Aldex (phenylephrine/pyrilamine) / Royalty - LARVOL DELTA

Metabarcoding Study of Fecal Bacterial and Eukaryotic Pathogens in Stray and Pet Cats in Seoul, South Korea, 2022. (PubMed, Public Health Rep) - "This study found distinct fecal microbial communities in stray versus pet cats, with a higher prevalence of potential pathogens in stray cats. These findings emphasize the need for public health planning and effective measures for controlling stray cats."

Journal

Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses. (PubMed, BMC Bioinformatics) - "Interval assumptions enhance the rigor and reproducibility of differential expression and differential abundance analyses. Our results add to a growing body of literature arguing that normalizations should be replaced with alternative methods that allow researchers to account for scale uncertainty. However, compared to recent alternatives like scale models and sensitivity analyses, interval assumptions are easier to use, are more robust to misspecification, and have stronger and more interpretable inferential guarantees."

Journal

Distinct bladder tumor microbiome profiles between responders and non-responders to intravesical Bacillus Calmette-Guérin therapy in high-risk non-muscle invasive bladder cancer (EACR 2025) - "We conducted alpha and beta diversity analyses on responders and non-responders, followed by differential analysis using ANOVA-Like Differential Expression tool (ALDEx2).Result and In the study of bladder tumor microbiome profiles in HR-NMIBC naïve to BCG therapy, significant differences were found between responders and non-responders in microbial diversity and composition... Our findings revealed significant differences in the bladder tumor microbiome composition between BCG responders and non-responders in the HR-NMIBC. While microbiota richness and evenness were significantly lower in BCG responders compared to non-responders, certain species were still more predominant in responders. These results suggest that the bladder tumor microbiome may influence treatment outcomes, underscoring its potential as a predictive biomarker for BCG therapy."

Late-breaking abstract • Bladder Cancer • Genito-urinary Cancer • Oncology • Solid Tumor

Distinct bladder tumor microbiome profiles between responders and non-responders to intravesical Bacillus Calmette-Guérin therapy in high-risk non-muscle invasive bladder cancer (EACR 2025) - "We conducted alpha and beta diversity analyses on responders and non-responders, followed by differential analysis using ANOVA-Like Differential Expression tool (ALDEx2).Result and In the study of bladder tumor microbiome profiles in HR-NMIBC naïve to BCG therapy, significant differences were found between responders and non-responders in microbial diversity and composition... Our findings revealed significant differences in the bladder tumor microbiome composition between BCG responders and non-responders in the HR-NMIBC. While microbiota richness and evenness were significantly lower in BCG responders compared to non-responders, certain species were still more predominant in responders. These results suggest that the bladder tumor microbiome may influence treatment outcomes, underscoring its potential as a predictive biomarker for BCG therapy."

Bladder Cancer • Genito-urinary Cancer • Oncology • Solid Tumor

Impact of smoking status on microbiome diversity and taxonomic shifts in bladder cancer (EACR 2025) - "Differential abundance (DA) analysis was conducted using ANOVA-Like Differential Expression tool (ALDEx2).Result and Analysis of alpha diversity metrics, including the Chao1 and Shannon indices, revealed no statistically significant differences in species richness or evenness among current smokers, former smokers, and non-smokers (all p > 0.05)... These findings suggest that while smoking status does not significantly impact overall microbiome diversity in bladder cancer tissues, it induces specific taxonomic shifts, particularly affecting Lactobacillales and Proteobacteria. These microbiome alterations may contribute to the understanding of microbiome-mediated mechanisms underlying smoking-related bladder cancer development."

Bladder Cancer • Genito-urinary Cancer • Oncology • Solid Tumor

Long-Term Human Necrobiome Dynamics: Bacterial DNA Profiling of New York African Burial Ground Soil Samples (ASM Microbe 2025) - "Relative and differential abundance analyses (ALDEx2, ANCOM, LEfSe) revealed significant taxonomic shifts (p < 0.05) in NYABG soils, with increased representation of Firmicutes, Akkermansia muciniphila, and Acinetobacter lwoffii—taxa typically found in gut and skin microbiomes—distinguishing them from non-burial soil controls...It underscores the relevance of microbial legacies in understanding historical epidemiology. By integrating metagenomic approaches, this study provides a roadmap for future investigations into historical population health and microbial evolution while motivating the incorporation of human genomics to deepen insights."

