John MacSharry

• BSc (Hons) Microbiology, PhD Microbiology and Immunology
• Lecturer at University College Cork

Endometriosis is a chronic systemic disease, which results in endometrial-type tissue growing outside the uterus, and affects approximately 10% of reproductive-aged women worldwide. Its aetiology is poorly understood, and there is currently no long-term cure. Development and persistence of the disease depend on several coexisting factors including...

The global outbreak of human monkeypox (mpox) in 2022, declared a Public Health Emergency of International Concern by the WHO, has underscored the urgent need for effective diagnostic tools. In August 2024 WHO again declared mpox as a Public Health Emergency of International Concern. This study presents an innovative approach using artificial intel...

Introduction Immunoglobulins play a vital role in host immune response and in the pathogenesis of conditions like asthma. Therapeutic agents such as monoclonal antibodies target specific elements of the asthmatic inflammatory cascade. Decisions to utilize these medications are often based on systemic inflammatory profiling without direct insight in...

Human milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing...

As the COVID-19 pandemic winds down, it leaves behind the serious concern that future, even more disruptive pandemics may eventually surface. One of the crucial steps in handling the SARS-CoV-2 pandemic was being able to detect the presence of the virus in an accurate and timely manner, to then develop policies counteracting the spread. Nevertheles...

Background: Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these stud...

How the gut microbiome develops during the first three years of life can affect a child’s health for years to come, but antibiotic use in infancy can impair microbiome development, potentially leading to long-term health problems. Unfortunately, most studies on this topic have used antibiotics that aren’t typically prescribed in infants, making it...

The lungs have their own microbiota which seems to be altered in disease processes such as asthma. Viral infection accounts for many asthma exacerbations. Little is known about the lung virome, and the role that viruses play in non-exacerbating asthmatics. We aimed to assess if detection of virus in bronchoscopy samples of asthmatic patients in a n...

Early life dietary patterns and timely maturation of mucosa‐associated microbial communities are important factors influencing immune development and for establishing robust immune tolerance networks. Microbial fermentation of dietary components in vivo generates a vast array of molecules, some of which are integral components of the molecular circ...

DNA sensor pathways can initiate inflammasome, cell death and type I interferon (IFN) signalling in immune-mediated inflammatory diseases (IMIDs); including type I interferonopathies. We investigated the involvement of these pathways in the pathogenesis of ulcerative colitis (UC); by analysing expression of DNA sensor, inflammasome, and type I IFN...

Almost 2 years ago, the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered to be the causative agent of the disease COVID-19. Subsequently, SARS-CoV-2 has spread across the world infecting millions of people, resulting in the ongoing COVID-19 pandemic. The current ‘gold standard’ for COVID-19 diagnosis in...

Diet exerts a major influence upon host immune function and the gastrointestinal microbiota. Although components of the human diet (including carbohydrates, fats, and proteins) are essential sources of nutrition for the host, they also influence immune function directly through interaction with innate and cell-mediated immune regulatory mechanisms....

As the COVID-19 pandemic continues to affect the world, a new variant of concern, B.1.1.529 (Omicron), has been recently identified by the World Health Organization. At the time of writing, there are still no available primer sets specific to the Omicron variant, and its identification is only possible by using multiple targets, checking for specif...

Objective This study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the Abbott antinucleocapsid IgG chemiluminescent microparticle immunoassay (CMIA) assay, in five prespecified healthcare worker (HCW) subgroups following the first wave of the COVID-19 pandemic. Setting An 800-bed tertiary-level teaching hospital in the s...

Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium . One of the limitations of using such insertion vectors is the pres...

The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective properties onto strains as well as allowing the user to introduce or knock out/in selected genes for phenotypic characterization purposes. We have generalized on the plasmi...

Background Endometriosis is a chronic gynaecological disease whose aetiology is still unknown. Despite its prevalence among women of reproductive age, the pathology of the disease has not yet been elucidated and only symptomatic treatment is available. Endometriosis has high latency and diagnostic methods are both limited and invasive. Aim of Revi...

The COVID-19 pandemic has resulted in increased need for diagnostic testing using reverse transcriptase real-time PCR (RT-PCR). An exponential increase in demand has resulted in a shortage of numerous reagents in particular those associated with the lysis buffer required to extract the viral RNA. Herein, we describe a rapid collective effort by hos...

