A Research Genetic sequencing laboratory
Scholarly Publications
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
MedRXiv (Preprint)
Objective: To compare gut microbiome diversity and composition in SARS-CoV-2 polymerase chain reaction (PCR)-confirmed positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls.
Effectiveness of Ivermectin-Based Multidrug Therapy in Severe Hypoxic Ambulatory COVID-19 Patients
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
MedRXiv (Preprint)
Ivermectin is a safe, inexpensive and effective early COVID-19 treatment validated in 20+ RCTs. Having developed combination therapies for Helicobacter pylori, we tested various COVID-19 combinations and describe the most effective. In 24 consecutive COVID-19 subjects with high risk features, hypoxia and untreated modera
MedRXiv (Preprint)
Ivermectin is a safe, inexpensive and effective early COVID-19 treatment validated in 20+ RCTs. Having developed combination therapies for Helicobacter pylori, we tested various COVID-19 combinations and describe the most effective. In 24 consecutive COVID-19 subjects with high risk features, hypoxia and untreated moderate-severe symptoms averaging 9 days, we trialed this novel combination comprising ivermectin, doxycycline, zinc, and Vitamins D and C. It was highly effective. All subjects resolved symptoms in 11 days on average, and oxygen saturation improved in 24hrs (87.4% to 93.1%, p=0.001). Hospitalizations and deaths were significantly fewer (p<0.002 or 0.05, respectively) than in background-matched controls from the CDC database. Triple combination therapy is safe and effective even in moderate-severe patients with hypoxia treated in the outpatient setting.
n-6 High Fat Diet Induces Gut Microbiome Dysbiosis and Colonic Inflammation
The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
International Journal of Molecular Sciences / Vol. 22 / Issue 13
Concerns are emerging that a high-fat diet rich in n-6 PUFA (n-6HFD) may alter gut microbiome and increase the risk of intestinal disorders. Research is needed to model the relationships between consumption of an n-6HFD starting at weaning and development of gut dysbiosis
International Journal of Molecular Sciences / Vol. 22 / Issue 13
Concerns are emerging that a high-fat diet rich in n-6 PUFA (n-6HFD) may alter gut microbiome and increase the risk of intestinal disorders. Research is needed to model the relationships between consumption of an n-6HFD starting at weaning and development of gut dysbiosis and colonic inflammation in adulthood. We used a C57BL/6J mouse model to compare the effects of exposure to a typical American Western diet (WD) providing 58.4%, 27.8%, and 13.7% energy (%E) from carbohydrates, fat, and protein, respectively, with those of an isocaloric and isoproteic soybean oil-rich n-6HFD providing 50%E and 35.9%E from total fat and carbohydrates, respectively on gut inflammation and microbiome profile. Methods: At weaning, male offspring were assigned to either the WD or n-6HFD through 10–16 weeks of age. The WD included fat exclusively from palm oil whereas the n-6HFD contained fat exclusively from soybean oil. We recorded changes in body weight, cyclooxygenase-2 (COX-2) expression, colon histopathology, and gut microbiome profile. Results: Compared to the WD, the n-6HFD increased plasma levels of n-6 fatty acids; colonic expression of COX-2; and the number of colonic inflammatory and hyperplastic lesions. At 16 weeks of age, the n-6HFD caused a marked reduction in the gut presence of Firmicutes, Clostridia, andLachnospiraceae, and induced growth of Bacteroidetes and Deferribacteraceae. At the species level, then-6HFD sustains the gut growth of proinflammatory Mucispirillum schaedleri and Lactobacillus murinus.Conclusions: An n-6HFD consumed from weaning to adulthood induces a shift in gut bacterial profile associated with colonic inflammation.
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
Journal of Experimental Pathology / Vol. 2 / Issue 2
In this mini-review, we summarise the significant body of evidence for the treatment of Clostridioides difficile infection (CDI) with Faecal Microbiota Transplantation (FMT) and propose the transition of FMT from ‘last resort’ treatment to the forefront of CDI management. To address the
Journal of Experimental Pathology / Vol. 2 / Issue 2
In this mini-review, we summarise the significant body of evidence for the treatment of Clostridioides difficile infection (CDI) with Faecal Microbiota Transplantation (FMT) and propose the transition of FMT from ‘last resort’ treatment to the forefront of CDI management. To address the feasibility of this proposal, we examined the rates of efficacy in FMT treated patients with CDI and also reviewed the safety of FMT across available published studies. A considered view of safety, efficacy, product standardisation, quality control and Good Manufacturing Practices (GMP) allows for a prudent approach in positioning FMT as the primary or initial treatment for CDI.