Cholera • Infectious Disease

Duckweed Surfaces Are Selectively Colonized by a Subset of Environmental Bacteria (ASM Microbe 2025) - "ALDEx2 was used to analyze differential abundance of taxa between the conditions and identified four taxa as enriched in water microbiomes relative to duckweed microbiomes...The colonized microbiomes were not distinct from those of the inoculant, as measured by Bray-Curtis similarity, and no taxa were differentially abundant between the microbiomes. This inconsistency between wild and laboratory findings brings into question the common practice of using laboratory inoculation experiments to define core taxa in the duckweed microbiome and suggests that further work is required to design a laboratory microcosm for duckweed that effectively approximates the microbial conditions encountered by this plant in the wild."

Infectious Disease

Community Profiling of Patient-Matched Pediatric Oral Plaque and Odontogenic Abscess Samples Reveals Sample-Type Specific Trends (ASM Microbe 2025) - "Significantly enriched taxa between plaque and abscess communities were rigorously evaluated using a combination of three different algorithms (MaAsLin2, ANCOMBC2, and ALDEx2)...This analysis captured abscess-enriched microbial topics, including collections of Fusobacterium, Treponema, and Prevotella, which provides insights into polymicrobial dynamics with odontogenic abscesses when compared to oral plaque. These findings will help guide future clinical work identifying bacterial biomarkers for oral disease progression within the polymicrobial environment of the oral cavity."

Clinical • Late-breaking abstract • Pediatrics

Microbial community structure and functional characteristics across the mucosal surfaces of olive flounder (Paralichthys olivaceus). (PubMed, Front Microbiol) - "To elucidate the unique roles of commensal microbes in external and internal organs, we used PICRUSt2 and ALDEx2, respectively, to predict metabolic functions and identify differential abundances of microbes...Conversely, the intestine was characterized by functions such as beta-lactamase and phenicol resistance, glycosidases, LPS synthesis, and vitamin K2 production. These findings support the idea that while the microbiota of internal organs primarily supports digestive and immunological processes, the symbionts of external organs may play crucial roles in neutralizing toxic compounds from aquaculture practices, such as reduced nitrogen and sulfur compounds, and maintaining the integrity of the mucosal barrier."

Journal

FOOD PROTEIN-INDUCED ENTEROCOLITIS SYNDROME IN CHILDREN IS ASSOCIATED WITH GUT AND SALIVARY DYSBIOSIS, WITH PARTIAL RESOLUTION AT THE END OF FOLLOW-UP AFTER TOLERANCE (ESPGHAN 2025) - "16S rRNA gene sequencing (V3-V4 regions) and biostatistical analyses (ANCOM-BC, DESeq2, LEfSe, paired ALDEx2 and MaAsLIN2) were used to compare microbiota composition between groups...Understanding the underlying mechanisms of dysbiosis is crucial to prevent and or to help in management of FPIES. A prolonged follow-up could determine if dysbiosis resolution could be complete, and if this early-infancy dysbiosis has long-term consequences on health."

Clinical • Dysbiosis • Food Hypersensitivity • Gastrointestinal Disorder • Immunology

Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization. (PubMed, Genome Biol) - "In practice, scale models can drastically reduce false positives and false negatives rates. We introduce updates to the popular ALDEx2 software package, available on Bioconductor, facilitating scale model analysis."