Background Increased numbers of blood and sputum eosinophils are associated with higher exacerbation frequency and increased asthma severity. In clinical trials, targeting Interleukin-5 has been shown to be a useful therapeutic strategy for patients with severe eosinophilic asthma. Methods Twenty-six patients have been commenced on Reslizumab in o...

Background It is suggested that airway fungi, in particular Aspergillus may impinge on clinical phenotype in asthma. Indeed, the term severe asthma with fungal sensitization (SAFS) has been coined. We aimed to ascertain whether the presence of fungi, in particular Aspergillus fumigatus, in the airway correlated with asthma severity and control. Fur...

Since bifidobacteria are among the pioneering colonizers of the human infant gut, their interaction with their host is believed to start soon following birth. Several members of the Bifidobacterium genus are purported to exert various health-promoting effects at local and systemic levels, e.g., limiting pathogen colonization/invasion, influencing g...

Urinary tract infections (UTIs) are common, in general caused by intestinal Uropathogenic E. coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels competitive overgrowth of intestinal E. coli , both pathogenic enterohaemorrhagic E. coli and commensal strains. During UTI ure...

Once regarded as obscure, the cohabitation of man and microbe has gained increasing recognition as a determinant of the health status of the host. Pharmacokinetic research at the host-microbe interface has been primarily directed towards effects on metabolism, with comparatively fewer investigations considering effects on the absorption process. We...

Breast cancer is the second most common cancer in women. Recent evidence identifies a unique microbiome in breast tissue; a site previously thought to be sterile. The identification that this microbiome varies considerably from healthy subjects to cancer patients has prompted investigations into the role of specific bacterial species in oncogenesis...

Gastro-Oesophageal Reflux (GOR) has been associated with chronic airway diseases while the passage of foreign matter into airways and lungs through aspiration has the potential to initiate a wide spectrum of pulmonary disorders. The clinical syndrome resulting from such aspiration will depend both on the quantity and nature of the aspirate as well...

The Republic of Ireland reports a relatively low prevalence of Johne’s disease (JD) compared to international counterparts. Postulated reasons for this include a lower average herd size and a grass-based production system. Ireland also engages in high levels of bovine tuberculosis (bTB) testing. As interferon-gamma (IFN-γ) is believed to play a key...

Recent findings point toward diet having a major impact on human health. Diets can either affect the gut microbiota resulting in alterations in the host’s physiological responses or by directly targeting the host response. The microbial community in the mammalian gut is a complex and dynamic system crucial for the development and maturation of both...

Most analyzed Lactococcus lactis strains are predicted to harbor one or more prophage genomes within their chromosome; however, the true extent of the inducibility and functionality of such prophages cannot easily be deduced from sequence analysis alone. Chemical treatment of lysogenic strains with Mitomycin C is known to cause induction of tempera...

Background: Many asthmatics remain sub-optimally controlled despite current treatments. Reasons include comorbidities that could aggravate asthma, including gastro-esophageal reflux (GER). We aimed to investigate whether aspiration occurs in asthmatic patients and if so does it correlate with asthma control. Methods: Patients had ACQ-7, FeNO, an...

Statins are the most widely prescribed medications worldwide for the treatment of hypercholesterolemia. They inhibit the activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-R), an enzyme involved in cholesterol synthesis in higher organisms and in isoprenoid biosynthesis in some bacteria. We hypothesized that statins may influence the...

Asthma is a chronic respiratory disease whose prevalence is increasing in the western world. Recently research has begun to focus on the role the microbiome plays in asthma pathogenesis in the hope of further understanding this respiratory disorder. Considered sterile until recently, the lungs have revealed themselves to contain a unique microbiota...

Disruptions to circadian rhythm in mice and humans have been associated with an increased risk of obesity and metabolic syndrome. The gut microbiota is known to be essential for the maintenance of circadian rhythm in the host suggesting a role for microbe-host interactions in the regulation of the peripheral circadian clock. Previous work suggested...

Effect of bile acid on cell viability and membrane integrity. A) Caco2 cells were treated with bile acids DCA or CDCA or their corresponding bile salts at 100 μM or with vehicle for 24 hours. The percentage cell viability was determined and plotted in graph. B) Caco2 cells were seeded on the polycarbonate insert and allowed to form an intact monola...

