Aldex (phenylephrine/pyrilamine) / Royalty - LARVOL DELTA

Gut Microbiome Taxa Associated With Response to Chemo-Immunotherapy in NSCLC: A Multi-Method Differential Abundance Analysis (IASLC-WCLC 2026) - P2 | "The NADIM II trial is a multicenter, randomized phase II study demonstrating the efficacy of perioperative nivolumab in combination with platinum-based chemotherapy (experimental arm) compared with chemotherapy alone (control arm) in patients with resectable stage IIIA-B NSCLC...As many DAA methods rely on count data, estimated absolute counts were also used to perform complementary analyses with ALDEx2, ANCOM2, Corncob, DESeq2, edgeR, LEfSe, MaAsLin3, and metagenomeSeq...Conclusions : A consensus-based approach integrating multiple statistical methods identified robust taxa associated with pCR and survival outcomes. These findings highlight the importance of methodological standardization and support the use of integrative analytical strategies to improve the reproducibility of microbiome-based biomarkers."

IO biomarker • Gastroenterology • Gastrointestinal Disorder • Immunology • Lung Cancer • Non Small Cell Lung Cancer • Solid Tumor

Gut Microbiota Profiles Associated with Bronchopulmonary Dysplasia in Very and Extremely Preterm Infants (ERS 2026) - "A total of 8 genera and 9 species were found to be significantly different between the GA and BPD groups using ALDEx2. Among the identified taxa, the genus Clostridioides was associated with GA, while Blautia showed the strongest association with BPD severity (P < 0.001). At the species level, Clostridioides difficile ATCC 9689 was significantly associated with both GA and BPD (P < 0.01)."

Gut Microbiota • Prematurity • Bronchopulmonary Dysplasia • Pulmonary Disease • Respiratory Diseases

The Oral Microbiome Demonstrates Potential as a Biomarker for Primary Lung Malignancy (IASLC-WCLC 2026) - "To identify the optimal microbial biomarkers, taxa were ranked using a composite ALDEx2-based scoring pipeline...We demonstrated that a panel of microbial species could be selected based on differential abundance and used to differentiate benign vs malignant disease with strong discrimination. Our study provides rationale for further investigation and development of non-invasive microbiome-based biomarkers."

Biomarker • Lung Cancer • Oncology • Oral Cancer

Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring. (PubMed, Int J Mol Sci) - "Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2)...Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences-particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes-though this link has not been tested directly and remains a hypothesis for future work."

Journal • BACE1

Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data. (PubMed, PLoS Comput Biol) - "Implementing a scale model in ALDEx2 or ALDEx3 ameliorated unacceptably high FDRs; however, there was an inherent trade-off between satisfactory FDR control and high sensitivity- no tool offered both...Critically, we leveraged a 'real-world', non-permuted analysis of an RNA-seq dataset to demonstrate that the latter effect is not a result of our thinning/permutation approach. Overall, our work highlights the potentially unwitting choice between sensitivity and FDR control that all researchers are making when analysing sequencing data and provides guidance on choosing an appropriate amount of scale uncertainty for the analysis of HTS data."

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Full-length 16S ribosomal RNA sequencing of foal synovial fluid shows substantial agreement with microbial culture. (PubMed, Am J Vet Res) - "Differential taxa were identified with ALDEx2...Next-generation sequencing and culture results were substantially aligned. Next-generation sequencing may aid diagnosis in suspected septic arthritis cases with negative culture results."

Journal • Immunology • Rheumatology

SIPdb: a stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using reverse ecology. (PubMed, ISME Commun) - "SIPdb provides a standardized pipeline accommodating the three most common SIP gradient fractionation strategies (binary, multi-fraction, and density-resolved), two incorporator designation strategies (fixed- and sliding-window), and four complementary differential abundance methods (DESeq2, edgeR, limma-voom, and ALDEx2)...Finally, reanalysis of a non-SIP study of 1,4-dioxane degradation showed how SIPdb can both validate known degraders and uncover additional candidate taxa involved in community metabolism. SIPdb establishes a scalable platform for reverse ecology, enabling hypothesis generation, cross-study meta-analysis, and linking taxa to metabolic processes, while serving as an open, extensible resource to accelerate ecological interpretation in microbiome research."

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Effects of Intestinal Microbiota on Individual Growth and Development of Pontastacus leptodactylus. (PubMed, Microorganisms) - "ALDEx2 analysis identified six ASVs significantly enriched in the LGP group, assigned to Methylobacterium, Devosia, order Rhizobiales, Renibacterium, Stenotrophomonas, and class Mollicutes, which were near-absent in the HGP group...COG analysis revealed eight downregulated functional genes in HGP (p < 0.01), suggesting more complex host-microbiota interactions. This study identifies distinct intestinal microbial signatures associated with growth performance in P. leptodactylus, providing candidate targets for probiotic development and aquaculture management, while causal verification remains the critical next step."

