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At least 19 recordsLinked to original sources

PubMed2025

Integrated genomics and morphological approach reveals interspecific gene flow cases and decodes the origin of selected feathergrasses (Poaceae, Stipa).

Central Asia is a diversity hotspot of arid-adapted grasses from the genus Stipa, with approximately 100 taxa found in the region. Recent studies in the steppe areas of Kazakhstan revealed specimens displaying intermediate morphology, distinguishing them from other taxa that grow sympatrically. Using integrative taxonomy, we investigated whether these individuals resulted from natural speciation or hybridisation, and if so, we would like to know which species were involved in this process feathergrasses. Research conducted in steppes of central Kazakhstan (Kyzylorda region), revealed the existence of individuals morphologically intermediate between S. arabica and S. richteriana, suggesting that these are probably of hybrid origin. Morphology and SNP markers validated the specimens as F1 hybrid between the aforementioned species by cladding separately based on neighbor-joining phylogenetic tree. Moreover, genetic structure displayed a separate cluster and showed almost equal genetic admixture between S. arabica and S. richteriana. Additionally, fastStructure analysis detected two geographically separated cryptic genotypes within S. richteriana population and their involvement in the hybridisation resulted in occurrence of S. × heptapotamica, S. × czerepanovii and S. × korshinskyi which recently were suggested as hybrids. Based on these evidences, we described a new nothospecies S. × kyzylordensis, as F1 hybrid. Furthermore, morphologically, the nothospecies delimited with other hybrids in Kazakh steppe area, marking the first report of hybridisation between S. arabica and S. richteriana, along with molecular evidence for the origin of further species supposed to be hybrids. This finding is crucial to understanding species diversity and hybridisation process in morphologically and genetically distant Stipa species.

Poaceae↗

PubMed2026

Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae).

Taxonomic assignments based only on morphology are often insufficient for delimiting species, particularly in complexes shaped by hybridization and polyploidy, where species boundaries are unclear. This limitation hinders progress in ecological, biogeographic and conservation research. The genus Romulea, distributed across Africa and the Mediterranean Basin, exemplifies this challenge. Despite its remarkable diversity, Mediterranean Romulea has not received much attention from genetic and molecular studies. Here, we present the first multilocus genotype analysis of Mediterranean Romulea taxa, focusing on the Tyrrhenian biogeographic province. Using target-capture sequencing with the universal Angiosperms353 kit, we generated genomic data for 272 individuals representing 18 putative taxa. Our findings reveal genetic groups that align with current taxonomy, the existence of cryptic divergence, and highlight the role of hybridization. Furthermore, analysis of intra-individual genetic diversity suggests one or several allopolyploid origins for Mediterranean Romulea. Four taxa (R. assumptionis, R. revelieri, R. ligustica, R. rollii) are consistently well differentiated across nuclear and plastid datasets, supporting their recognition as distinct species. In contrast, the widespread species R. ramiflora and R. columnae contain well-differentiated groups that may represent cryptic speciation. Several other taxa, including R. x melitensis, R. corsica, and R. bulbocodium, exhibit genomic signatures consistent with hybrid origins. Plastid and nuclear variation patterns are consistent with a hypothesis of rapid radiation in the Tyrrhenian region. These results provide a primary genomic framework for the integrative taxonomy of Romulea.

Genetic Variation↗

PubMed1978

Future prospects in lymphoma and leukemia.

Possible advances in leukemia and lymphomas can, in my opinion, derive from continued consideration of viral etiopathogenesis, possibly demonstrated by therapeutic impact of antiviral therapy. Terminology is in constant flux, and a classification based on biochemical (such as asparagine dependence) and immunologic (such as surface marker) characteristics should displace older terms such as chronic and acute. There is a constellation of neoplasms of lymphoid cells and their derivatives--leukemias, lymphomas, and plasmacytomas which need an integrated taxonomy. New diagnostic tests, new strategies of adapting therapy to tumor cell kinetics perturbed by the preceding treatment, and interesting clinical and preclinical combination of drugs provide new basis for favorable expectations. Immunotherapy is just emerging as a potent therapeutic tool. A technique for standardizing clinical results of different institutions to the age and sex of the population who develop the disease in question is much needed. Controls in trials of leukemias and lymphomas are found to be dispensable if one is measuring qualitative differences; for quantitative assessment of remission frequency or response duration, however, controls are requisite.

Antineoplastic Agents↗

PubMed2026

Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.

BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications. RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty. CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.

Metagenome↗

PubMed2026

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.

Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.

Dysbiosis↗

PubMed2026

Painting new pathways: Castilleja enters the genomic era.