Effect of bile acids DCA and CDCA on the DBP gene expression in synchronised Caco2 cells. Caco2 cells were synchronized via serum starvation followed by a serum shock and treated with bile acids at 100 μM or with their corresponding bile salts. The cells were harvested for every 6h for a total of 48 hours. The relative expression levels of DBP gene...

List of mouse primer and sequences used for qRT-PCR analysis. (PDF)

List of human primer and sequences used for qRT-PCR analysis. (PDF)

Background: Statins have been long known for their lipid-lowering properties however there has been recent interest in their potential to positively influence clinical outcomes in pulmonary disease processes manifesting primarily as airway disorders. Objectives: We review the potential use of statin therapy in respiratory medicine, with particular...

Background: Statins have been long known for their lipid-lowering properties however there has been recent interest in their potential to positively influence clinical outcomes in pulmonary disease processes manifesting primarily as airway disorders. Objectives: We review the potential use of statin therapy in respiratory medicine, with particul...

Pregnancy-specific glycoproteins (PSGs) are immunoglobulin superfamily members related to the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family and are encoded by ten genes in the human. They are secreted at high levels by placental syncytiotrophoblast into maternal blood during pregnancy, and are implicated in immunoregulatio...

Disorders affecting smooth muscle structure/function may require technologies that can generate large scale, differentiated and contractile smooth muscle cells (SMC) suitable for cell therapy. To date no clonal precursor population that provides large numbers of differentiated SMC in culture has been identified in a rodent. Identification of such c...

The innate immune system is currently seen as the likely initiator of events which culminate in the development of Inflammatory Bowel Disease (IBD) with Toll-Like Receptors (TLRs) known to be involved in this disease process. Many regulators of TLRs have been described and dysregulation of these may also be important in the pathogenesis of IBD. The...

Enzyme-linked immunosorbent assays (ELISA) of milk and serum samples are a routinely used method of screening herds for Mycobacterium avium subspecies paratuberculosis (MAP). Infection with MAP causes granulomatous enteritis of ruminants known as Johne’s disease (JD). The sensitivity (Se) and specificity (Sp) of MAP ELISAs leads to difficulties in...

There is now convincing evidence that liver X receptor (LXR) is an important modulator of the inflammatory response; however, its mechanism of action remains unclear. This study aimed to examine the effect of LXR on the IL-12 family of cytokines and examined the mechanism by which LXR exerted this effect. We first demonstrated that activation of mu...

Significance It is known that the gastrointestinal microbiota influences adiposity and weight gain in the host. However the mechanisms by which gut microorganisms coordinate host physiological processes are currently unclear. We demonstrate that a single, widely distributed function of the gut microbiota, bile salt hydrolase (BSH) activity, signifi...

The pathogenic gram-positive bacteria, Listeria monocytogenes is a facultative infectious intracellular pathogen that causes listeriosis. Effective elimination of infection is dependent upon a functioning innate immune system and activation of inflammatory responses by pathogen recognition receptors (PRRs). In this review, we trace the route of L....

Listeria monocytogenes is a Gram-positive bacterium that can cause septicemia and meningitis. TLRs are central receptors of the innate immune system that drive inflammatory responses to invading microbes such as L. monocytogenes. Although intestinal epithelial cells (IECs) represent the initial point of entry used by L. monocytogenes for infection,...

Intestinal epithelial cells (IECs) represent the initial point of invasion for the pathogen Listeria monocytogenes however; the role of epithelial pattern recognition receptors (PRRs) engagement and subsequent inflammatory cascades remains poorly characterised. The aim of our study was to determine which PRRs are involved in initiating the immune r...

The outcome following infection depends on the generation of an immune response that results in control of the pathogenic microorganism, while limiting inflammatory collateral damage to the host. Bifidobacterium infantis 35624 was shown to be protective against Salmonella associated host injury via a Treg-dependent mechanism. In this study, we furt...

Subunit and DNA-based vaccines against Mycobacterium avium ssp. paratuberculosis (MAP) attempt to overcome inherent issues associated with whole-cell formulations. However, these vaccines can be hampered by poor expression of recombinant antigens from a number of disparate hosts. The high G+C content of MAP invariably leads to a codon bias througho...

Microorganisms live in a myriad of ecological niches. The human intestine is among the most densely populated environments; here, a multitude of bacteria appear to have co-evolved to impact beneficially upon the health of their human host. The precise molecular mechanisms and signaling pathways employed by commensal bacteria, including those that f...

