Current Opinion in Microbiology, Journal Year: 2025, Volume and Issue: 83, P. 102578 - 102578
Published: Jan. 8, 2025
Language: Английский
MedComm, Journal Year: 2023, Volume and Issue: 4(6)
Published: Nov. 4, 2023
The gut microbiota and its homeostasis play a crucial role in human health. However, for some diseases related to the microbiota, current traditional medicines can only relieve symptoms, it is difficult solve root causes or even cause side effects like disturbances microbiota. Increasing clinical studies evidences have demonstrated that probiotics, prebiotics, postbiotics prevent treat various diseases, but currently they be used as dietary supplements rather than medicines, which restricts application of probiotics field medicine. Here, this review analyzes importance health problems systematically summarizes effectiveness mechanisms maintaining treating based on animal models trials. And research outcomes development trends field, challenges prospects their health, alleviating are analyzed. It hoped promote disease treatment open up new frontiers probiotic research.
Language: Английский
Citations
144
Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(10), P. 1424 - 1433
Published: Feb. 20, 2023
Abstract Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale lack phenotype–genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology genomic data maximize diversity microbes isolated enable targeted picking specific genera. Application this fecal samples 20 humans yields personalized gut biobanks totaling 26,997 represented >80% all abundant taxa. Spatial analysis >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae , Bacteroidaceae Coriobacteriaceae Bifidobacteriaceae families suggest important interactions. Comparative 1,197 high-quality genomes these shows interesting intra- interpersonal evolution, selection horizontal gene transfer. This culturomics framework should empower new research efforts systematize collection quantitative imaging-based phenotypes with high-resolution genomics many emerging studies.
Language: Английский
Citations
123
Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 31(5), P. 712 - 733
Published: May 1, 2023
Language: Английский
Citations
120
Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(12), P. 1716 - 1728
Published: Oct. 30, 2023
Language: Английский
Citations
102
Journal of Environmental Management, Journal Year: 2023, Volume and Issue: 346, P. 119004 - 119004
Published: Sept. 19, 2023
Language: Английский
Citations
65
npj Biofilms and Microbiomes, Journal Year: 2023, Volume and Issue: 9(1)
Published: Sept. 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.
Language: Английский
Citations
47
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: July 26, 2024
Abstract Ionizable lipid nanoparticles (LNPs) are seeing widespread use in mRNA delivery, notably SARS-CoV-2 vaccines. However, the expansion of therapies beyond COVID-19 is impeded by absence LNPs tailored for diverse cell types. In this study, we present AI-Guided Lipid Engineering (AGILE) platform, a synergistic combination deep learning and combinatorial chemistry. AGILE streamlines ionizable development with efficient library design, silico screening via neural networks, adaptability to lines. Using AGILE, rapidly synthesize, evaluate lipids selecting from vast library. Intriguingly, reveals cell-specific preferences lipids, indicating tailoring optimal delivery varying These highlight AGILE’s potential expediting customized LNPs, addressing complex needs clinical practice, thereby broadening scope efficacy therapies.
Language: Английский
Citations
24
Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(12), P. 1229 - 1240
Published: June 5, 2024
Recent studies of dynamic interactions between epigenetic modifications a host organism and the composition or activity its associated gut microbiota suggest an opportunity for to shape microbiome through alterations that lead changes in gene expression noncoding RNA activity. We use insights from microbiota-induced review potential epigenetically regulate microbiome, which bidirectional 'epigenome–microbiome axis' emerges. This axis embeds environmentally induced variation, may influence adaptive evolution host–microbe interactions. furthermore present our perspective on how epigenome–microbiome can be understood investigated within holo-omic framework with applications applied health food sciences.
Language: Английский
Citations
19
Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(8), P. 807 - 822
Published: Feb. 3, 2024
The microbiota of solid tumors was identified >100 years ago; however, heterogeneous composition and diversity have been revealed only recently. Growing evidence has suggested that several functional mechanisms the intratumoral affect tumorigenesis progression, suggesting is a promising biomarker for multiple cancers. low biomass poses major challenge to related research, thus necessitating use multiple-modality integrated framework resolve this dilemma. Advanced techniques such as single-cell sequencing provide significant clues, gradual optimization experiments culture-based methods enables deeper investigation underlying involved. In review, we outline current state research on describe challenges comprehensive strategies future research.
Language: Английский
Citations
18
iMeta, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 17, 2025
Abstract The rapid growth of microbiome research has generated an unprecedented amount multi‐omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for This integrates essential bioinformatics workflows with pipelines provides 82 distinct visualization cases interpreting datasets. By incorporating basic tutorials advanced R‐based strategies, MicrobiomeStatPlots enhances accessibility usability researchers. Users can customize plots, contribute to the platform's expansion, access wealth knowledge freely on GitHub ( https://github.com/YongxinLiu/MicrobiomeStatPlot ). Future plans include extending support metabolomics, viromics, metatranscriptomics, along seamless integration into omics workflows. bridges gaps visualization, paving way more efficient, impactful research.
Language: Английский
Citations
3