Microbiome Diversity in a Patient Treated With Serum-Derived Bovine Immunoglobulin/Protein Isolate
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
Microbiome Diversity in a Patient Treated With Serum-Derived Bovine Immunoglobulin/Protein Isolate
The American Journal of Gastroenterology / Vol. 115 / Issue - p S1196
Crohn's disease (CD) is a chronic relapsing inflammatory disease that can affect any part of the GI tract. Recent evidence suggests that changes in the composition of gut microbiota are a common feature in CD. This is paving the way for novel therapeutics that target th
The American Journal of Gastroenterology / Vol. 115 / Issue - p S1196
Crohn's disease (CD) is a chronic relapsing inflammatory disease that can affect any part of the GI tract. Recent evidence suggests that changes in the composition of gut microbiota are a common feature in CD. This is paving the way for novel therapeutics that target the microbiome. Recently, serum-derived bovine Ig/protein isolate (SBI) has emerged as a novel therapeutic for different GI pathologies. SBI is uniquely designed to increase gut Ig levels, over 50% of which is IgG. SBI works by neutralizing microbial components, maintaining gut microbiota, managing gut barrier function, and sustaining GI immune balance. We present a patient with CD who sought to avoid immune-suppression. We introduced SBI to modify the composition of the gut microbiome, restore intestinal diversity and thus achieve clinical remission.
Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing
Faecal Microbiota Transplantation as Primary Treatment for Clostridioidoes difficile Infection-evidence for Change
Microbiome Diversity in a Patient Treated With Serum-Derived Bovine Immunoglobulin/Protein Isolate
Gut Pathogens / Vol. 13 / Article 7
SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients.
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Reviews in Cardiovascular Medicine / Vol. 21 / Issue (4)
The SARS-CoV-2 virus spreading across the world has led to surges of COVID-19 illness, hospitalizations, and death. The complex and multifaceted pathophysiology of life-threatening COVID-19 illness including viral mediated organ damage, cytokine storm, and thrombosis warrants earl
Reviews in Cardiovascular Medicine / Vol. 21 / Issue (4)
The SARS-CoV-2 virus spreading across the world has led to surges of COVID-19 illness, hospitalizations, and death. The complex and multifaceted pathophysiology of life-threatening COVID-19 illness including viral mediated organ damage, cytokine storm, and thrombosis warrants early interventions to address all components of the devastating illness. In countries where therapeutic nihilism is prevalent, patients endure escalating symptoms and without early treatment can succumb to delayed in-hospital care and death. Prompt early initiation of sequenced multidrug therapy (SMDT) is a widely and currently available solution to stem the tide of hospitalizations and death. A multipronged therapeutic approach includes...
Shotgun Metagenomic Sequencing Identifies Dysbiosis in Triplet Sibling with Gastrointestinal Symptoms and ASD
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Children / Vol. 7 / Issue 12
The gut microbiome profile of a child with autism spectrum disorder (ASD) and co-occurring gastrointestinal (GI) symptoms was compared to that of her healthy triplet siblings to determine if she exhibited intestinal dysbiosis. Shotgun metagenomic sequencing was performed in individual fecal samples, and rel
Children / Vol. 7 / Issue 12
The gut microbiome profile of a child with autism spectrum disorder (ASD) and co-occurring gastrointestinal (GI) symptoms was compared to that of her healthy triplet siblings to determine if she exhibited intestinal dysbiosis. Shotgun metagenomic sequencing was performed in individual fecal samples, and relative microbial abundance and diversity was determined. Microbial diversity was lower in sibling #3, coupled with a higher Bacteroidetes/Firmicutes ratio, a lower relative abundance of Actinobacteria, and an increased relative abundance of Proteobacteria. Our findings are suggestive of gut dysbiosis in a child with ASD and co-occurring GI symptoms, compared to her two healthy triplet siblings.
Anti–Siglec-8 Antibody for Eosinophilic Gastritis and Duodenitis
Multifaceted highly targeted sequential multidrug treatment of early ambulatory high-risk SARS-CoV-2 infection (COVID-19)
Rapid improvement in Alzheimer’s disease symptoms following fecal microbiota transplantation
The New England Journal of Medicine
Eosinophilic gastritis and duodenitis are characterized by gastrointestinal mucosal eosinophilia, chronic symptoms, impaired quality of life, and a lack of adequate treatments. Mast-cell activity may contribute to the pathogenesis of the conditions. AK002 (lirentelimab) is an anti–Siglec-8 antibody that
The New England Journal of Medicine
Eosinophilic gastritis and duodenitis are characterized by gastrointestinal mucosal eosinophilia, chronic symptoms, impaired quality of life, and a lack of adequate treatments. Mast-cell activity may contribute to the pathogenesis of the conditions. AK002 (lirentelimab) is an anti–Siglec-8 antibody that depletes eosinophils and inhibits mast cells and that has shown potential in animal models as a treatment for eosinophilic gastritis and duodenitis.