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Occupational exposure to Baijiu fermentation environments alters nasal microbiota composition: a comparative analysis of Strong-flavor and Sesame-flavor production systems. (PubMed, Microbiol Spectr) - "ALDEx2 revealed six genera depleted in both exposed groups (FDR < 0.05): Caproiciproducens, Petrimonas, Proteiniphilum, Sporosarcina, Syntrophomonas, and an uncultured genus...These findings connect microbial ecology with occupational health and support practical interventions: improving Daqu storage and ventilation, routine microbial surveillance, and preserving traditional fermentation practices without compromising safety. This work advances our understanding of human environment microbial exchange in traditional food systems with implications for global fermentation industries."

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Oral microbiome diversity and mortality in metabolic syndrome: a cohort study. (PubMed, J Oral Microbiol) - "ALDEx2 was employed for differential abundance analysis in the high-diversity subgroup...However, in the high-diversity subgroup, ecological network disruption, rather than alpha diversity or differential taxonomic richness, differentiates the deceased patients from the alive counterparts. This suggests that community structure is a promising risk marker with a higher sensitivity than diversity alone."

Journal • Metabolic Disorders

Nasopharyngeal microbiota profiles and lytA-PCR status in adult pneumococcal pneumonia: distinct microbial communities and diagnostic implications. (PubMed, Pneumonia (Nathan)) - "Among adults with pneumococcal pneumonia, nasopharyngeal lytA-PCR identified two distinct patterns of nasopharyngeal microbiota composition. These findings support the coexistence of colonization-driven and invasion-driven disease pathways and highlight the added value of integrating microbiota profiling with molecular diagnostics to better understand pneumococcal disease pathogenesis in adults."

Journal • Infectious Disease • Pneumococcal Infections • Pneumonia • Respiratory Diseases

rbims: an R package for integrative functional profiling and pathway-level discrimination in metagenome-assembled genomes. (PubMed, Front Bioinform) - "Beyond descriptive profiling, rbims implements an exploratory discriminant framework that combines compositional differential analysis (ALDEx2) with random forest-based feature ranking to prioritize candidate metabolic traits associated with environmental factors...The workflow identified widespread hexadecane and phenanthrene degradation potential, detected enriched oxidoreductase-related protein families, and revealed a strong pathway-level directional bias toward deep-water MAGs for phenanthrene, naphthalene, and hexadecane degradation pathways. By integrating annotation parsing, quantitative trait analysis, statistical discrimination, and visualization in a reproducible framework, rbims provides a user-friendly platform for functional interpretation in genome-resolved metagenomics."

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Microbiome differential abundance methodologies to detect relevant taxa associated with chemotherapy toxicity rate in colorectal cancer. (PubMed, Bioinform Adv) - "We then evaluated six widely used DAA methods (ALDEx2, ANCOM-BC, DESeq2, LEfSe, LinDA, and ZicoSeq) to assess how analytical variability affects the detection of microbiome signatures associated with chemotherapy-related toxicity...View collectively, our results support a context-dependent approach to DAA method selection in clinical microbiome studies. The data supporting this study are available at NCBI SRA database (PRJNA911189) and NCBI SRA database (PRJNA893853)."

Journal • Colorectal Cancer • Oncology • Solid Tumor

Subtype-Specific Differences in the Fecal Metabolome and Gut Microbiota in Breast Cancer Patients (JBCS 2026) - "AMP, asparagine, diethanolamine, N-acetylglucosamine 1-phosphate, NAD⁺, nicotinamide, riboflavin, terephthalic acid, and UMP were elevated in the breast cancer patient group...In the ALDEx2 analysis, changes in Clostridiales and Bacteroidales were observed at the ocular level when comparing the healthy female group with the breast cancer patient group (effect size > 0.4, p < 0.01, adjusted p = 0.27, 0.19)...In particular, several metabolites were suggested as potential biomarkers that could distinguish breast cancer patients from healthy women. Furthermore, gut microbiota diversity was reduced in breast cancer patients, and the gut microbiota may differ among breast cancer subtypes, suggesting that further investigation with additional cases is necessary."

Clinical • Gut Microbiota • Breast Cancer • HER2 Breast Cancer • HER2 Negative Breast Cancer • HER2 Positive Breast Cancer • Hormone Receptor Breast Cancer • Hormone Receptor Positive Breast Cancer • Oncology • Solid Tumor • Triple Negative Breast Cancer • HER-2

Longitudinal multiomic features of host fecal miRNAs and the gut microbiome reveal distinct recovery dynamics in post-operative colorectal cancer (EACR 2026) - "For microbiome, taxa found significant in at least two of the three differential abundance testing methods applied (ALDEx2, ANCOM-BC2, MaAsLin3) are defined as robust signatures... Our findings reveal a loss of crosstalk between host miRNAs and microbiome in post-operative CRC. While host fecal miRNAs are largely tumor-dependent and recover following surgery, the microbiome remained altered in dysbiosis, failing to revert to a healthy state at six months. These results provide novel insights into post-operative monitoring of CRC, emphasizing the distinct behaviour of the omic layers."

