iMeta Science

Functional metagenomics reveals novel antibiotic resistomes in polar soils Using a robust functional metagenomics approach, we demonstrated that polar environments are important reservoirs of novel antibiotic resistance genes (ARGs). DNA was initially extracted from culture...

Functional #metagenomics reveals novel antibiotic resistomes in polar soils onlinelibrary.wiley.com/doi/10.1002/...
#antibiotics #ARG #microbiome

Early #matrine intervention of gut #microbiota for type 2 diabetes prevention #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#T2D #microbiome

A portable device for probiotic counting and viability assessment based on microfluidic chip and image recognition A portable, low-cost system enables rapid (3 min), on-site quantification of viable probiotics using a microfluidic chip with a fluorescent biosensor and image recognition. It distinguishes live/dead...

A portable #device for probiotic counting and viability assessment based on #microfluidic chip and image recognition #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#probiotics #biosensor #microbiome

RTTAP: Empowering metatranscriptomic data analysis with a read‐based total‐infectome taxonomic solution Metatranscriptomic data analysis is a complex task due to its sheer volume and the need for sophisticated bioinformatics tools. To address this, we developed the Read-based Total-infectome Taxonomic ...

RTTAP: Empowering metatranscriptomic data analysis with a read‐based total‐infectome taxonomic solution #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#Bioinformatics #taxonomy #diversity

Distinctive metabolic disturbances associated with redox homeostasis, nervous and hormonal functions during gut microbial enrichment upon polystyrene microplastic exposure Microplastic-induced gut microbial enrichment was dominated by bacteria within Eubacteriales, correlated with the virome, and accompanied by colitis. The polyamine synthetic pathway was activated to ...

Distinctive metabolic disturbances associated with redox homeostasis, nervous and hormonal functions during gut microbial enrichment upon polystyrene microplastic exposure #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#Microplastics #microbiome #metabolomics #RedoxBiology #Environment

Gut microbial‐derived 3,4‐dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome By integrating multi-level and multi-omics analyses, we identify 3,4-dihydroxyphenylacetic acid (DHPAA), a gut microbiota-derived degradation product of dietary flavonoids, as a key bioactive end-pro...

Gut microbial‐derived 3,4‐dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome onlinelibrary.wiley.com/doi/10.1002/...
#galactosidase #PCOS #microbiome #DHPAA

GitHub - mujiezhang/PSOSP: PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding t... PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding to target DNA, classifyin...

🧪Struggling to induce #prophage?
🧬 Meet PSOSP, a tool to predict prophage induction mode!
🚀Distinguishes SOS-dependent vs independent prophages.
🖥️Available on web server: vee-lab.sjtu.edu.cn/PSOSP and Github: github.com/mujiezhang/P...
#Bioinformatics #phage #viruse #microbiome #GutHealth

Multiomics integration unravels genotype‐microbiome interactions shaping the conjunctival transcriptome The effects of genotype and microbiome on molecular phenotypes, such as host gene expression, can vary interdependently. Through an integrative analysis of conjunctival multi-omics data from 120 pair...

#Multiomics integration unravels genotype‐microbiome interactions shaping the conjunctival transcriptome #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#transcriptome #MachineLearning #microbiome #Bioinformatics

Harnessing gut microbiota for longevity: Insights into mechanisms and genetic manipulation Overview of Gut Microbiota's Role in Aging and Potential for Genetic Manipulation. The relationship between gut microbiota and aging is complex, with significant implications for both health and dise....

Harnessing gut #microbiota for #longevity: Insights into mechanisms and genetic manipulation #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#microbiome #aging #SCFA

Global meta‐analysis reveals the drivers of gut #microbiome variation across vertebrates #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#antibiotics #diet

Akkermansia muciniphila‐derived hypoacylated rough‐type lipopolysaccharides alleviate diet‐induced obesity via activation of TLR4−IL‐23−IL‐22 immune axis This study demonstrates that hypoacylated, rough-type lipopolysaccharides (LPS) derived from Akkermansia muciniphila strain HW07 (ALPS) alleviates diet-induced obesity. ALPS acts as a weak TLR4 agoni...