The sphingosine-1-phosphate (S1P) analogue FTY720 is therapeutically efficacious in multiple sclerosis and in the prevention of transplant rejection. It prevents the migration of lymphocytes to sites of pathology by trapping them within the peripheral lymph nodes, mesenteric lymph nodes (MLNs), and Peyer's patches. However, evidence suggests that i...

This work reports on the identification and molecular characterization of the two-component regulatory system (2CRS) PhoRP, which controls the response to inorganic phosphate (Pi) starvation in Bifidobacterium breve UCC2003. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted Pi transporter system...

Lactobacillus salivarius strain UCC118 is a human intestinal isolate that has been extensively studied for its potential probiotic effects in human and animal models. The objective of this study was to determine the effect of L. salivarius UCC118 on gene expression responses in the Caco-2 cell line to improve understanding of how the strain might m...

Background A balanced microbiota is important in preventing intestinal disorders and microbial infections. Objective To evaluate the effects of feeding Bifidobacterium longum AH1206, Bifidobacterium breve AH1205, and Lactobacillus salivarius AH102, all of human origin, on Citrobacter rodentium infected mice. Methods C. rodentium infected mice (N=...

Background Respiratory syncytial virus (RSV) causes respiratory tract infections in infants and immunocompromised individuals and has been associated with the development of asthma. Objective To evaluate the effect of feeding Bifidobacterium longum AH1206, Bifidobacterium breve AH1205, and Lactobacillus salivarius AH102 to RSV infected mice. Meth...

Different rates of bacterial translocation across the gut mucosa have been reported but few studies have examined translocation of commensals at the level of the gut epithelial microfold (M) cell. We used an in vitro M-cell model to quantify translocation and determine the transcriptional response of M cells to various commensal bacteria. The trans...

Bifidobacteria comprise a significant proportion of the human gut microbiota. Several bifidobacterial strains are currently used as therapeutic interventions, claiming various health benefits by acting as probiotics. However, the precise mechanisms by which they maintain habitation within their host and consequently provide these benefits are not f...

Bifidobacteria comprise a significant proportion of the human gut microbiota. Several bifidobacterial strains are currently used as therapeutic interventions, claiming various health benefits by acting as probiotics. However, the precise mechanisms by which they maintain habitation within their host and consequently provide these benefits are not f...

Cellodextrins, the incomplete hydrolysis products from insoluble cellulose, are accessible as a carbon source to certain members of the human gut microbiota, such as Bifidobacterium breve UCC2003. Transcription of the cldEFGC gene cluster of B. breve UCC2003 was shown to be induced upon growth on cellodextrins, implicating this cluster in the metab...

The pathogenesis of irritable bowel syndrome (IBS) is poorly understood. One contributory factor may be low-grade mucosal inflammation, perhaps initiated by the microbiota. Toll-like receptors (TLRs) are a family of pathogen-recognition receptors of the innate immune system. The aim of this study was to evaluate the potential involvement of TLRs in...

Method for in vivo bioluminescence imaging as a valuable strategy for pre-clinical evaluation of leukocyte trafficking as shown here for small molecule α4-integrin antagonists as a promising therapeutic for IBD. Leukocyte trafficking is a therapeutic target in IBD. The integrins α4β7 and α4β1 regulate leukocyte migration into tissues and lymphoid o...

Toll-like receptor (TLR) signalling shapes dendritic cell (DC) responses by inducing co-stimulatory molecule up-regulation and cytokine secretion while TLR regulatory proteins inhibit this process. We aimed to determine if gene expression of TLRs and TLR regulatory proteins underpins the functionally different lipopolysaccharide (LPS) responses of...

The incidence of atopic disease has increased dramatically during recent decades and the potential immunoregulatory influence of the microbiota in these individuals is under investigation. The aim of our study was to identify a bacterial strain that is protective in murine allergy models and to determine if microbial induction of T regulatory cells...

Growth of Bifidobacterium breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI-type regulator encoded by rbsR, loca...

Fig. S1. Growth of E. coli mutants complemented with a cloned fragment of the rbsK gene of B. breve UCC2003 on M9 agar plates supplemented with 0.2% ribose. Fig. S2. A. A schematic representation of the relevant rbs regions of the B. breve UCC2003 and B. breve UCC2003::rbsA chromosomes. Chromosomal DNA is represented by a thin line, the rbsA gene i...