Ecology and genomics of Actinobacteria: new concepts for natural product discovery

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(10), С. 546 - 558

Опубликована: Июнь 1, 2020

Язык: Английский

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Actinobacteria in natural products research: Progress and prospects

Microbiological Research, Год журнала: 2021, Номер 246, С. 126708 - 126708

Опубликована: Янв. 22, 2021

Язык: Английский

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Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

npj Biofilms and Microbiomes, Год журнала: 2023, Номер 9(1)

Опубликована: Сен. 22, 2023

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir microbial biodiversity, yet majority desert microorganisms remain uncharacterized are seen as "microbial dark matter". Here, we introduce multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, shotgun metagenomic sequencing. The results showed CBM captured amount taxonomic functional diversity missed in direct sequencing by increasing recovery amplicon sequence variants (ASVs) high/medium-quality metagenome-assembled genomes (MAGs). Importantly, allowed post hoc microbes interest (e.g., novel or specific taxa), even those with extremely low abundance culture. Furthermore, strain-level analyses based on revealed soils harbored considerable number bacterial candidates (1941, 51.4%), which 1095 (from CBM) were culturable. However, would not exactly reflect relative true composition pathways situ environment, its use coupled could provide greater insight into microbiomes. Overall, this study exemplifies strategy high-resolution is an ideal way to deeply explore untapped resources soils, substantially expands our knowledge matter hidden vast expanse deserts.

Язык: Английский

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Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls

Pharmaceutical Research, Год журнала: 2020, Номер 37(7)

Опубликована: Июнь 11, 2020

Язык: Английский

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Perspectives on the microorganism of extreme environments and their applications

Current Research in Microbial Sciences, Год журнала: 2022, Номер 3, С. 100134 - 100134

Опубликована: Янв. 1, 2022

Extremophiles are organisms that can survive and thrive in conditions termed as "extreme" by human beings. Conventional methods cannot be applied under extreme like temperature pH fluctuations, high salinity, etc. for a variety of reasons. function adapted to these environments sustainable, cheaper, efficient, therefore, they serve better alternatives the traditional methods. They adapt with biochemical physiological changes produce products extremolytes, extremozymes, biosurfactants, etc., which found useful wide range industries sustainable agriculture, food, cosmetics, pharmaceuticals. These also play crucial role bioremediation, production biofuels, biorefinery, astrobiology. This review paper comprehensively lists out current applications extremophiles their various explores prospects same. help us understand underlying basis biological mechanisms exploring boundaries life thus origin evolution on Earth. helps research extra-terrestrial space exploration. The structure properties along any possible long-term effects need investigated further.

Язык: Английский

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Actinobacteria From Desert: Diversity and Biotechnological Applications

Frontiers in Microbiology, Год журнала: 2021, Номер 12

Опубликована: Дек. 9, 2021

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 2021, 129 new species been continuously reported from 35 deserts worldwide. The two largest numbers of members genera Streptomyces Geodermatophilus , followed by other extremophilic strains such alkaliphiles, halotolerant species, thermophiles, psychrotolerant species. Improved isolation strategies recovery culturable unculturable desert crucial exploration their diversity offer a better understanding survival mechanisms under stresses. main bioprospecting processes involve target on selective media incubation selection representatives plates further investigations. Bioactive compounds obtained being explored potential, especially in medicine. To date, there more than 50 novel discovered these gifted potential antimicrobial activities, including anti-MDR anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, cytotoxic activities. A range plant growth-promoting abilities inspired great interest agricultural In addition, several degradative, oxidative, enzymes can be applied industry environment. This review aims provide comprehensive overview environments remarkable source while rich offers underexplored resource exploitations.

Язык: Английский

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Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

Cell Genomics, Год журнала: 2022, Номер 2(12), С. 100213 - 100213

Опубликована: Ноя. 11, 2022

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae renowned producers of secondary metabolites commercial interest, yet only a small part its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context phylum-wide analysis 6,700 including public isolates metagenome-assembled (MAGs). We estimate that 30%–50% projected phylogenetic possesses genomic representation via MAGs. A comparison gene functions reveals novel determinants host-microbe interaction as well environment-specific adaptations such potential antimicrobial peptides. identify plasmids prophages across uncover extensive prophage structured mainly host taxonomy. Analysis >80,000 biosynthetic clusters horizontal transfer loss shape metabolite repertoire taxa. Our observations illustrate essential role need for high-quality genome sequences.

Язык: Английский

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OMICS and Other Advanced Technologies in Mycological Applications

Journal of Fungi, Год журнала: 2023, Номер 9(6), С. 688 - 688

Опубликована: Июнь 19, 2023

Fungi play many roles in different ecosystems. The precise identification of fungi is important aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate taxonomy, higher-level classifications. However, some species, referred to "dark taxa", lack distinct physical features that makes their challenging. High-throughput metagenomics environmental samples provide a solution identifying new lineages fungi. This paper discusses approaches including PCR amplification rDNA, multi-loci phylogenetic analyses, the importance various omics (large-scale molecular) techniques for understanding fungal applications. use proteomics, transcriptomics, metatranscriptomics, metabolomics, interactomics provides comprehensive These advanced technologies are critical expanding knowledge Kingdom Fungi, its impact food safety security, edible mushrooms foodomics, secondary metabolites, mycotoxin-producing fungi, biomedical therapeutic applications, antifungal drugs drug resistance, data novel development. also highlights exploring from extreme environments understudied areas identify dark taxa.

Язык: Английский

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Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 24, 2023

Abstract Natural products biosynthesised by microbes are an important component of the pharmacopeia with a vast array biomedical and industrial applications, in addition to their key role mediating many ecological interactions. One approach for discovery these metabolites is identification biosynthetic gene clusters (BGCs), genomic units which encode molecular machinery required producing natural product. Genome mining has revolutionised BGCs, yet metagenomic assemblies represent largely untapped source products. The imbalanced distribution BGC classes existing databases restricts generalisation detection patterns limits ability methods recognise broader spectrum BGCs. This problem further intensified datasets, where genes may be incomplete. work presents SanntiS, new machine learning-based tool identifying SanntiS achieved high precision recall both effectively capturing broad range Application MGnify led resource containing 1.9 million predictions associated contextual data from diverse biomes demonstrates significant fraction novelty compared equivalent isolate genomes datasets. Subsequent experimental validation novel antimicrobial peptide detected solely potential this uncovering bioactive compounds.

Язык: Английский

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Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Июнь 2, 2023

More than 20,000 species of prokaryotes (less 1% the estimated number Earth's microbial species) have been described thus far. However, vast majority microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little known regarding ecological functions biotechnological potential these underexplored extremophiles, representing a untapped uncharacterized biological resource. Advances in cultivation approaches are key for detailed comprehensive characterization roles shaping environment and, ultimately, their exploitation, such as extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, pigments, among others), astrobiology, space exploration. Additional efforts to enhance culturable diversity required due challenges imposed by culturing plating conditions. In review, we summarize methods technologies used recover environments, while discussing advantages disadvantages associated with each approaches. Additionally, review describes alternative strategies retrieve novel taxa unknown genes, metabolisms, roles, ultimate goal increasing yields more efficient bio-based products. This summarizes unveil hidden microbiome discusses directions future studies matter its applications biotechnology astrobiology.

Язык: Английский

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