Colorectal Cancer • Oncology • Solid Tumor • MIR451A

16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis. (PubMed, J Microbiol) - "Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping...The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License."

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Recolonization dynamics of the middle ear microbiota following MESNA-assisted dissection in pediatric cholesteatomatous chronic otitis media. (PubMed, Front Cell Infect Microbiol) - "We employed a Compositional Data Analysis (CoDA) framework, centering on Aitchison distances, ALDEx2 for differential abundance, and consensus co-occurrence networks (SparCC, SPIEC-EASI, and CLR-Pearson). While MESNA disrupts the dysbiotic equilibrium, it does not fully restore a healthy stable climax community within the studied timeframe, as defined in ecological succession theory. These results support a paradigm shift from simple pathogen eradication toward ecological restoration as a strategy to prevent disease recurrence in CCOM patients."

Journal • Otorhinolaryngology • Pediatrics

A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou. (PubMed, Front Microbiol) - "Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups...Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions."

Journal • Cardiovascular • Hypertension • Metabolic Disorders

Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study. (PubMed, Int Endod J) - "Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation."

Journal • Dental Disorders • Gastrointestinal Disorder • Infectious Disease • Inflammation • Periodontitis

Debaryomyces hansenii Reshapes the Fungal Community of Iberian Cured Pork Loin: An ITS1 Metabarcoding Approach. (PubMed, Microorganisms) - "Ion Torrent ITS1 amplicon sequencing, QIIME2/DADA2 pipeline, and ALDEx2 differential abundance analysis were applied to this study...The findings confirm that the inoculation of D. hansenii can substantially reduce fungal contamination risks. Overall, the results contribute valuable insights into microbial interactions during meat curing and underscore the practical benefits of targeted starter cultures for enhancing food safety and quality."

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Oral squamous cell carcinoma is associated with altered salivary microbiome structure and reduced community evenness. (PubMed, Sci Rep) - "Microbial diversity and composition were analyzed using complementary bioinformatic and statistical approaches, including four differential abundance methods (MaAsLin2, ANCOM-BC2, LinDA, and ALDEx2)...These findings support the existence of an OSCC-associated salivary dysbiosis characterized by ecological restructuring rather than global diversity loss. The identified taxa represent exploratory candidate microbial signatures associated with OSCC that require validation in larger, independent, and longitudinal cohorts before any potential clinical application can be considered."

Journal • Oncology • Oral Cancer • Squamous Cell Carcinoma

Characteristics of gut microbiota changes in patients with nasopharyngeal carcinoma during radiotherapy. (PubMed, J Transl Med) - "Our findings demonstrate that NPC patients exhibit significant gut microbial dysbiosis compared with healthy controls, characterized by reduced alpha diversity and altered genus-level composition. Longitudinal analyses further revealed that radiotherapy is associated with dynamic alterations in gut microbial diversity, composition, and structure in NPC patients. Notably, these temporal shifts in the gut microbiota are strongly stratified by chemotherapy regimen, with pronounced changes observed in patients receiving CCRT alone but a stable microbial profile in those receiving induction chemotherapy followed by CCRT. Collectively, these results highlight the profound impact of oncological treatment on the gut microbiome in NPC patients and identify treatment regimen as a critical modifier of microbial dynamics during radiotherapy."

Journal • Mucositis • Nasopharyngeal Carcinoma • Oncology • Solid Tumor

Longitudinal Follow-Up of Gut and Salivary Microbiota in Children With Food Protein-Induced Enterocolitis Syndrome. (PubMed, Allergy) - "The faecal and salivary dysbiosis observed in allergic patients with FPIES partially resolved after tolerance acquisition. Understanding the underlying mechanisms of dysbiosis is crucial to prevent and help manage FPIES. A prolonged follow-up could determine whether dysbiosis resolution may be complete, and whether this early infancy dysbiosis has long-term consequences on health."

Journal • Gastrointestinal Disorder

Associations among diet, gut microbiota, and hypertension: a cross-sectional study in Thai subjects. (PubMed, PeerJ) - "Differential abundance and microbial-functional associations were evaluated using ALDEx2 and HAllA, respectively...Functional analysis revealed a profound restructuring of the gut ecosystem in the HT group, characterized by functional dysbiosis where microbial-functional association patterns shift distinct from changes abundance. These findings suggest that the gut microbiota's potential role in hypertension may involve altered interaction dynamics, which may provide a new perspective for targeted interventions in the Thai population."

Journal • Observational data • Cardiovascular • Gastrointestinal Disorder • Hypertension

Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress. (PubMed, Sci Rep) - "Compositional differential abundance testing (ALDEx2) detected no significantly altered taxa for primary antibiotic contrasts (T1 vs. T3, T2 vs. T3), indicating context-driven rather than antibiotic-driven compositional changes...The selective enrichment of antibiotic degradation pathways suggests potential for microbiome-assisted mitigation of pharmaceutical residues in agricultural systems. These results provide insights for developing compartment-specific microbiome management strategies that integrate with One Health approaches to enhance agricultural resilience under increasing pharmaceutical pressure in agroecosystems."

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