#Akkermansia muciniphila‐derived hypoacylated rough‐type lipopolysaccharides alleviate #diet‐induced obesity via activation of TLR4−IL‐23−IL‐22 #immune axis onlinelibrary.wiley.com/doi/10.1002/...
#microbiome

Integrated #omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by #LP533401 #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#serotonin #metabolomics #microbiome #vitamin

Saliva MicroAge: A salivary microbiome based machine learning model for noninvasive aging assessment and health state prediction Saliva MicroAge is a machine learning-based model designed to estimate biological age and assess health status using globally sourced salivary microbiome data. Trained on 4532 healthy samples, the mo...

Saliva MicroAge: A salivary #microbiome based machine learning model for noninvasive #aging assessment and health state prediction #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#MachineLearning #OralHealth

Emerging role of gut microbiota extracellular vesicle in neurodegenerative disorders and insights on their therapeutic management Gut microbiota extracellular vesicles play (GMEVs) a vital role in maintaining the health of the digestive system and facilitating proper brain functioning. Gut dysbiosis exacerbates gut inflammation...

Emerging role of gut #microbiota extracellular vesicle in #neurodegenerative disorders and insights on their therapeutic management #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#inflammation #microbiome #GutHealth

Genome assembly and genomic architecture of a prominent cold‐resistant rapeseed germplasm The genomic landscape of cold-tolerant winter rapeseed (Brassica napus, L) has been poorly characterized. We assembled a high-quality reference genome of a prominent cold-tolerant winter rapeseed cul...

Genome #assembly and genomic architecture of a prominent cold‐resistant rapeseed germplasm #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#Bioinformatics #genome #phylogenetics #methylation

HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively...

HiFi based metagenomic assembly strategy provides accuracy near isolated #genome resolution in MAG #assembly onlinelibrary.wiley.com/doi/10.1002/...
#iMetaOmics #microbiome #Bioinformatics #MAG

Electroacupuncture reshapes the microbial co‐occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease Microbial keystone species and gut microbiota composition are highly variable during the pathological development of the behavioral and psychological symptoms of dementia (BPSD) in Alzheimer's diseas...

Electroacupuncture reshapes the microbial co‐occurrence networks related to the behavioral and psychological symptoms of dementia in #Alzheimer's disease #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#microbiome

Commentary on LRAs targeting NF‐κB with #epigenetic and mutational impacts on #HIV latency #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#methylation #epigenetics

Multi‐omics analysis of gut‐organ axes reveals the high‐altitude adaptation in Tibetan chicken The Qinghai-Tibet Plateau is an extreme ecosystem subject to special climatic conditions that require unique adaptations for its inhabiting organisms. In addition to genetic characteristics, the gut ...

Multi‐omics analysis of #gut‐organ axes reveals the high‐altitude adaptation in Tibetan #chicken onlinelibrary.wiley.com/doi/10.1002/...
#iMetaOmics #poultry #GutHealth #microbiome

TBCancer: A database for exploring characteristics and functions of tissue‐biased genes in cancer This study defined 10,921 tissue-biased genes across 54 normal tissues and 41 cancer types. Tumor-associated tissue-biased genes exhibit downregulation, mutations, and epigenetic modifications, corre...

TBCancer: A #database for exploring characteristics and functions of tissue‐biased genes in #cancer #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#scRNA #TME #immun

When the microbiome meets One Health principle: Leading to the Holy Grail of biology and contributing to overall well‐being and social sustainability Unveiling the microbiome as a cornerstone for interdisciplinary solutions to global health challenges, this theory integrates microbiome research with the One Health approach to develop innovative st....