Castilleja (Orobanchaceae), commonly known as Indian paintbrush, is a genus of approximately 200 hemiparasitic species found primarily across the Americas. Long studied for its taxonomic complexity, vibrant floral displays, and ecological interactions with host plants, Castilleja has recently emerged as a versatile research system spanning parasitic biology, specialized metabolism, conservation genetics, and pharmacology. The availability of whole-genome sequencing is transforming the field, revealing expanded gene families involved in host recognition, enabling genomic species delimitation of cryptic taxa, and providing frameworks for mapping biosynthetic pathways of bioactive compounds, including iridoid glycosides and phenylethanoid glycosides. This review synthesizes advances across these disciplines and highlights how genomics serves as an integrative force connecting taxonomy, ecology, phytochemistry, and parasitic biology in this genus.

Castilleja↗

PubMed2026

Genetic and metabolite diversity of Sundaland Heptapleurum (Araliaceae) insight into evolutionary and specialized metabolite.

BACKGROUND: The genus Heptapleurum Gaertn (previously treated as Schefflera J.R.Forst. & G.Forst.) within the Araliaceae family is recognized for its significant medicinal value and complex taxonomy. However, an integrated understanding of its evolutionary and metabolite diversity remains unexplored, especially in the Sundaland region (i.e., Java and Sumatra). Here, we integrate genomics and metabolomics to unravel the evolutionary relationships and metabolite diversity of 10 Heptapleurum species from Sundaland. RESULTS: We assembled 10 new complete plastid genomes (plastomes) and 45S nuclear ribosomal DNA (nrDNA) sequences, identifying significant variation and potential key molecular markers. Metabolomics identified 152 metabolites, mainly phenolics and terpenoids. Metabolite profiles of H. rhynchocarpum and H. capituliferum were more correlated with phylogeny than with geography; these two species were separate from the main Heptapleurum clade. Four species, H. farinosum, H. longifolium, H. rigidum, and H. fastigiatum, have almost identical plastomes and 45S nrDNA structures, suggesting they may represent closely related species with different phenotypes, as evidenced by distinctive metabolite compositions. CONCLUSIONS: Crucially, there is an incongruence between the genetic and chemical phylogenies, underscoring that while chemotaxonomy reflects functional diversity, genetic data remains the definitive standard for evolutionary inference, with the potential for reclassifying H. rhynchocarpum and H. capituliferum. This study provides a foundation for future taxonomic revisions, conservation, and drug discovery of Heptapleurum.

Phylogeny↗

PubMed1978

[The experience in dental education of Cayetano Heredia University of Peru].

This article describes the educational experience gained in the dentistry program of Cayetano Heredia University in Peru. The programs for professional and auxiliary personnel training were drawn up after analyzing the health needs of the population and the services required to meet them, which resulted in the elaboration of an original methodology and taxonomy. Learning is an integral experience, one that takes place in the dental clinic, the hospital, and the community. The curriculum includes the following components: units for the intensive learning of clinical functions, fewer preclinical activities, clinical training with the ongoing assistance of auxiliary staff, extended interaction with marginal urban communities, rural internships, and hospital externships. A summary account is given of the gains made, the difficulties encountered, and plans for devising in-service teaching approaches that more effectively meet the needs of the community.

Community Dentistry↗

PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

PubMed2025

Hybridization as driving force for cryptic species diversity in the Caribbean coral genus Madracis.

Species boundaries in scleractinian corals remain highly elusive due to conflicting patterns between morphological and molecular phylogenies, often caused by morphological plasticity, occurrence of cryptic species, incomplete lineage sorting or introgressive hybridization. Here, we use an integrated systematics approach, which combines reduced representation genome sequencing (nextRAD), micro-morphometric characterization, SEM analyses and compilation of life history traits, to infer phylogenetic relationships among closely related species in the Caribbean coral genus Madracis. In total, we analyzed 235 Madracis specimens from Curaçao and Bermuda collected from 10-90 m depth. Sequence- and SNP-based analyses for 115 samples generated unprecedented species resolution in Madracis, greatly supporting the morphology-based taxonomy of the current, accepted Caribbean species M. senaria, M. decactis, M. formosa, M. carmabi and M. mirabilis (M. auretenra). The exception was M. pharensis, in which we found evidence for three separate lineages, and for which we found signatures of admixture and introgression. These three M. pharensis lineages showed distinct depth distributions (thus classified as shallow, deep and very deep) and were partially distinguishable on the basis of fine microstructural elements of the collumella, septa and coenosteum. Further taxonomic comparisons are needed to formalize these putative cryptic species. Overall, our integrated systematics approach further resolves species relationships in the Caribbean genus Madracis, supports the morphological descriptions for most of the recognized species, but also reveals the existence of cryptic diversity in groups marked by high admixture, thus suggesting hybridization as a driving force in coral species diversity.

