Journal of Hazardous Materials, Год журнала: 2024, Номер 479, С. 135669 - 135669
Опубликована: Авг. 27, 2024
Язык: Английский
Natural Product Reports, Год журнала: 2025, Номер unknown
Опубликована: Янв. 1, 2025
The article highlights the available data on Antarctic bacteria, their biosynthetic potential, and successful NP discoveries while addressing challenges in research advocating for systematic, collaborative Antarctica.
Язык: Английский
Процитировано
0
Microbial Ecology, Год журнала: 2025, Номер 88(1)
Опубликована: Март 14, 2025
Abstract The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales Chlamydiae ). Here, we provide detailed comprehensive account on the current knowledge . First, acknowledging up-to-date phylogenetic reconstructions recent nomenclatural proposals, reevaluate their taxonomy, thus re-ranking them as suborder, i.e. Holosporineae , within Rhodospirillales Then, examine diversity presenting 20 described genera many yet undescribed sub-lineages, well variety respective environments provenance which belong several different supergroups. Noteworthy representatives are infectious intranuclear Holospora host manipulator ‘ Caedimonas ’, farmed shrimp pathogen Candidatus Hepatobacter’. Next, put these in context whole by comparing available data least studied representatives, including genome sequences. Accordingly, reason most probable trajectories for interactions, specificity, emergence potential pathogens aquaculture possibly humans, future research directions investigate those open points
Язык: Английский
Процитировано
0
Food Bioscience, Год журнала: 2025, Номер unknown, С. 107009 - 107009
Опубликована: Июнь 1, 2025
Язык: Английский
Процитировано
0
Current Opinion in Microbiology, Год журнала: 2023, Номер 75, С. 102335 - 102335
Опубликована: Июнь 15, 2023
Язык: Английский
Процитировано
6
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown
Опубликована: Июнь 15, 2023
ABSTRACT Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome of BGCFlow incorporates several and tools grouped into five common stages analysis such as; i) data selection, ii) functional annotation, iii) phylogenetic analysis, iv) mining, v) comparative analysis. Furthermore, provides easy configuration different projects, parallel distribution, scheduled job monitoring, an interactive database visualize tables, exploratory Jupyter notebooks, customized reports. demonstrate the application by investigating distribution various gene clusters detected 42 Saccharopolyspora genus, known produce industrially important secondary/specialized metabolites. BGCFlow-guided predicted more accurate dereplication BGCs guided targeted selected RiPPs. scalable, interoperable, adaptable, re-entrant, reproducible nature will provide effective way ever-growing genomic datasets biotechnologically relevant species. downloading at https://github.com/NBChub/bgcflow .
Язык: Английский
Процитировано
6
Microbiology Resource Announcements, Год журнала: 2024, Номер 13(2)
Опубликована: Янв. 11, 2024
Myxobacteria are known as prolific producers of secondary metabolites with a unique and wide spectrum bioactivities. Here, we report draft genome sequences KH5-1 NO1, myxobacteria isolated from activated sludge, which consist 9.89 9.86 Mb, both have G + C contents 70.7%.
Язык: Английский
Процитировано
2
PLoS ONE, Год журнала: 2023, Номер 18(11), С. e0294843 - e0294843
Опубликована: Ноя. 27, 2023
Biological control agents (BCAs), beneficial organisms that reduce the incidence or severity of plant disease, have been expected to be alternatives replace chemical pesticides worldwide. To date, BCAs screened by culture-dependent methods from various environments. However, previously unknown BCA candidates may buried and overlooked because this approach preferentially selects only easy-to-culture microbial lineages. overcome limitation, as a small-scale test case, we attempted explore novel employing shotgun metagenomic information activated sludge (AS) microbiome, which is thought contain unutilized biological resources. We first performed genome-resolved metagenomics for AS taken municipal sewage treatment obtained 97 nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS)-related gene sequences 43 assembled bins, most were assigned phyla Proteobacteria Myxococcota. Furthermore, these NRPS/PKS-related genes are predicted they genetically dissimilar known NRPS/PKS clusters. Of these, condensation domain syringomycin-related NRPS cluster was detected in Rhodoferax- Rhodocyclaceae-related its homolog found reported metagenomes well genomes three strains available culture collections, implying their potential ability. Then, tested antimicrobial activity against phytopathogenic fungi investigate ability vitro cultivation successfully confirmed actual antifungal harboring possibly cluster. Our findings provide possible strategy discovering environment using metagenomics.
