Molecular beacons to identify gifted microbes for genome mining

Baltz, Richard H.

doi:10.1038/ja.2017.1

Cited by 27 publications

(26 citation statements)

References 58 publications

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“…A large number of contigs in the genome assembly can lead to BGCs, especially PKS-I and NRPS, to be broken across pieces and not being identified by available software and tools. A great example of such issue was demonstrated by Baltz who showed that draft genomes containing large NRPS/PKS-I genes were incorrectly assembled due to being largely fragmented which resulted in overestimation of such BGCs by antiSMASH 3.0 [57]. However, since then, new updated versions of antiSMASH have been released in which the location of the gene cluster close to the contig edge is flagged.…”

Section: Discussionmentioning

confidence: 99%

Comparative Metabologenomics Analysis of Polar Actinomycetes

et al. 2021

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Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.

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Section: Discussionmentioning

confidence: 99%

Comparative Metabologenomics Analysis of Polar Actinomycetes

et al. 2021

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“…Moreover, resistome is now identified in almost every microbial community, including soil, activated sludge, human gut and oral microbiomes, and animal gut microbiomes [ 539 , 540 ]. On the other hand, it is now extremely difficult to find an effective antibiotic against resistant pathogenic bacteria, although every effort has been taken to discover new antibiotics [ 541 , 542 , 543 ]. One of the steps to solve this problem is to know precisely the mechanisms of drug resistance in the various kingdoms once more.…”

Section: Discussionmentioning

confidence: 99%

Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms

Ogawara

2018

Molecules

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Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.

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“…The advances in genome sequencing of extremophilic microorganisms have allowed us to provide a comprehensive understanding of their applications [93][94][95]. Moreover, microbes with large genomes, usually inhabiting complex harsh environments, can produce a vast array of secondary metabolites [96,97].…”

Section: Biotechnological Potential Of Prokaryotes Inhabiting Dhabsmentioning

confidence: 99%

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

2020

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Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.

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Molecular beacons to identify gifted microbes for genome mining

Cited by 27 publications

References 58 publications

Comparative Metabologenomics Analysis of Polar Actinomycetes

Comparative Metabologenomics Analysis of Polar Actinomycetes

Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

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