MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta‐omics and bioinformatics DOI Creative Commons

Defeng Bai,

Chuang Ma,

Jiani Xun

et al.

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

Dietary restriction of isoleucine increases healthspan and lifespan of genetically heterogeneous mice DOI Creative Commons
Cara L. Green,

Michaela E. Trautman,

Krittisak Chaiyakul

et al.

Cell Metabolism, Journal Year: 2023, Volume and Issue: 35(11), P. 1976 - 1995.e6

Published: Nov. 1, 2023

Language: Английский

Citations

55
An atlas of cells in the human tonsil DOI Creative Commons
Ramon Massoni-Badosa, Sergio Aguilar-Fernández, Juan C. Nieto

et al.

Immunity, Journal Year: 2024, Volume and Issue: 57(2), P. 379 - 399.e18

Published: Jan. 31, 2024

Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas human tonsil composed >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well spatial transcriptomics. This census identified 121 cell types states, defined developmental trajectories, enabled understanding functional units tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer locally active in follicle-associated T B cells, SIX5 putative transcriptional regulator plasma maturation. Analyses validation cohort confirmed presence, annotation, markers tonsillar provided evidence age-related compositional shifts. demonstrate value this resource by annotating from cell-derived mantle lymphomas, linking heterogeneity to normal differentiation states

Language: Английский

Citations

51
shinyCircos‐V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features DOI Creative Commons
Shaobin Wang, Lihua Jia,

Ge Tian

et al.

iMeta, Journal Year: 2023, Volume and Issue: 2(2)

Published: May 1, 2023

We previously developed shinyCircos, an interactive web application for creating Circos diagrams, which has been widely recognized its graphical user interface and ease of use. Here, we introduce shinyCircos-V2.0, upgraded version shinyCircos that includes a new with enhanced usability many features advanced plots. To help users get started provide detailed tutorials example input data sets. The is available online at https://venyao.xyz/shinyCircos/ https://asiawang.shinyapps.io/shinyCircos/, or can be installed locally using the source code deposited in GitHub (https://github.com/YaoLab-Bioinfo/shinyCircos-V2.0).

Language: Английский

Citations

50
Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis DOI Creative Commons
Pin Su, Houxiang Kang, Qianze Peng

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 2, 2024

In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as phyllosphere microbiota. However, underlying mechanisms of host-driven assembly these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment rice microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals strong between genotype members four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales Xanthomonadales. Some associations are to distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified main driver enrichment bacteria belonging Pseudomonadales. 4-HCA can be synthesized by plant's OsPAL02 from phenylpropanoid biosynthesis pathway. knockout mutant results in reduced Pseudomonadales abundance, dysbiosis microbiota consequently higher susceptibility plants disease. Our provides direct link metabolite homeostasis opening possibilities new breeding strategies.

Language: Английский

Citations

50
Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams DOI Creative Commons
Mei Yang, Tong Chen, Yongxin Liu

et al.

iMeta, Journal Year: 2024, Volume and Issue: 3(3)

Published: April 11, 2024

Abstract Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such metabolomics, genomics, transcriptomics, and proteomics, utility is undeniable. However, the operational complexity has been compounded by absence standardized data formats need switch between various platforms generating different diagrams. To address these challenges, we introduce EVenn platform, a versatile tool offering unified interface efficient exploration visualization ( http://www.ehbio.com/test/venn ) streamlines upload process with format, enhancing capabilities multimodule analysis. This comprehensive protocol outlines applications EVenn, featuring representative results multiple diagrams, uploads in centralized center, step‐by‐step case demonstrations. Through functionalities, emerges valuable user‐friendly in‐depth multiomics data.

Language: Английский

Citations

44
Multi‐omics analysis of disulfidptosis regulators and therapeutic potential reveals glycogen synthase 1 as a disulfidptosis triggering target for triple‐negative breast cancer DOI Creative Commons
Jindong Xie, Xinpei Deng, Yi Xie

et al.

