Aldex (phenylephrine/pyrilamine) / Royalty - LARVOL DELTA

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

Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype. (PubMed, Int J Mol Sci) - "According to the enterotypes, LEfSe, ALDEx2, XGBoost, and DCiPatho were utilized to identify differential abundances and pathogenic microbes in the gut between the MAFLD and non-MAFLD groups...In conclusion, P. copri emerged as a potential microbial biomarker for MAFLD. These findings enhance our understanding of the pathological mechanisms of MAFLD mediated through the gut microbiota, providing insights for future interventions."

Journal • Genetic Disorders • Hepatology • Metabolic Disorders • Metabolic Dysfunction-Associated Steatotic Liver Disease • Obesity

Gut microbiome and intestinal inflammation in preclinical stages of rheumatoid arthritis. (PubMed, RMD Open) - "We could not identify microbiome profiles associated with preclinical stages of RA. Only in a subgroup of individuals with the most pronounced phenotypes did we modestly retrieve the previously reported associations."

Journal • Preclinical • Immunology • Inflammation • Inflammatory Arthritis • Inflammatory Bowel Disease • Musculoskeletal Pain • Rheumatoid Arthritis • Rheumatology

EFFECTS OF HYPERBARIC OXYGEN THERAPY ON SALIVARY AND FECAL MICROBIOTA IN PATIENTS WITH MULTIPLE MYELOMA UNDERGOING AUTOLOGOUS HEMATOPOIETIC CELL TRANSPLANTATION (EBMT 2023) - P2 | "Melphalan 200 mg/m2 was given on day -1. Antibacterial prophylaxis (oral vancomycin and ciprofloxacin) was administered from the onset of neutropenia (days 5-8 in this trial) until neutrophil recovery to 0.5 k/uL or fever. Cefepime and metronidazole were used for neutropenic fever...ALDEx2 was used for differential abundance analysis... HBOT may affect salivary and fecal microbiota composition. HBOT appeared to decrease microbiota diversity loss after autologous HCT. Increased oxygen pressure near the intestinal epithelium after HBOT may make the lumen a more favorable habitat for obligate anaerobic commensals, hence their enhanced fecal detection."

Clinical • Febrile Neutropenia • Hematological Disorders • Hematological Malignancies • Multiple Myeloma • Neutropenia • Oncology • Solid Tumor • Transplantation • Wilms Tumor • ARPP19

Gut Microbiome and Intestinal Inflammation in Preclinical Stages of Rheumatoid Arthritis (ACR Convergence 2023) - "Microbial community composition and differential analysis were conducted using non-parametric tests, such as PERMANOVA, Wilcoxon and Kruskal-Wallis, or Aldex2 R-package to account for data compositionality... Prevotellaceae abundance, or bacterial cell counts, are associated with RA-autoimmunity only in the most pronounced phenotypes of preclinical RA stages. But in the larger overall FDR population, specific bacterial taxa were not associated with pre-clinical RA stages."

Preclinical • Immunology • Inflammation • Inflammatory Arthritis • Inflammatory Bowel Disease • Mucositis • Musculoskeletal Pain • Rheumatoid Arthritis • Rheumatology

Glomerular Spatial Transcriptomics and Integrated Gut Microbiome Analysis Reveals Pathogenetic Importance of Short-Chain Fatty Acid in IgA Nephropathy (KIDNEY WEEK 2023) - "PICRUSt2 analysis was used to predict metagenome functions, which were compared by ALDEx2 between the groups. We identified 1209 consistently highly expressed genes in the IgAN glomerulus, mainly annotated in major histocompatibility protein binding, immune cell adhesion, and extracellular matrix formation gene ontologies... We identified that short-chain fatty acid and related signal receptors, G-protein-coupled receptors, were significantly lowly expressed in the IgAN glom, linked to the alteration of acetate, a representative short-chain fatty acid, metabolism pathway in the IgAN microbiome. Further experimental validation studies are ongoing to investigate the pathogenetic significance of the current findings."

Diabetic Nephropathy • Focal Segmental Glomerulosclerosis • Glomerulonephritis • IgA Nephropathy • Immunology • Inflammatory Arthritis • Lupus • Lupus Nephritis • Nephrology • Renal Disease

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data. (PubMed, Brief Bioinform) - "We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis...This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones."

Journal • Dental Disorders • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammation • Inflammatory Bowel Disease

Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals. (PubMed, Int J Mol Sci) - "Within ET-L, Bifidobacterium, Blautia, Clostridium, Collinsella, and Corynebacterium were significantly higher in the DP group in the LDA and ANOVA-like differential expression-2 (ALDEx2) analyses...These findings provide insights into the gut-brain axis and its role in the pathogenesis of depression, thus contributing to our understanding of the underlying mechanisms in Asian individuals. Further research is warranted to explain the mechanistic links between gut microbiota and depression and to explore their potential for use in precision medicine interventions."

Journal • CNS Disorders • Depression • Mood Disorders • Psychiatry

Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight. (PubMed, Biomedicines) - "To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used...However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota."

Journal

Glucose-lowering effects of a synbiotic combination containing Pediococcus acidilactici in C. elegans and mice. (PubMed, Diabetologia) - "Our data suggest that the combination of pA1c with PC and BGC could be a potential synbiotic for blood glucose regulation and may help to fight insulin resistance, diabetes and obesity."

Journal • Preclinical • Diabetes • Genetic Disorders • Metabolic Disorders • Obesity • Type 2 Diabetes Mellitus • CCL2 • IGF1 • SLC2A1

Hair cortisol, cortisone and DHEA concentrations and the composition of microbiota in toddlers. (PubMed, Psychoneuroendocrinology) - "The bacterial core genus level analyses were conducted using DESeq2 and ALDEx2...These findings in toddlers suggest that long-term HPA axis activity may be related to genera abundancies but not to ecosystem-level measures in gut microbiota. The influence of these observed interrelations on later child health and development warrants further research."

Journal

Conditional Forest Models Built Using Metagenomic Data Accurately Predicted Salmonella Contamination in Northeastern Streams. (PubMed, Microbiol Spectr) - "The taxa that were most informative for accurately predicting Salmonella contamination based on CF were compared to taxa identified by ALDEx2 as being differentially abundant between Salmonella-positive and -negative samples...These putative indicators warrant further research to assess whether they are consistent indicators of Salmonella contamination across regions, waterways, and years not represented in the data set used in this study. Validated indicators identified using microbiome data may be used as targets in the development of rapid (e.g., PCR-based) detection assays for the assessment of microbial safety of agricultural surface waters."

Journal