Thomas Borody

Centre for Digestive Diseases, Sydney · Clinical

Characterized by the presence of amyloid plaques, neurofibrillary tangles and neuroin-flammation, Alzheimer's disease (AD) is a progressive neurodegenerative disorder with no known treatment or cure. Global disease projections warrant an urgent and rapid therapeutic for the treatment of this devastating disease. Fecal microbiota transplantation (FM...

Despite the fundamental role of strain variation in gut microbiota function, the number of unique strains of a species that can stably colonize the human gut is still unknown. In this work, we determine the strain richness of common gut species using thousands of sequenced bacterial isolates and metagenomes. We find that strain richness varies acro...

Background: The use of faecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) has frequently failed to induce long-term symptomatic improvement. The use of multiple FMT infusions is one proposed mechanism through which the efficacy of FMT can be amplified. Aims: To evaluate the safety and efficacy of a novel six-month FMT trea...

Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indicatio...

Fecal microbiota transplantation (FMT) has been used as a core therapy for treating dysbiosis-related diseases by remodeling gut microbiota. The methodology and technology for improving FMT are stepping forward, mainly including washed microbiota transplantation (WMT), colonic transendoscopic enteral tubing (TET) for microbiota delivery, and purifi...

Objective Faecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FM...

Objective: The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 PCR-positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls. Design: Using a cross-sectional design, we performed shotgun next-generation sequencing on stool samples to evaluate gut microbiome comp...

Aims: Ivermectin is a safe, inexpensive and effective early COVID-19 treatment validated in 20+ random, controlled trials. Having developed combination therapies for Helicobacter pylori, the authors present a highly effective COVID-19 therapeutic combination, stemming from clinical observations. Patients & methods: In 24 COVID-19 subjects refusing...

Background Faecal microbiota transplantation (FMT) delivered via colonoscopic infusion or enemas have been shown to induce remission in a proportion of patients with active ulcerative colitis. Whether orally administered FMT is effective in ulcerative colitis is unknown. We aimed to assess the efficacy of oral lyophilised FMT for the treatment of a...

Background: The effectiveness of fecal microbiota transplantation (FMT), a treatment for Clostridioides difficile infection (CDI), is dependent on successful engraftment (incorporation) of donor stool. We present a method for evaluating engraftment success based on next-generation sequencing (NGS)-based profiling of bacterial strains present in do...

Faecal microbiota transplantation (FMT) involves homogenisation and infusion of stool from a healthy, highly screened individual into the bowel of an unwell recipient. Dietary intake is an important modulator of the gut microbiota. Currently there are no clinical practice recommendations available to provide patients or stool donors with dietary ad...

Introduction: Collagenous Colitis (CC) is a subtype of microscopic colitis, which presents with chronic, non-bloody, watery diarrhoea > 3 stools/d. Onset is often gradual, but may be sudden in approximately 40% of patients accompanied by urgency (70%), incontinence (40%), nocturnal episodes (50%), weight loss and abdominal pain. The colon is unrem...

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. Design: Using a cross-sectional study design, we used shotgun next-generation sequencing (NGS) to evaluate microbiome composi...

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 averagin...

Background Vonoprazan fumarate is a novel potassium-competitive acid blocker more effective in suppressing acid production than proton pump inhibitors (PPIs) and when combined with antibiotics has been used to eradicate Helicobacter pylori (H. pylori) infection. However, it has not yet been examined in an Australian setting. This study aimed to rep...

Background Faecal microbiota transplantation (FMT) administered via the lower GI tract effectively induces remission in ulcerative colitis (UC). Orally administered FMT capsules may improve patient tolerability and facilitate maintenance therapy while it is unclear if pre-FMT antibiotics enhance therapeutic efficacy. Methods We performed a dual-ce...

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 effica...

This study reports on the dietary intake of recipients of faecal microbiota transplantation (FMT), comparing this with dietary guidelines, and investigates the relationship between dietary intake and clinical outcomes. Males and females aged ≥ 16 years with irritable bowel syndrome or inflammatory bowel disease undergoing FMT were invited to comple...

Background and Aims: Colonoscopy surveillance depends on effective bowel preparation. Inadequate bowel preparation can lead to inaccurate clinical diagnosis, insufficient visualization of the colon and increased risk of missed diagnosis. This study aimed to compare the efficacy and safety of a novel Capsule Bowel Preparation (RitePrep), high-volume...

Oral lyophilized fecal microbiota transplantation (FMT) is effective in recurrent Clostridioides difficile infection (CDI); however, limited data exist on its efficacy in primary CDI and long-term microbial engraftment. Patients with primary or recurrent CDI were prospectively enrolled to receive oral FMT. Changes in the bacterial and fungal commun...

For decades, Mycobacterium avium subspecies paratuberculosis (MAP) has been linked to the pathogenesis of Crohn's disease. Despite many investigations and research efforts, there remains no clear unifying explanation of its pathogenicity to humans. Proponents argue Crohn's disease shares many identical features with a granulomatous infection in rum...

Objectives To determine the age‐standardised prevalence of inflammatory bowel disease (IBD) in a metropolitan area of Sydney, with a focus on its prevalence among older people. Design, setting Population‐based epidemiological study of people with IBD in the City of Canada Bay, a local government area in the inner west of Sydney, during 1 March 201...