Journal

DIFFERENCES IN IBD WITH AND WITHOUT ATOPIC DISEASE: DIFFERENTIAL ABUNDANCE OF SHORT-CHAIN FATTY ACID PRODUCERS IN THE INTESTINAL MUCOSAL MICROBIOME AND ASSOCIATIONS WITH VEDOLIZUMAB USE. (DDW 2025) - "ALDEx2 was used to assess differential relative abundance in those with vs without AD. This is the first study comparing the intestinal mucosal microbiota in IBD with and without AD. Several anti-inflammatory SCFA-producing microbes were differentially abundant between groups. VDZ use was associated with a history of AD and there were related microbiome differences in AD patients on VDZ, suggesting a shared mechanism by which microbiota modulate immune responses in both AD and IBD."

Allergic Rhinitis • Asthma • Atopic Dermatitis • Dermatitis • Dermatology • Gastroenterology • Gastrointestinal Disorder • Inflammatory Bowel Disease • Respiratory Diseases • IL10 • TNFA

MUCOSA-ASSOCIATED INTESTINAL MICROBIOTA COMPOSITION VARIES ACROSS EIMS OF IBD (DDW 2025) - "ALDEx2 was used to assess differential relative abundances in taxa between groups at the univariate level... Our study is the first to compare the intestinal mucosal microbiome in multiple EIMs, particularly while accounting for sex, a variable known to be significantly different across most primary EIMs. Both ocular and dermatologic EIMs predominantly occurred in females, and differences in the microbiome in those with vs without dermatologic EIMs were only in part accounted for by differences in sex distribution. Notably, taxa identified differed from those previously observed as associated with joint EIMs, suggesting potentially unique contributions from the gut microbiome to different primary EIMs which warrants further study."

Dermatology • Gastroenterology • Gastrointestinal Disorder • Inflammatory Bowel Disease • Ocular Inflammation • Ophthalmology • Pyoderma Gangrenosum • Scleritis • Uveitis

Evaluation of extended-spectrum β-lactamase producing bacteria in feces of shelter dogs as a biomarker for altered gut microbial taxa and functional profiles. (PubMed, Front Microbiol) - "Differential abundance of taxa, gut microbiome functions, and differential abundance of microbiome functions were analyzed using DESeq2, PICRUSt2, and ALDEx2, respectively, with Wilcoxon rank and Kruskal-Wallis tests for comparisons between dog groups...Dog's demography and fertility status modify the alterations, indicating host factors and ESBL bacteria interplay to shape gut microbiota. ESBL bacteria or other factors reprogram gut microbiome functions through down and upregulating multiple metabolic and biosynthesis pathways to promote ESBL bacteria colonization."

Biomarker • Journal

ATOPY IN INDIVIDUALS WITH IBD IS ASSOCIATED WITH DIFFERENTIAL ABUNDANCE OF SHORT-CHAIN FATTY ACID PRODUCERS IN INTESTINAL MUCOSAL MICROBIOME (CCCongress 2025) - "ALDEx2 was used to assess differential relative abundance in those with vs without AD... This is the first study to compare the intestinal mucosal microbiome in IBD with and without AD. Alpha diversity was lower in patients with concomitant AD. Several anti-inflammatory short-chain fatty acid producers were differentially abundant between the two groups, indicating a potential mechanism whereby microbes may modulate mucosal immune responses in these diseases."

Clinical • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammation • Inflammatory Bowel Disease • IL10 • IL17A • TNFA

Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies. (PubMed, Microbiome) - "Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract."

Clinical • Journal • Retrospective data • CNS Disorders • Vaginitis

Oral microbial changes, oral mucositis and febrile neutropenia during myelosuppressive chemotherapy in patients diagnosed with a solid tumor or lymphoma. (PubMed, Front Oral Health) - "Furthermore, differential abundances were analyzed using ALDEx2v1.32.0...Changes in the oral microbiome were observed during the CT-regimen and when OM was present. Furthermore, changes of the oral microbiota during FN episodes were observed; however, larger studies should be performed to substantiate our results."