Animals↗

PubMed2026

RePo index: a multidimensional framework to quantify genetic resilience in data-limited amphibian faunas.

This study explores the resilience of Chilean amphibians to environmental disturbances through an integrative approach that combines ecological, demographic, bibliometric, and molecular information. A total of 58 species distributed across 14 genera and 9 families were evaluated via the resilience potential (RePo) index, which incorporates eleven criteria grouped into five dimensions: distribution, population trends, emerging diseases, evolutionary history, and genetic records. The results revealed high ecological vulnerability: 83% of the species were classified as non resilient (45% with no resilience and 38% with low resilience), and none reached the high-resilience category. At the family level, Telmatobiidae presented the lowest resilience values, whereas Leptodactylidae presented the highest. At the genus level, Insuetophrynus was identified as the most vulnerable taxon, with no molecular records and an extremely restricted distribution. In contrast, species such as Rhinella spinulosa and Pleurodema thaul presented moderate resilience, suggesting greater adaptive potential and relevance for functional studies. From a bibliometric perspective, a bias toward classical research topics (distribution, physiology, and taxonomy) was detected, with limited representation of integrative approaches such as genetic conservation or climate change. The conceptual modularity in the literature was low (Q = 0.1328), indicating weak thematic differentiation and little integration of omics tools. Most species lack transcriptomic and genomic data, severely limiting the assessment of their adaptive mechanisms. In this context, the RePo index has emerged as an integrative tool useful for operationalizing concepts such as evolutionarily significant units (ESUs) and management units (MUs), which are essential for evidence-based conservation. Finally, this study highlights the need to incorporate high-throughput sequencing (HTS) technologies and to participate in international initiatives, such as the Amphibian Genomics Consortium, as a strategic path forward for advancing adaptive conservation of Chilean amphibians.

Animals↗

PubMed2026

"Updates on diagnostic and prognostic molecular biomarkers of CNS tumors".

The diagnosis and classification of central nervous system (CNS) tumors has undergone a paradigm shift over the past decade, evolving from a purely histology-based approach to an integrated framework that incorporates molecular and epigenetic features. This review summarizes recent updates in key genomic and epigenomic biomarkers across major CNS tumor categories, with a focus on their diagnostic, prognostic, and therapeutic implications. DNA methylation profiling has emerged as a valuable tool for tumor classification, subgrouping, and grading, complementing traditional histopathologic assessment. Across diffuse gliomas, newly characterized molecular alterations have refined grading criteria and clarified the boundaries between tumor types, including important caveats about the use of individual molecular features as sole diagnostic criteria. In ependymomas, medulloblastomas, atypical teratoid/rhabdoid tumors, meningiomas, pineal tumors, and embryonal tumors, methylation profiling now defines biologically and clinically meaningful subgroups that inform risk stratification and treatment selection. The emerging recognition of mismatch repair-deficient gliomas and fusion-driven tumor entities further underscores the expanding complexity of CNS tumor taxonomy. As molecular technologies continue to advance, the integration of genomic, epigenomic, histopathologic, and clinical data will be essential to improving diagnostic precision, guiding therapy, and ultimately enhancing patient outcomes.

Embryonal↗

PubMed2026

Advances in the diagnosis and classification of B-ALL: comparative insights from updated guidelines.

Accurate molecular classification is essential for diagnosis, risk stratification, and treatment selection in B-cell lymphoblastic leukemia (B-ALL). In this study, we performed a comprehensive, real-world reclassification of 1015 consecutively diagnosed B-ALL patients using the fifth edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO-HAEM5) and the International Consensus Classification (ICC). An integrative genomic strategy that combined whole transcriptome sequencing, fusion detection, mutational analysis, and cytogenetics enabled reclassification according to both the WHO-HAEM5 and ICC frameworks, thereby substantially reducing the proportion of unclassifiable B-ALL from 41.9% (2016 WHO revision [WHO-HAEM4R]) to 15.9% (WHO-HAEM5) and 11.9% (ICC). Distinct clinical and prognostic features were identified across newly defined subtypes. Multivariable analysis confirmed that this genomic classification is a robust, independent predictor of survival after adjusting for age, minimal residual disease status, and transplant intervention. Specifically, HLF-rearranged and MEF2D-rearranged B-ALL conferred a persistently poor prognosis across all age groups despite allogeneic hematopoietic stem cell transplantation, highlighting an urgent need for novel therapeutic strategies. Gene expression profiling resolved cryptic subtypes, including ETV6::RUNX1-like, ZNF384-rearranged-like, and BCR::ABL1-like B-ALL, and uncovered diagnostic ambiguity in patients with concurrent lesions. In addition, we report emerging high-risk groups, including IDH1/2- and ZEB2 Q1072-mutated B-ALL, that may warrant recognition as distinct molecular entities. Our findings demonstrate the clinical use of integrative transcriptomic profiling in refining B-ALL taxonomy in guiding risk-adapted therapies and informing future revisions of diagnostic standards. This study supports the incorporation of high-throughput molecular diagnostics into routine leukemia classification and precision treatment planning.

