scholarly journals The natural product biosynthetic potential of Red Sea nudibranch microbiomes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10525
Author(s):  
Samar M. Abdelrahman ◽  
Nastassia V. Patin ◽  
Amro Hanora ◽  
Akram Aboseidah ◽  
Shimaa Desoky ◽  
...  
Keyword(s):  
Antitumor Activity ◽  
16S Rrna ◽  
Microbial Communities ◽  
Natural Product ◽  
Red Sea ◽  
High Throughput Sequencing ◽  
Marine Invertebrates ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Biosynthetic Gene

Background Antibiotic resistance is a growing problem that can be ameliorated by the discovery of novel drug candidates. Bacterial associates are often the source of pharmaceutically active natural products isolated from marine invertebrates, and thus, important targets for drug discovery. While the microbiomes of many marine organisms have been extensively studied, microbial communities from chemically-rich nudibranchs, marine invertebrates that often possess chemical defences, are relatively unknown. Methods We applied both culture-dependent and independent approaches to better understand the biochemical potential of microbial communities associated with nudibranchs. Gram-positive microorganisms isolated from nudibranchs collected in the Red Sea were screened for antibacterial and antitumor activity. To assess their biochemical potential, the isolates were screened for the presence of natural product biosynthetic gene clusters, including polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, using PCR. The microbiomes of the nudibranchs were investigated by high-throughput sequencing of 16S rRNA amplicons. Results In screens against five model microorganisms, 51% of extracts displayed antimicrobial activity against more than one organism, and 19% exhibited antitumor activity against Ehrlich’s ascites carcinoma. Sixty-four percent of isolates contained PKS and NRPS genes, suggesting their genomes contain gene clusters for natural product biosynthesis. Thirty-five percent were positive for more than one class of biosynthetic gene. These strains were identified as belonging to the Firmicutes and Actinobacteria phyla via 16S rRNA gene sequencing. In addition, 16S rRNA community amplicon sequencing revealed all bacterial isolates were present in the uncultured host-associated microbiome, although they were a very small percentage of the total community. Taken together, these results indicate that bacteria associated with marine nudibranchs are potentially a rich source of bioactive compounds and natural product biosynthetic genes.

scholarly journals Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

2012 ◽  
Vol 78 (10) ◽  
pp. 3744-3752 ◽  
Author(s):  
Boojala Vijay B. Reddy ◽  
Dimitris Kallifidas ◽  
Jeffrey H. Kim ◽  
Zachary Charlop-Powers ◽  
Zhiyang Feng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Natural Product ◽  
Gene Sequence ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Type I ◽  
Adenylation Domain ◽  
Biosynthetic Gene ◽  
Bacterial Phyla

ABSTRACTThe number of bacterial species estimated to exist on Earth has increased dramatically in recent years. This newly recognized species diversity has raised the possibility that bacterial natural product biosynthetic diversity has also been significantly underestimated by previous culture-based studies. Here, we compare 454-pyrosequenced nonribosomal peptide adenylation domain, type I polyketide ketosynthase domain, and type II polyketide ketosynthase alpha gene fragments amplified from cosmid libraries constructed using DNA isolated from three different arid soils. While 16S rRNA gene sequence analysis indicates these cloned metagenomes contain DNA from similar distributions of major bacterial phyla, we found that they contain almost completely distinct collections of secondary metabolite biosynthetic gene sequences. When grouped at 85% identity, only 1.5% of the adenylation domain, 1.2% of the ketosynthase, and 9.3% of the ketosynthase alpha sequence clusters contained sequences from all three metagenomes. Although there is unlikely to be a simple correlation between biosynthetic gene sequence diversity and the diversity of metabolites encoded by the gene clusters in which these genes reside, our analysis further suggests that sequences in one soil metagenome are so distantly related to sequences in another metagenome that they are, in many cases, likely to arise from functionally distinct gene clusters. The marked differences observed among collections of biosynthetic genes found in even ecologically similar environments suggest that prokaryotic natural product biosynthesis diversity is, like bacterial species diversity, potentially much larger than appreciated from culture-based studies.

scholarly journals In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghofran Othoum ◽  
Salim Bougouffa ◽  
Rozaimi Razali ◽  
Ameerah Bokhari ◽  
Soha Alamoudi ◽  
...  
Keyword(s):  
Natural Product ◽  
Red Sea ◽  
In Silico ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

scholarly journals Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

2020 ◽  
Vol 8 (2) ◽  
pp. 198
Author(s):  
Mingyue Li ◽  
Tiezhu Mi ◽  
Zhigang Yu ◽  
Manman Ma ◽  
Yu Zhen
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Liaohe River ◽  
Estuarine Wetland ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

scholarly journals Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products

2021 ◽  
Vol 9 (7) ◽  
pp. 1347
Author(s):  
Tânia Keiko Shishido ◽  
Matti Wahlsten ◽  
Pia Laine ◽  
Jouko Rikkinen ◽  
Taina Lundell ◽  
...  
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Indigenous Communities ◽  
Gene Clusters ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Shotgun Metagenomics

Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.

scholarly journals Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments

2014 ◽  
Vol 8 (12) ◽  
pp. e3240 ◽  
Author(s):  
Katrine L. Whiteson ◽  
Vladimir Lazarevic ◽  
Manuela Tangomo-Bento ◽  
Myriam Girard ◽  
Heather Maughan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rrna Gene

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.

scholarly journals Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library

2020 ◽  
Vol 11 ◽  
Author(s):  
Alinne L. R. Santana-Pereira ◽  
Megan Sandoval-Powers ◽  
Scott Monsma ◽  
Jinglie Zhou ◽  
Scott R. Santos ◽  
...  
Keyword(s):  
Natural Product ◽  
Soil Microorganisms ◽  
Polyketide Synthase ◽  
Metagenomic Library ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Type I ◽  
Biosynthetic Gene ◽  
Pcr Screening ◽  
Natural Product Discovery

Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

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