Journal • Febrile Neutropenia • Hematological Disorders • Hematological Malignancies • Infectious Disease • Lymphoma • Mucositis • Neutropenia • Oncology • Solid Tumor • Stomatitis

Physical Therapy for Knee Pain Relief Induces Changes in Gut Microbiome Composition: A Secondary Analysis of Data From a Randomized Controlled Trial. (PubMed, Sports Health) - "Amplicon sequence variants (ASVs) that changed after the program were identified with ALDEX2, and correlations between these ASVs and measures of physical function, muscle strength, and interleukin-6 (IL-6) were explored...This is particularly relevant for patients with osteoarthritis, who are known to have a high prevalence of cardiometabolic comorbidities. Integrating physiotherapy protocols that positively influence the gut microbiome can thus enhance overall patient outcomes."

Journal • Immunology • Inflammation • Musculoskeletal Pain • Osteoarthritis • Pain • Rheumatology • IL6

Reshaping gut microbiota affects pain and anxiety behaviors in sickle cell transgenic mice (IASP 2024) - " To explore the changes in the gut microbiome, we employed 16S rRNA sequencing from fecal samples and identified compositional differences and specific genera with differential abundance between sickle cell transgenic mice and their healthy non-sickle littermates using ALDEx2... These findings provide new insights on the impact of gut dysbiosis and bidirectional signaling of the gut-brain axis on sickle cell pain, highlighting the differential gut microbial communities and gut-derived metabolites which may serve as potential intervention targets and may ultimately lead to rational design of new pain therapies."

Gut Microbiota • Preclinical • Genetic Disorders • Hematological Disorders • Mood Disorders • Pain • Psychiatry • Sickle Cell Disease

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions. (PubMed, Front Microbiol) - "Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment...In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations."

Journal • Gastrointestinal Disorder

The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study. (PubMed, J Oral Microbiol) - "In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1)...Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required."

Clinical • Journal • Dental Disorders

PROFILING THE GUT MICROBIOME IN SARCOIDOSIS (DDW 2024) - "Central log ratio transformation was applied before calculating diversity measures using phyloseq and performing differential analysis of microbial taxa and KO pathways using ALDEx... Our findings highlight the potential role of gut microbiome composition and function in inflammatory processes that are associated with granuloma formation in sarcoidosis."

Immunology • Inflammation • Sarcoidosis

INDIVIDUALS WITH IBD-ASSOCIATED ARTHRITIS HAVE INCREASED ABUNDANCE OF CORYNEBACTERIUM IN INTESTINAL MUCOSAL MICROBIOME (DDW 2024) - "ALDEx2 was used to assess differential bacterial taxa amplicon sequence variants (ASVs) relative abundances between those with vs without IBD-associated arthritis... This is the first study to compare the intestinal mucosal microbiome across several locations in subjects with and without IBD-associated arthritis. Similar bacteria were found across the terminal ileum, proximal colon, and distal colon in individuals, but lower concordance was seen in those with IBD-associated arthritis. Notably, the relative abundance of Corynebacterium and Roseburia ASVs was altered in those with vs without joint manifestations; these bacteria represent promising targets for future studies."

Clinical • Crohn's disease • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammatory Arthritis • Inflammatory Bowel Disease • Musculoskeletal Diseases • Musculoskeletal Pain • Orthopedics • Pain • Rheumatology • Ulcerative Colitis

Rapamycin and Inulin for Third-Dose Vaccine Response Stimulation (rivastim): A Multicenter, Randomised, Double-Blinded, Placebo-Controlled Trial of Dietary Inulin to Improve SARS-CoV-2 Vaccine Response in Kidney Transplant Recipients (ATC 2024) - "*Purpose: Kidney transplant recipients (KTR) are at an increased risk of hospitalisation and death from SARS-CoV-2 infection. Pre-biotic fibre supplementation is a feasible and effective strategy to enhance the gut microbiota in KTRs, and warrants further investigations as an adjuvant to enhance vaccine-induced immunity.Figure 1. There was no difference in vaccine specific immune responses between groups. Figure 2."

Clinical • Infectious Disease • Novel Coronavirus Disease • Respiratory Diseases • Transplantation

Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study. (PubMed, Int Endod J) - "The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP."

Biomarker • Journal • Next-generation sequencing • Dental Disorders • Gastrointestinal Disorder • Infectious Disease • Periodontitis