Background: Medical therapy for strictures is limited and first-line treatment consists of endoscopic balloon dilatation, strictureplasty or surgical resection. Mycobacterium tuberculosis, Helicobacter pylori and Streptococcus can all cause stenosis, for which antibiotic treatment achieves stricture resolution. Mycobacterium avium ssp. paratubercu...

Background: Faecal microbiota transplantation (FMT) administered via the lower gastrointestinal tract effectively induces remission in ulcerative colitis (UC). Orally administered lyophilized FMT capsules may improve patient tolerability and facilitate maintenance therapy. Antibiotics before FMT may further enhance the therapeutic efficacy of FMT i...

INTRODUCTION: A bowel preparation comprising of a Low Residue Diet (LRD) compared to a Clear Fluid Diet (CFD) increases both the quality and tolerability of conventional bowel preparations such as; Polyethylene Glycol and Sodium Picosulfate. Despite this, many patients still experience side effects when consuming such bowel preparations. We aimed...

The population structure of strains within a bacterial species is poorly defined, despite the functional importance of strain variation in the human gut microbiota on health. Here we analyzed >1000 sequenced bacterial strains from the fecal microbiota of 47 individuals from two countries and combined them with >150,000 bacterial genomes from NCBI t...

Introduction: Clostridium difficile (C. difficile) infection (CDI) is commonly recognised as a nosocomial infection but is increasingly identified in patients in the community. Antimicrobial exposure which compromises gut microbiota is the main risk factor for CDI, although antibiotics remain the main treatment for this infection. Faecal microbiot...

Significance Composition of gut microbiota is altered in many human diseases, including inflammatory bowel disease. Some hope that restoring microbiota to a healthy state could help treat such diseases. We have used mice colonized with microbiotas from humans with inflammatory bowel disease to study what happens when these mice receive a microbiota...

Background: Blastocystis hominis (B. hominis) and Dientamoeba fragilis (D. fragilis) are two protozoan parasites of human bowel that are found throughout the world. There is still debate about the pathogenicity of these protozoans, despite them being commonly associated with gastrointestinal symptoms and can cause health issue in both children and...

Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been successfully applied to ulcerative colitis. However, only a subset of patients responds to FMT, and there is a pressing need for biomarkers of responsiveness. Fungi (the mycobiota) represent a highly immunologically reactive component of the gut microbiota. We analyze...

Objective Faecal microbiota transplantation (FMT) has proved to be an extremely effective treatment for recurrent Clostridioides difficile infection, and there is interest in its potential application in other gastrointestinal and systemic diseases. However, the recent death and episode of septicaemia following FMT highlights the need for further a...

We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal sample taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality.

The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases, where clinical trials of fecal microbiota transplant have shown some efficacy. To aid the development of novel microbiota-targeted therapies...

INTRODUCTION Approximately one third of patients with Crohn’s disease (CD) will develop strictures within 10 years of diagnosis, commonly in the terminal ileum and ileocecal valve (ICV). Strictures often lead to abdominal pain, obstruction and are a risk factor for developing internal fistulae and cancer. Current treatment involves endoscopic ballo...

INTRODUCTION Ulcerative colitis (UC) is characterised by inflammation in the colon and the rectum. The primary symptoms include abdominal pain, diarrhoea, fever, weight loss and anaemia. Fusobacterium varium (F. varium) is present in the colonic mucosa of approximately 80% of patients with UC. Butyric acid, a derivative of F. varium culture superna...

Background & Aims: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. Methods: We performed a double-blind trial of 81 patients wi...

Background In the FOCUS study, multidonor FMT was effective in the treatment of active ulcerative colitis (UC).¹ Here we characterise the bacterial taxonomic and functional changes associated with outcome. Methods A total of 314 fecal and 160 colonic biopsy samples were collected at specific intervals from 70 patients. A total of 113 fecal samples...

Introduction: Crohn's disease (CD) is a relapsing-remitting, incurable inflammatory bowel disease. Current therapies target inflammation but neglect to treat the underlying causal infection(s)[1]. Combined antibiotics used with Fecal Microbiota Transplantation (FMT) in CD can sporadically result in endoscopic remission and deep mucosal healing with...

Introduction: Ulcerative Colitis (UC) is a chronic relapsing-remitting inflammatory disease of the large intestine. It is thought that UC is a result of an aberrant reaction of the mucosa to the normal gut microbiome in genetically predisposed individuals. The use of trans-colonoscopic/enema fecal microbiota transplantation (FMT) in UC has succeede...

Introduction: Postinfectious irritable bowel syndrome (PI-IBS) is a sequela of acute infective gastroenteritis (IGE), impacting 10-30% of those who suffer from the initial event [1].Probiotic use in an animal model of PI-IBS provided symptomatic improvement [2] and the use of fecal microbiota transplantation (FMT) in a human cohort suffering from r...

Background: The intestinal microbiota is implicated in the pathogenesis of ulcerative colitis. Faecal microbiota transplantation is a novel form of therapeutic microbial manipulation, but its efficacy in ulcerative colitis is uncertain. We aimed to establish the efficacy of intensive-dosing, multidonor, faecal microbiota transplantation in active...