Humans↗

PubMed2025

Easy and interactive taxonomic profiling with Metabuli App.

SUMMARY: Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often requires command-line proficiency and high-performance computing resources. To lower these barriers, we developed Metabuli App, an all-in-one desktop application that efficiently runs taxonomic profiling locally on a consumer-grade computer. It features user-friendly graphical interfaces for custom database curation, raw read quality control (QC), taxonomic profiling, and interactive result visualization. AVAILABILITY AND IMPLEMENTATION: GPLv3-licensed source code and prebuilt apps for Windows, macOS, and Linux are available at https://github.com/steineggerlab/Metabuli-App and are archived at https://doi.org/10.5281/zenodo.15876171. Analysis scripts are available at https://github.com/jaebeom-kim/metabuli-app-analysis. The Sankey-based taxonomy visualization component is available at https://github.com/steineggerlab/taxoview for easy integration into other web projects.

Software↗

PubMed1977

[The species C. diphtheriae].

Corynebacteria (C. diphtheriae var. gravis, mitis, minimus, intermedius, C. belfanti, C. ovis, C. ulceraus) producing diphtheria toxin are found as variants sharply differing from one another morphologically (from long branching rods to coccobacilli), culturally, biochemically and by other signs. The toxin synthesis in them was determined by genetically heterogeneous prophages tox+; tox+ virus exchange is possible between the corynebacteria. Since production of specific toxin, the cardinal sign of C. diphtheriae species, is connected with the genoms of genetically heterogeneous viruses tox+, the circle of whose hosts is very wide, it can be supposed that there is no genetically homogeneous taxonomic category "diphtheriae species". Several species of corynebacteria--lysogenized (toxigenic) or capable of being lysogenized (nontoxigenic) with tox+ viruses are included into the composition of the corynebacteria groups which medicine considers as "species" for over 80 years. A possiblity of becoming a diphtheria causative agent is determined by the capacity of corynebacteria to become infected with the circle of viruses tox+ the DNA of which can become stably integrated with the gene of this bacterium. The mentioned approach to taxonomy is possibly applicable to microorganisms in which the pathogenicity signs (the toxin) were determined, as in C. diphtheriae, in the virus genoms (Bac. botulinus).

Bacteriophage Typing↗

PubMed2026

Mutual Information-based Prognostic Biomarker Discovery in Cancer Genomics: Conceptual Framework and Representative Applications of MI-POG.

Mutual information (MI)-based approaches have increasingly been applied to cancer genomics; however, their use for genome-wide prognostic biomarker discovery remains relatively underexplored. The present article summarizes the conceptual workflow of Mutual Information-based Prognostic Omics Gene (MI-POG) based on previously published applications in breast cancer, lower-grade glioma, and other cancer datasets. The framework consists of clinical endpoint discretization, genome-wide MI-based screening, candidate ranking, and downstream validation using conventional survival-analysis approaches. Previous MI-POG applications identified solute carrier family 20 member 1 (SLC20A1) as a prognostic biomarker in hormone receptor-positive breast cancer. Elevated SLC20A1 expression was associated with unfavorable survival outcomes and was independently validated in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort. Methodological analyses demonstrated how survival endpoints can be integrated into an information-theoretic framework through fixed-time outcome discretization, enabling model-independent assessment of molecular-clinical dependencies. Applications across multiple cancer datasets suggested the potential applicability of the framework across biologically distinct tumor types, although further validation will be required to establish its robustness and generalizability. In conclusion, MI-POG can be formalized as an information-theoretic framework for genome-wide identification of prognostic biomarkers by quantifying molecular-clinical dependencies using mutual information. Representative applications from previously published studies suggest that MI-POG may complement conventional survival-analysis approaches and provide a useful strategy for biomarker discovery, although additional benchmarking and prospective validation will be required.

Humans↗

PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