome structure to improve assembly. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read assemblers in the recovery of full-length coronavirus genomes. This should allow to better understand the coronaviridae spread and diversity.

Epigenetic modification, co-culture and genomic methods for natural product discovery

2018 ◽  
Vol 4 (4) ◽  
Author(s):  
Sergi Herve Akone ◽  
Cong-Dat Pham ◽  
Huiqin Chen ◽  
Antonius R. B. Ola ◽  
Fidele Ntie-Kang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Bioactive Compounds ◽  
Epigenetic Modification ◽  
Gene Clusters ◽  
Histone Deacetylation ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Mixed Fermentation ◽  
Silent Genes ◽  
Promising Source

Abstract Fungi and bacteria are encountered in many habitats where they live in complex communities interacting with one another mainly by producing secondary metabolites, which are organic compounds that are not directly involved in the normal growth, development, or reproduction of the organism. These organisms appear as a promising source for the discovery of novel bioactive natural products that may find their application in medicine. However, the production of secondary metabolites by those organisms when cultured axenically is limited as only a subset of biosynthetic genes is expressed under standard laboratory conditions leading to the search of new methods for the activation of the silent genes including epigenetic modification and co-cultivation. Biosynthetic gene clusters which produce secondary metabolites are known to be present in a heterochromatin state in which the transcription of constitutive genes is usually regulated by epigenetic modification including DNA methylation and histone deacetylation. Therefore, small-molecule epigenetic modifiers which promote changes in the structure of chromatin could control the expression of silent genes and may be rationally employed for the discovery of novel bioactive compounds. Co-cultivation, which is also known as mixed-fermentation, usually implies two or more microorganisms in the same medium in which the resulting competition is known to enhance the production of constitutively present compounds and/or to lead to the induction of cryptic metabolites that were not detected in axenic cultures of the considered axenic microorganism. Genomic strategies could help to identify biosynthetic gene clusters in fungal genomes and link them to their products by the means of novel algorithms as well as integrative pan-genomic approaches. Despite that all these techniques are still in their infancy, they appear as promising sources for the discovery of new bioactive compounds. This chapter presents recent ecological techniques for the discovery of new secondary metabolites that might find application in medicine.

scholarly journals Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Stephen C. Heinsch ◽  
Szu-Yi Hsu ◽  
Lindsey Otto-Hanson ◽  
Linda Kinkel ◽  
Michael J. Smanski
Keyword(s):  
Microbial Communities ◽  
Natural Product ◽  
De Novo ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Sequencing Data ◽  
Biosynthetic Gene Clusters ◽  
Contig Assembly ◽  
Sample Number

Abstract Background Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays. Results Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93–23, Streptomyces sp. 3211–3, and Streptomyces sp. S3–4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution. Conclusions Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93–23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.

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