BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Meleshko, Dmitry; Mohimani, Hosein; Tracanna, Vittorio; Hajirasouliha, Iman; Medema, Marnix H.; Korobeynikov, Anton; Pevzner, Pavel A.

doi:10.1101/gr.243477.118

Cited by 49 publications

(50 citation statements)

References 51 publications

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“…3A). It was previously shown that NRPS/PKS gene clusters often result in fragmented assemblies from short reads (22). While we saw 1,100 CD and 939 KS domains in total on contigs of Ͼ10 kb across our genomes, we also saw 555 CD and 417 KS domains on contigs of Ͻ10 kb, indicating that a large fraction of BGCs in the genomes of these microbes may not have been analyzed here.…”

Section: Resultsmentioning

confidence: 52%

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Sharrar

Crits-Christoph

Méheust

et al. 2020

mBio

139

104

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Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles.

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Section: Resultsmentioning

confidence: 52%

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Sharrar

Crits-Christoph

Méheust

et al. 2020

mBio

139

104

View full text Add to dashboard Cite

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“…We found an overwhelming majority of C and KS domain sequences having sequence identity scores well below 85% to their predicted natural product ( Supplementary Tables S2, S3 ). It was previously shown that shotgun metagenomics may lead to fragments of NRPS/PKS gene clusters which may account for the large number of low identity scores ( Meleshko et al, 2019 ). On the contrary, scores below the threshold may imply potential novelty in NRPS and PKS products, although further studies would be required to assess the extent of this novelty.…”

Section: Resultsmentioning

confidence: 99%

Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats

et al. 2020

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Microbial mats are geobiological multilayered ecosystems that have significant evolutionary value in understanding the evolution of early life on Earth. Shark Bay, Australia has some of the best examples of modern microbial mats thriving under harsh conditions of high temperatures, salinity, desiccation, and ultraviolet (UV) radiation. Microorganisms living in extreme ecosystems are thought to potentially encode for secondary metabolites as a survival strategy. Many secondary metabolites are natural products encoded by a grouping of genes known as biosynthetic gene clusters (BGCs). Natural products have diverse chemical structures and functions which provide competitive advantages for microorganisms and can also have biotechnology applications. In the present study, the diversity of BGC were described in detail for the first time from Shark Bay microbial mats. A total of 1477 BGCs were detected in metagenomic data over a 20 mm mat depth horizon, with the surface layer possessing over 200 BGCs and containing the highest relative abundance of BGCs of all mat layers. Terpene and bacteriocin BGCs were highly represented and their natural products are proposed to have important roles in ecosystem function in these mat systems. Interestingly, potentially novel BGCs were detected from Heimdallarchaeota and Lokiarchaeota, two evolutionarily significant archaeal phyla not previously known to possess BGCs. This study provides new insights into how secondary metabolites from BGCs may enable diverse microbial mat communities to adapt to extreme environments.

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“…No BGC was shared between all six strains, however, the BGC predicted by antiSMASH to encode enzymes required for biosynthesis of an N -tetradecanoyl tyrosine-like compound was identified in all strains, except for P. maricaloris LMG 19692 T . Since only two of the genomes are complete genomes, it is likely that this BGC would also be identified in P. maricaloris LMG 19692 T , as BGCs are known to be difficult to detect in contig-based genomes due to the repeat regions in BGCs 30 . The predicted BGCs in all six strains shared little to no sequence homology to already known BGCs (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov.

Paulsen

Isbrandt

Kirkegaard

et al. 2020

Sci Rep

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Novel antimicrobials are urgently needed due to the rapid spread of antibiotic resistant bacteria. In a genome-wide analysis of Pseudoalteromonas strains, one strain (S4498) was noticed due to its potent antibiotic activity. It did not produce the yellow antimicrobial pigment bromoalterochromide, which was produced by several related type strains with which it shared less than 95% average nucleotide identity. Also, it produced a sweet-smelling volatile not observed from other strains. Mining the genome of strain S4498 using the secondary metabolite prediction tool antiSMASH led to eight biosynthetic gene clusters with no homology to known compounds, and synteny analyses revealed that the yellow pigment bromoalterochromide was likely lost during evolution. Metabolome profiling of strain S4498 using HPLC-HRMS analyses revealed marked differences to the type strains. In particular, a series of quinolones known as pseudanes were identified and verified by NMR. The characteristic odor of the strain was linked to the pseudanes. The highly halogenated compound tetrabromopyrrole was detected as the major antibacterial component by bioassay-guided fractionation. Taken together, the polyphasic analysis demonstrates that strain S4498 belongs to a novel species within the genus Pseudoalteromonas, and we propose the name Pseudoalteromonas galatheae sp. nov. (type strain S4498T = NCIMB 15250T = LMG 31599T).

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BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Cited by 49 publications

References 51 publications

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats

Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov.

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