Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences

Libis, Vincent; Antonovsky, Niv; Zhang, Mengyin; Shang, Zhuo; Montiel, Daniel; Maniko, Jeffrey; Ternei, Melinda A.; Calle, Paula Y.; Lemetre, Christophe; Owen, Jeremy G.; Brady, Sean F.

doi:10.1038/s41467-019-11658-z

Cited by 53 publications

(61 citation statements)

References 20 publications

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“…Very recently, other studies have also aimed at linking taxonomic diversity to functionality. Thus, Libis et al (37) analyzed metagenomic cosmid libraries from soil and subjected them to amplicon sequencing followed by statistical analysis of cooccurrence patterns in order to build complete BGCs. Although the study did not focus on the taxonomic origin of these BGCs, their findings corroborate our findings with respect to the high proportion of BGCs originating from low abundance organisms (37).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, Libis et al (37) analyzed metagenomic cosmid libraries from soil and subjected them to amplicon sequencing followed by statistical analysis of cooccurrence patterns in order to build complete BGCs. Although the study did not focus on the taxonomic origin of these BGCs, their findings corroborate our findings with respect to the high proportion of BGCs originating from low abundance organisms (37). Borsetto et al (28) combined 16S rRNA and NRPS/PKS amplicon sequencing and used Mantel and Procrustes tests in the search for overall taxonomic associations at the phylum level.…”

Section: Discussionmentioning

confidence: 99%

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Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity

et al. 2020

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Novel natural products have traditionally been sourced from culturable soil microorganisms, whereas marine sources have been less explored. The purpose of this study was to profile the microbial biosynthetic potential in coastal surface seawater and sandy sediment samples and to evaluate the feasibility of capturing this potential using traditional culturing methods. Amplicon sequencing of conserved ketosynthase (KS) and adenylation (AD) domains within polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes showed that seawater and, in particular, sandy sediment had a high biosynthetic potential with 6,065 and 11,072 KS operational biosynthetic units (OBUs) and 3,292 and 5,691 AD OBUs, respectively, compared to that of four soil samples collected by Charlop-Powers et al. (Z. Charlop-Powers, C. C. Pregitzer, C. Lemetre, M. A. Ternei, et al., Proc Natl Acad Sci U S A 113:14811–14816, 2016, https://doi.org/10.1073/pnas.1615581113) with 7,067 KS and 1,629 AD OBUs. All three niches harbored unique OBUs (P = 0.001 for KS and P = 0.002 for AD by permutational multivariate analysis of variance [PERMANOVA]). The total colonial growth captured 1.9% of KS and 13.6% of AD OBUs from seawater and 2.2% KS and 12.5% AD OBUs from sediment. In a subset of bioactive isolates, only four KS OBUs and one AD OBU were recovered from whole-genome sequencing (WGS) of seven seawater-derived strains and one AD OBU from a sediment-derived strain, adding up to 0.028% of the original OBU diversity. Using a pairwise regression model of classified amplicon sequence variants (ASVs) to the species level, and OBUs, we suggest a method to estimate possible links between taxonomy and biosynthetic potential, which indicated that low abundance organisms may hold a disproportional share of the biosynthetic potential. Thus, marine microorganisms are a rich source of novel bioactive potential, which is difficult to access with traditional culturing methods. IMPORTANCE Since bacterial resistance to antibiotics is developing worldwide, new antibiotics are needed. Most antibiotics discovered so far have been found in soil-dwelling bacteria, so we instead targeted marine environments as a novel source of bioactive potential. We used amplicon sequencing of bioactive gene clusters in the microbiome of coastal seawater and sandy sediments and found the bioactive potential to be comparable to, but distinct from, the bioactive potential of selected soil microbiomes. Moreover, most of this potential is not captured by culturing. Comparing the biosynthetic potential to the corresponding microbiome composition suggested that minor constituents of the microbiome likely hold a disproportionally large fraction of the biosynthesis potential.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity

et al. 2020

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“…Omnipeptin (Libis et al, 2019) Anisomycin (Zheng et al, 2017) Ashimides (Shi et al, 2019) Frigocyclinone (Mo et al, 2019) Locillomycins (Luo et al, 2019) PAC/BAC libraries…”

Section: Dna Fragmentationmentioning

confidence: 99%

“…The above-mentioned DNA assembly methods were developed in the past decades, and there are already many successful applications ( Table 1). For example, Libis et al (2019) have screened a 10 million cosmid library from soil metagenomic DNA samples using Co-occurrence Network Analysis of Targeted Sequences (CONKAT-seq), and identified omnipeptin. Moreover, Bok et al (2015) have constructed a novel Aspergillus-E. coli shuttle FAC expression vector coupling a BAC vector backbone with an autonomous fungal replicating element AMA1 from Aspergillus nidulans.…”

Section: Successful Applicationsmentioning

confidence: 99%

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Lin

Nielsen

Liu

2020

Front. Bioeng. Biotechnol.

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Since the discovery of penicillin, natural products and their derivatives have been a valuable resource for drug discovery. With recent development of genome mining approaches in the post-genome era, a great number of natural product biosynthetic gene clusters (BGCs) have been identified and these can potentially be exploited for the discovery of novel natural products that can find application as pharmaceuticals. Since many BGCs are silent or do not express in native hosts under laboratory conditions, heterologous expression of BGCs in genetically tractable hosts becomes an attractive route to activate these BGCs to discover the corresponding products. Here, we highlight recent achievements in cloning and discovery of natural product biosynthetic pathways via intact BGC capturing, and discuss the prospects of high-throughput and multiplexed cloning of rational-designed gene clusters in the future.

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“…Previous work has demonstrated the potential for deep “shotgun” metagenomic sequencing to directly characterize BGCs from environmental samples 10 11 , but the assembly of full-length BGCs from short reads is associated with significant limitations 12 . Alternative techniques include the use of clone libraries 1 or innovative sequence-based analyses 13, 14 including the reconstruction of uncultivated microbes as metagenome-assembled genomes (MAGs; reviewed in 15 ).…”

mentioning

confidence: 99%

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Goethem

Osborn

Bowen

et al. 2021

Preprint

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Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 695 novel, full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night in cyanobacteria but not in other phyla, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

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Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences

Cited by 53 publications

References 20 publications

Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity

Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

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