When the #microbiome meets One Health principle: Leading to the Holy Grail of biology and contributing to overall well‐being and social #sustainability #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#OneHealth #ecology

OUTPOST: A comprehensive analysis software for whole‐metagenome shotgun sequencing incorporating group stratification The whole metagenOme shotgun seqUencing sTream Pipeline that is cOmprehensive and uSeful for mulTi groups experiments (OUTPOST) is a comprehensive analysis software for whole-metagenome shotgun seque....

OUTPOST: A comprehensive analysis software for whole‐metagenome shotgun sequencing incorporating group stratification #iMetaOmics
onlinelibrary.wiley.com/doi/10.1002/...
#metagenome #microbiome #Bioinformatics

SynCom‐mediated herbicide degradation activates microbial carbon metabolism in soils Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture re....

SynCom‐mediated #herbicide degradation activates microbial #carbon metabolism in soils onlinelibrary.wiley.com/doi/10.1002/...
#microbiome #SoilHealth

A gut microbiota‐bile acid axis inhibits the infection of an emerging coronavirus by targeting its cellular receptor aminopeptidase N Bacteroides fragilis employs bile salt hydrolase to reprogram host bile acid metabolism, generating lithocholic acid that directly blocks porcine deltacoronavirus infection by disrupting spike protei....

A gut #microbiota‐bile acid axis inhibits the infection of an emerging #coronavirus by targeting its cellular receptor aminopeptidase N #microbiome
onlinelibrary.wiley.com/doi/10.1002/...

Arabidopsis multiomics reveals the role of autophagy in root microbiome assembly Upon mutation of the core autophagy protein ATG5, disrupted autophagy pathways result in alterations in several biological processes important for plant-root microbe interaction mechanisms, including....

#Arabidopsis multiomics reveals the role of #autophagy in root #microbiome assembly #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...

Probiotics restore enteric HDL3 secretion and improve prognosis in patients with end‐stage renal disease Randomized double-blind trials have shown that probiotic mixtures significantly increase high-density lipoprotein (HDL) levels and reduce the risk of cardiovascular disease mortality in end-stage ren....

#Probiotics restore enteric HDL3 secretion and improve prognosis in patients with end‐stage renal disease onlinelibrary.wiley.com/doi/10.1002/...
#ESRD #kidneyhealth

PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes We developed PMAT2, an advanced toolkit for lineage-specific de novo assembly of plant, animal, and fungal mitochondrial genomes, as well as plant chloroplast genome. PMAT2 leverages optimized graph-...

PMAT2: An efficient graphical #assembly toolkit for comprehensive organellar genomes, available at
onlinelibrary.wiley.com/doi/10.1002/...
github.com/aiPGAB/PMAT2
#mitochondria #chloroplast #Bioinformatics

Novel insights into immunopathogenesis and crucial biomarkers between primary open‐angle glaucoma and systemic lupus erythematosus This study revealed a novel correlation between systemic lupus erythematosus (SLE) and primary open-angle glaucoma (POAG) through comprehensive bioinformatics analysis and experimentation, identifyin...

Novel insights into #immunopathogenesis and crucial #biomarkers between primary open‐angle #glaucoma and systemic lupus erythematosus onlinelibrary.wiley.com/doi/10.1002/...
#scRNA #SLE #PPI #MachineLearning

Microbiota humanization drives human‐like metabolic and immune transcriptomic shifts in pigs This study successfully established gut microbiota-humanized pigs, achieved human-like remodeling of the serum metabolome, and uncovered transcriptional alterations in immune cell subsets. These find....

#Microbiota humanization drives human‐like metabolic and immune transcriptomic shifts in pigs #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#FMT #metabolome

Culture dependent and independent approaches reveal the role of specific bacteria in human skin aging In total, 822 facial microbial samples and 14 skin phenotypes were assessed in a Chinese cohort. We profiled skin microbiome dynamics associated with age and skin aging phenotypes. Using machine lear...

Culture dependent and independent approaches reveal the role of specific #bacteria in human #skin #aging #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#microbiome