Язык: Английский
Процитировано
4
Frontiers in Microbiology, Год журнала: 2023, Номер 14
Опубликована: Дек. 12, 2023
The Greenland Ice Sheet is a biome which mainly microbially driven. Several different niches can be found within the glacial for those microbes able to withstand harsh conditions, e.g., low temperatures, nutrient high UV radiation in summer, and contrasting long dark winters. Eukaryotic algae form blooms during summer on ice surface, interacting with communities of bacteria, fungi, viruses. Cryoconite holes snow are also habitats their own microbial community. Nevertheless, microbiome supraglacial remains poorly studied, leading lack representative genomes from these environments. Under-investigated extremophiles, like living Sheet, may provide an untapped reservoir chemical diversity that yet discovered. In this study, inventory biosynthetic potential organisms made, through cataloging presence gene clusters genomes. There were 133 high-quality metagenome-assembled (MAGs) 28 whole bacteria obtained samples sheet cryoconite, biofilm, using culturing-dependent -independent approaches. AntiSMASH BiG-SCAPE used mine subsequently analyze resulting predicted clusters. Extensive sets Biosynthetic Gene Clusters (BGCs) collected genome collection, limited overlap between isolates MAGs. Additionally, little was among environments, suggesting specialization specific habitats. median number BGCs per significantly higher compared most talented producers Proteobacteria. We evidence capacity produce antimicrobials, carotenoid pigments, siderophores, osmoprotectants, indicating survival mechanisms cope extreme conditions. majority identified BGCs, including prevalent cluster families, have unknown functions, presenting substantial bioprospecting. This study underscores diverse genomes, revealing insights into strategies highlighting need further exploration characterization resources.
Язык: Английский
Процитировано
4
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Янв. 16, 2024
Abstract Filamentous Actinobacteria, previously Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences more than 1,000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera 389 species, including 244 likely novel species. All filamentous isolates class Actinomycetia NBC culture collection. The largest genus is Streptomyces with 886 742 We use this data to show that analysis can bring biological understanding not derived fragmented less systematic datasets. document central structured location core genes distal specialized metabolite duplicate linear chromosome, analyze content length terminal inverted repeats which characteristic for . then diversity trans-AT polyketide synthase clusters, encodes machinery a biotechnologically highly interesting compound class. These insights have both ecological biotechnological implications in importance high quality genomic resources complex role synteny plays biology.
Язык: Английский
Процитировано
1
mBio, Год журнала: 2024, Номер 15(5)
Опубликована: Март 27, 2024
ABSTRACT Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there scarce genomic information about the microbiota that perform this degradation. This study explores potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, brown macroalgae through in silico carbohydrate-active enzyme sulfatase sequences. Recovery metagenome-assembled genomes (MAGs) previously described gut metagenomes newly sequenced bioreactor enrichments reveals differences enzymatic capabilities between major taxa guts. The most versatile recovered MAGs were Bacteroidota phylum, whose house collections able decompose a variety algal polysaccharides. Unique enzymes predicted degradative capacities Bacillota (genus Vallitalea ) Verrucomicrobiota (order Kiritimatiellales highlight importance metabolic contributions multiple phyla broaden polysaccharide degradation capabilities. Few contain required fully any complex sulfated alone. distribution suitable originating different taxa, with widespread detection signal peptides candidate enzymes, consistent cooperative extracellular these carbohydrates. leverages evidence reveal an untapped diversity at strain level among decomposition. Bioreactor provide foundation for fermentative processes central translating knowledge gained system aquaculture bioenergy sectors. IMPORTANCE Seaweed has long been considered promising source sustainable biomass feed, but scalable industrial methods decomposing terrestrial compounds can struggle break down seaweed efficiently due unique structures. Fish genus feed on leveraging bacteria into simple sugars. reconstructs enhance our understanding fish digestion fermentation Investigations gene identify guts as seaweed-degrading ripe further characterization. These discoveries set stage future work incorporating marine communities
Язык: Английский
Процитировано
1