Aaron W. Miller
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View article: Evaluating the use of biobanked urine specimens for human urobiome studies
Evaluating the use of biobanked urine specimens for human urobiome studies Open
Case–control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. Wh…
View article: <b>Baseline abundance of oxalate-degrading bacteria determines response to</b> <i> <b>Oxalobacter formigenes</b> </i> <b>probiotic therapy</b>
<b>Baseline abundance of oxalate-degrading bacteria determines response to</b> <i> <b>Oxalobacter formigenes</b> </i> <b>probiotic therapy</b> Open
Oxalate, a compound derived from both diet and metabolism, contributes to multiple renal and vascular diseases. Certain gut bacteria degrade oxalate, limiting absorption and promoting secretion. This study examined microbial factors that i…
View article: Comment on: Measuring the perceived duration of post-ejaculatory penile detumescence: a pilot study in a real-life setting
Comment on: Measuring the perceived duration of post-ejaculatory penile detumescence: a pilot study in a real-life setting Open
View article: Impact of study design, contamination, and data characteristics on results and interpretation of microbiome studies
Impact of study design, contamination, and data characteristics on results and interpretation of microbiome studies Open
Advances in high-throughput molecular techniques have enabled microbiome studies in low-biomass environments, which pose unique challenges due to contamination risks. While best-practice guidelines can reduce contamination by over 90%, the…
View article: Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota
Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota Open
The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multi…
View article: Author response: Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Author response: Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
View article: Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet…
View article: Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet…
View article: Author response: Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Author response: Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
View article: The Prostate Microbiome Is Associated With Prostate Size and PSA Level, Independent of Age, in BPH Patients
The Prostate Microbiome Is Associated With Prostate Size and PSA Level, Independent of Age, in BPH Patients Open
Background The etiology of benign prostatic hyperplasia (BPH) is not well understood, though recent literature suggests that the urinary tract microbiome may play a role. We aimed to examine the prostatic microbiome in BPH and its associat…
View article: Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production
Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production Open
Excess amino acids from a protein-rich diet are mainly catabolized in the liver. However, it is still unclear to what extent the gut microbiota may be involved in the mechanisms governing this catabolism. Therefore, the aim of this study w…
View article: Inducing Oxalobacter formigenes Colonization Reduces Urinary Oxalate in Healthy Adults
Inducing Oxalobacter formigenes Colonization Reduces Urinary Oxalate in Healthy Adults Open
View article: Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet…
View article: Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet…
View article: Hypereosinophilic Syndrome in a Patient With Complex Pulmonary Hypertension and Sjogren’s Syndrome: A Case Report
Hypereosinophilic Syndrome in a Patient With Complex Pulmonary Hypertension and Sjogren’s Syndrome: A Case Report Open
We describe the case of a 73-year-old man who had been followed up by our clinic for pulmonary hypertension and asthma. He was later hospitalized and found to have significant and persistent eosinophilia compatible with hypereosinophilic s…
View article: Mitochondrial dysfunction signatures in idiopathic primary male infertility: a validated proteomics-based diagnostic approach
Mitochondrial dysfunction signatures in idiopathic primary male infertility: a validated proteomics-based diagnostic approach Open
Research question Male infertility accounts for almost half of all infertility cases worldwide, with idiopathic male infertility accounting for up to 30% of the cases. Sperm proteomics has revealed critical molecular pathway changes in men…
View article: Cefazolin shifts the kidney microbiota to promote a lithogenic environment
Cefazolin shifts the kidney microbiota to promote a lithogenic environment Open
View article: Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria
Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria Open
Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet…
View article: Editor's evaluation: Host-derived Lactobacillus plantarum alleviates hyperuricemia by improving gut microbial community and hydrolase-mediated degradation of purine nucleosides
Editor's evaluation: Host-derived Lactobacillus plantarum alleviates hyperuricemia by improving gut microbial community and hydrolase-mediated degradation of purine nucleosides Open
View article: Sacral neuromodulation device biofilm differs in the absence and presence of infection, harbors antibiotic resistance genes, and is reproducible in vitro
Sacral neuromodulation device biofilm differs in the absence and presence of infection, harbors antibiotic resistance genes, and is reproducible in vitro Open
Introduction/Purpose Sacral neuromodulation (SNM) is effective therapy for overactive bladder refractory to oral therapies, and non‐obstructive urinary retention. A subset of SNM devices is associated with infection requiring surgical remo…
View article: Uropathogenic Dysbiosis Pattern is Associated With Urethral Fibrosis
Uropathogenic Dysbiosis Pattern is Associated With Urethral Fibrosis Open
Purpose: Cellular mechanisms of stricture progression after repeated transurethral interventions are unclear. We hypothesize that urethral injury and mechanical stretch cause tears on the urethral epithelial cell lining leading to leaking …
View article: Local Inflammation But Not Kidney Cell Infection Associated with High APOL1 Expression in COVID-Associated Nephropathy
Local Inflammation But Not Kidney Cell Infection Associated with High APOL1 Expression in COVID-Associated Nephropathy Open
Key Points In coronavirus disease-19 biopsies, detection of severe acute respiratory syndrome coronavirus 2 was rare with no evidence of viral replication, whereas autopsy tissue failed quality control. In patients with FSGS, apolipoprotei…
View article: Sex-Specific Dysbiotic Bladder Microbiome in CKD Uncovered via High-Throughput Sequencing and Culture
Sex-Specific Dysbiotic Bladder Microbiome in CKD Uncovered via High-Throughput Sequencing and Culture Open
Background High-throughput techniques confirm the human bladder microbiome, but its relation to chronic kidney disease (CKD) remains unexplored. Bladder bacteria may migrate to the kidneys, affecting CKD. Methods A cross-sectional study re…
View article: Review of: "Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection"
Review of: "Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection" Open
View article: Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease
Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease Open
Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studie…
View article: Microbe-metabolite interaction networks, antibiotic resistance, and in vitro reconstitution of the penile prosthesis biofilm support a paradigm shift from infection to colonization
Microbe-metabolite interaction networks, antibiotic resistance, and in vitro reconstitution of the penile prosthesis biofilm support a paradigm shift from infection to colonization Open
View article: Biofilms on Indwelling Artificial Urinary Sphincter Devices Harbor Complex Microbe–Metabolite Interaction Networks and Reconstitute Differentially In Vitro by Material Type
Biofilms on Indwelling Artificial Urinary Sphincter Devices Harbor Complex Microbe–Metabolite Interaction Networks and Reconstitute Differentially In Vitro by Material Type Open
The artificial urinary sphincter (AUS) is an effective treatment option for incontinence due to intrinsic sphincteric deficiency in the context of neurogenic lower urinary tract dysfunction, or stress urinary incontinence following radical…
View article: Viral associations with kidney disease diagnosis and altered kidney metatranscriptome by kidney function
Viral associations with kidney disease diagnosis and altered kidney metatranscriptome by kidney function Open
View article: Mechanisms of the intestinal and urinary microbiome in kidney stone disease
Mechanisms of the intestinal and urinary microbiome in kidney stone disease Open
View article: Probiotic Oxalate-Degrading Bacteria: New Insight of Environmental Variables and Expression of the oxc and frc Genes on Oxalate Degradation Activity
Probiotic Oxalate-Degrading Bacteria: New Insight of Environmental Variables and Expression of the oxc and frc Genes on Oxalate Degradation Activity Open
Oxalate, a compound produced by many edible plants and as a terminal metabolite in the liver of mammals, is a toxin that has a detrimental role to human health. Humans and other mammals do possess enzymatic systems to degrade oxalate. More…