Rapid improvement in Alzheimer’s disease symptoms following fecal microbiota transplantation
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
Rapid improvement in Alzheimer’s disease symptoms following fecal microbiota transplantation
Journal of International Medical Research
Alzheimer’s disease (AD), the most common form of dementia, is a leading cause of death and a major cause of morbidity in older people. The disease is characterized by progressive memory loss, cognitive impairment, and the cerebral accumulation of amyloid-b peptide. Given the health and economic im
Journal of International Medical Research
Alzheimer’s disease (AD), the most common form of dementia, is a leading cause of death and a major cause of morbidity in older people. The disease is characterized by progressive memory loss, cognitive impairment, and the cerebral accumulation of amyloid-b peptide. Given the health and economic impacts of AD, treatments that target the underlying etiology of AD or modify the course of the disease are of significant interest. The gut microbiome has been increasingly implicated [...]
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
Gastroenterology / Vol. 158 / Issue 6
Toxigenic Clostridioides difficile infection (CDI) is the most common cause of nosocomial disease in the United States, however, its prevalence in the general population is poorly understood. In this study we sought to determine the presence of Clostridioides difficile colonizing a representative sampl
Gastroenterology / Vol. 158 / Issue 6
Toxigenic Clostridioides difficile infection (CDI) is the most common cause of nosocomial disease in the United States, however, its prevalence in the general population is poorly understood. In this study we sought to determine the presence of Clostridioides difficile colonizing a representative sample of 119 asymptomatic adult volunteers, 12 of which were physicians treating patients with CDI. Methods: Next generation sequencing (NGS) was performed on fecal samples from [...]
The Presence of Clostridioides difficile Strains in the Gut by Next Generation Shotgun Sequencing: Innocent Bystander or Villain?
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
Detection of Non-Toxigenic Clostridioides Difficile in the Gut Microbiome by Next Generation Sequencing Shotgun Utilizing Kraken Metagenomic Analysis
The American Journal of Gastroenterology / Vol. 114
Pathogenic Clostridioides difficile (C. difficile) is the most common cause of nosocomial infection in the United States. However, the prevalence of C. difficile colonization in the general population is poorly understood. We sought to determine the presence and nature of various C. diffi
The American Journal of Gastroenterology / Vol. 114
Pathogenic Clostridioides difficile (C. difficile) is the most common cause of nosocomial infection in the United States. However, the prevalence of C. difficile colonization in the general population is poorly understood. We sought to determine the presence and nature of various C. difficile strains colonizing a representative sample of 17 asymptomatic adult volunteers, consisting of 10 healthy and 7 stable Crohn's patients.
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The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
The BreathID®Hp urea breath test provides several advantages over other 13C breath analyzers for the detection of Helicobacter pylori. We evaluated the sensitivity and specificity of a new BreathID®Hp Lab System (Exalenz Bioscience Ltd, Israel), a 13C-urea breath test system using breath sampling bags that facilitates multiple testing in a multicenter international clinical study.
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The Relationship Between Parkinson’s Disease and the Microbiome
The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
Sabine Hazan, MD, Series Editor
Parkinson’s Disease (PD) is a central nervous system movement disorder characterized by the formation of spherical protein deposits in the brain (Lewy bodies) and the development of spindle-like Lewy neurites in the body of the affected neuron. These start in the medulla oblongata and spread in a predictable pattern, resulting in [...]
How Globalization Changes the Microbiome
The validity of breath collection bags method in detecting Helicobacter pylori using the novel BreathID®Hp Lab System: a multicenter clinical study in 257 subjects
How Globalization Changes the Microbiome
Sabine Hazan, MD, Series Editor
The digestive tract’s microbial ecosystem is tailored for specific geographic areas. Here we discuss how the rise of globalization has spurred a mass transition of the European and American microbiome worldwide, altering the unique digestive patterns and processes of other nations. We can partially attribute our global obesity epidemic [...]
Probiotics: What Do We Know So Far?
The Microbiome, Viscerosensory Signaling and Autism
How Globalization Changes the Microbiome
Sabine Hazan, MD, Series Editor
Probiotic is a general term for live, nonpathogenic microorganisms, many of which exist in a symbiotic relationship within the normal human gut flora. Here we discuss their growth in popularity, their use in treating Gastrointestinal (GI) and non-GI medical conditions, and the data demonstrating their [...]
The Microbiome, Viscerosensory Signaling and Autism
The Microbiome, Viscerosensory Signaling and Autism
The Microbiome, Viscerosensory Signaling and Autism
Sabine Hazan, MD, Series Editor
Throughout this series we have pointed to evidence of an increasingly complex understanding of the relationship between the gut, its commensal bacterial composition, and its link to various pathological states within different organ systems. Here we will briefly discuss the emerging research that [...]