MedComm, Journal Year: 2024, Volume and Issue: 5(3)

Published: Feb. 28, 2024

Disruption of disulfide homeostasis during biological processes can have fatal consequences. Excess disulfides induce cell death in a novel manner, termed as "disulfidptosis." However, the specific mechanism disulfidptosis has not yet been elucidated. To determine cancer types sensitive to and outline corresponding treatment strategies, we firstly investigated crucial functions regulators pan-cancer at multi-omics levels. We found that different tumor expressed dysregulated levels regulators, most which had an impact on prognosis. Moreover, calculated activity score tumors validated it using multiple independent datasets. Additionally, was correlated with classic pathways various cancers. Disulfidptosis also associated immune characteristics could predict immunotherapy outcomes. Notably, regulator, glycogen synthase 1 (

Language: Английский

Citations

34
Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS DOI Creative Commons
Frederickson Entila, Xiaowei Han, Akira Mine

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 11, 2024

Despite the plant health-promoting effects of microbiota, these assemblages also comprise potentially detrimental microbes. How immunity controls its microbiota to promote health under conditions remains largely unknown. We find that commensal bacteria isolated from healthy Arabidopsis plants trigger diverse patterns reactive oxygen species (ROS) production dependent on immune receptors and completely NADPH oxidase RBOHD selectively inhibited specific commensals, notably Xanthomonas L148. Through random mutagenesis, we L148 gspE, encoding a type II secretion system (T2SS) component, is required for damaging rbohD mutant plants. In planta bacterial transcriptomics reveals suppresses most T2SS gene expression including gspE. colonization protected against pathogen, when gspE was by ROS or mutation. Thus, negative feedback loop between tames leaf turns it into microbe beneficial host.

Language: Английский

Citations

32
Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae DOI Creative Commons
Xiaoqian Lin, Tongyuan Hu,

Zhinan Wu

et al.

iMeta, Journal Year: 2024, Volume and Issue: 3(2)

Published: Feb. 13, 2024

Abstract The Lachnospiraceae family holds promise as a source of next‐generation probiotics, yet comprehensive delineation its diversity is lacking, hampering the identification suitable strains for future applications. To address this knowledge gap, we conducted an in‐depth genomic and functional analysis 1868 high‐quality genomes, combining data from public databases with our new isolates. This set represented 387 colonization‐selective species‐level clusters, which eight genera multilineage clusters. Pan‐genome analysis, single‐nucleotide polymorphism (SNP) identification, probiotic predictions revealed that species taxonomy, habitats, geography together shape Lachnospiraceae. Moreover, analyses associations atherosclerotic cardiovascular disease (ACVD) inflammatory bowel (IBD) indicated several potentially novel possess capacity to reduce abundance opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on untapped enabling knowledge‐based selection development probiotics holding improving human management.

Language: Английский

Citations

26
Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation DOI Creative Commons
Uli Klümper, Giulia Gionchetta, Elisa Catão

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: June 8, 2024

Abstract When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat’s microbiome in long term if are able to overcome biotic resilience towards immigration. This process should more difficult with increasing biodiversity, as exploitable niches a given habitat reduced for immigrants when diverse competitors present. Consequently, microbial diversity could provide natural barrier resistance by reducing persistence time immigrating ARB ARG. To test this hypothesis, pan-European sampling campaign was performed structured forest soil dynamic riverbed environments low anthropogenic impact. In soils, higher diversity, evenness richness were significantly negatively correlated relative abundance >85% ARGs. Furthermore, number detected ARGs per sample inversely diversity. However, no such effects present riverbeds. Hence, serve dissemination stationary, environments, where long-term, diversity-based against immigration evolve.

Language: Английский

Citations

26
Paternal and induced gut microbiota seeding complement mother-to-infant transmission DOI Creative Commons
Léonard Dubois, Mireia Valles‐Colomer, Alise J. Ponsero

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(6), P. 1011 - 1024.e4

Published: June 1, 2024

Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess role both parents induced we analyzed two longitudinal metagenomic datasets (health early life microbiota [HELMi]: N = 74 infants, 398 samples, SECFLOR: 7 35 samples) with who received fecal transplantation (FMT). We found that father constitutes a stable source strains for infant independently delivery mode, cumulative contribution becoming comparable to mother 1 year. Maternal FMT increased mother-infant strain sharing raising average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate seeding partly complemented by support potential restore deviations this process.

Language: Английский

Citations

24