The Microbiome and the Heart
The Microbiome, Viscerosensory Signaling and Autism
The Microbiome, Viscerosensory Signaling and Autism
Sabine Hazan, MD, Series Editor
In this article, we discuss further understanding the gut microbiome along with its effect on metabolites and cardiovascular health. This understanding will give us opportunities to develop new test and therapeutic approaches to arteriosclerosis. In the future, stool transplantation with lean or low risk fo
Sabine Hazan, MD, Series Editor
In this article, we discuss further understanding the gut microbiome along with its effect on metabolites and cardiovascular health. This understanding will give us opportunities to develop new test and therapeutic approaches to arteriosclerosis. In the future, stool transplantation with lean or low risk for cardiovascular disease microflora may be a way of treating patients who are susceptible to [...]
The Microbiome and Obesity
The Microbiome and Inflammatory Bowel Disease
The Microbiome and Clostridium difficile
Sabine Hazan, MD, Series Editor
There is a growing body of research suggesting that obesity, metabolic syndrome, and insulin resistance are associated with predictable phyla and gene level compositional changes in the intestinal microbiome of humans and mice. With a better understanding of these changes, we can develop new, robust therape
Sabine Hazan, MD, Series Editor
There is a growing body of research suggesting that obesity, metabolic syndrome, and insulin resistance are associated with predictable phyla and gene level compositional changes in the intestinal microbiome of humans and mice. With a better understanding of these changes, we can develop new, robust therapeutic strategies. In this article, we will briefly discuss some of the definitive research related to [...]
The Microbiome and Clostridium difficile
The Microbiome and Inflammatory Bowel Disease
The Microbiome and Clostridium difficile
Sabine Hazan, MD, Series Editor
A new, emerging paradigm suggests that the susceptibility, severity, and duration of some diseases, even some previously thought to be independent of microbial involvement, are mediated by a complex interplay of host and microbe genomes. Already, nearly 10 million different microbial genes have been isolate
Sabine Hazan, MD, Series Editor
A new, emerging paradigm suggests that the susceptibility, severity, and duration of some diseases, even some previously thought to be independent of microbial involvement, are mediated by a complex interplay of host and microbe genomes. Already, nearly 10 million different microbial genes have been isolated from the human gut. In this series, we aim to shed light on some of the most promising research to date that [...]
The Microbiome and Inflammatory Bowel Disease
The Microbiome and Inflammatory Bowel Disease
The Microbiome and Inflammatory Bowel Disease
Sabine Hazan, MD, Series Editor
An IBD patient’s quality of life can be significantly diminished when treated with conventional therapies. However, like the trend of fecal microbiota transplantation (FMT) for the treatment of Clostridium difficile infection, there is promising evidence that a similar approach will prove efficacious in tre
Sabine Hazan, MD, Series Editor
An IBD patient’s quality of life can be significantly diminished when treated with conventional therapies. However, like the trend of fecal microbiota transplantation (FMT) for the treatment of Clostridium difficile infection, there is promising evidence that a similar approach will prove efficacious in treating UC and Crohn’s, especially given the increasingly predictable intestinal microbiome perturbation
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The Microbiome and Disease
Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: A phase 2, randomised, double-blind, active-controlled, non-inferiority study
The Microbiome and Inflammatory Bowel Disease
Sabine Hazan, MD, Series Editor
Simply and elegantly defined by Lynch and Pedersen in their December 2016 article in the New England Journal of Medicine, a microbiome is the collection of all genomes of microbes in an ecosystem. In the context of human beings and our health, it is the vastly diverse genetic information observable in the m
Sabine Hazan, MD, Series Editor
Simply and elegantly defined by Lynch and Pedersen in their December 2016 article in the New England Journal of Medicine, a microbiome is the collection of all genomes of microbes in an ecosystem. In the context of human beings and our health, it is the vastly diverse genetic information observable in the microbes colonizing the distal GI tract. Historically, the study of human microbiology has been one of a [...]
Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: A phase 2, randomised, double-blind, active-controlled, non-inferiority study
Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: A phase 2, randomised, double-blind, active-controlled, non-inferiority study
Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: A phase 2, randomised, double-blind, active-controlled, non-inferiority study
Background Clostridium difficile infection is the most common health-care-associated infection in the USA. We assessed the safety and efficacy of ridinilazole versus vancomycin for treatment of C difficile infection. Methods We did a phase 2, randomised, double-blind, active-controlled, non-inferiority study. Participants with signs and s
Background Clostridium difficile infection is the most common health-care-associated infection in the USA. We assessed the safety and efficacy of ridinilazole versus vancomycin for treatment of C difficile infection. Methods We did a phase 2, randomised, double-blind, active-controlled, non-inferiority study. Participants with signs and symptoms of C difficile infection and a positive diagnostic test result were recruited from 33 centres in the USA and Canada and randomly assigned (1:1) [...]