Uri Gophna

Tel Aviv University | TAU · School of Molecular Cell Biology and Biotechnology

Background The gut microbiome might play a role in neurodevelopment, however, evidence remains elusive. We aimed to examine the relationship between the intestinal microbiome and cognitive development of school-age children. Methods This cross-sectional study included healthy Israeli Arab children from different socioeconomic status (SES). The mic...

Background: The skin microbiome is important for skin health and protection against solar damage. Sun exposure can cause long-term harm and increase the risk of skin aging and skin cancer. Here we examined the effects of daily exposure to sun radiation on the skin microbiome in order to determine whether skin microbiome bacteria can contribute to...

CRISPR-Cas systems provide heritable acquired immunity against viruses to archaea and bacteria. Cas3 is a CRISPR-associated protein that is common to all Type I systems, possesses both nuclease and helicase activities, and is responsible for degradation of invading DNA. Involvement of Cas3 in DNA repair had been suggested in the past, but then set...

By reconstructing bacterial genomes from samples taken from specific sites within the human intestines, via aspiration, we show that strains at specific intestinal sites are genetically distinct yet interrelated and are derived from a single founder population. Organ-specific metagenomic information represents a powerful tool to generate insights i...

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes an...

The Mediterranean diet (MED) is associated with the modification of gut microbial composition. In this pilot study, we investigate the feasibility of a microbiota-targeted MED-based lifestyle intervention in healthy subjects. MED intervention integrating dietary counseling, a supporting mobile application, and daily physical activity measurement us...

Polyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an ‘evolutionary trap’ that by the notion of the Muller’s ratchet will inevitably conclude in the species’ decline or even extinction due to a grad...

Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their...

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis rev...

Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains larg...

Most known CRISPR‐Cas systems primarily provide acquired, heritable immunity to bacteria and archaea against invasion by selfish DNA elements. Consequently, the main activity of these systems is to destroy incoming DNA that matches their immune memory–spacers within the CRISPR array. This chapter discusses, the evidence for and against such a trade...

Here, we examined the skin microbiome of two groups of healthy volunteers living on the Mediterranean coast with different exposures to sun radiation. One group, exposed to the sun in the summer, was compared with a group covered with clothing throughout the year. The seasonal effects on the skin microbiome of three body sites were determined befor...

Viroids and viroid-like agents are unique, minimal RNA replicators that typically encode no proteins and hijack cellular enzymes for their genome replication. As the extent and diversity of viroid-like agents are poorly understood, we developed a computational pipeline to identify viroid-like covalently closed circular (ccc) RNAs and applied it to...

Background and Aims Escherichia coli is over-abundant in the gut microbiome of patients with IBD. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages. Methods We investigated E. coli genomes from patients with UC, CD or a pouch and healthy subjects. The majority of which were reconstructed from metagenomic samples...

Background and aims: The Mediterranean diet (MED) is associated with the modification of gut microbial composition. Here we conducted a pilot study of a microbiota targeted MED-based nutritional education program investigating its feasibility and effects on dietary habits, inflammatory markers, and microbial composition of healthy individuals. Meth...

Polyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an ‘evolutionary trap’ that by the notion of the Muller’s ratchet will inevitably conclude in the species’ decline or even extinction due to a grad...

The development of the gut microbiome occurs mainly during the first years of life; however, little is known on the role of environmental and socioeconomic exposures, particularly within the household, in shaping the microbial ecology through childhood. We characterized differences in the gut microbiome of school-age healthy children, in associatio...

We thank Weaver et al¹ for the interest in our study focusing on antibiotic use patterns and safety profile in a cohort of patients with ulcerative colitis who underwent total abdominal proctocolectomy with ileal pouch–anal anastomosis.² We read with interest their letter describing antibiotic regimen choice and duration in patients with chronic an...

High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny s...

Locust plagues are a notorious, ancient phenomenon. These swarming pests tend to aggregate and perform long migrations, decimating cultivated fields along their path. When population density is low, however, the locusts will express a cryptic, solitary, non‐aggregating phenotype that is not considered a pest. Although the transition from the solita...

Background Primary prevention trials have demonstrated that the traditional Mediterranean diet is associated with a reduction in cardiovascular mortality and morbidity. However, this benefit has not been proven for secondary prevention after an acute coronary syndrome (ACS). We hypothesized that a high-intensity Mediterranean diet intervention afte...

Objective Escherichia coli is over-abundant in the gut microbiome of patients with IBD, yet most studies have focused on the adherent-invasive E. coli pathotype. Here, we aimed to identify IBD-specific or phenotype-specific genomic functions of diverse E. coli lineages. Design We investigated E. coli from patients with UC, CD and a pouch and healt...

Introduction Pouchitis, often developing after colectomy and ileal pouch-anal anastomosis for ulcerative colitis, is highly responsive to antibiotics. Ciprofloxacin and/or metronidazole are commonly used, often for prolonged periods. We report patterns of antibiotic use, adverse events, and resistant infections in patients with pouchitis with long-...

Prolonged exposure to psychiatric pharmacological agents is often associated with marked gastrointestinal phenomena, including changes in food intake, bowel motility, gastric emptying, and transit time. Those changes are reflected in the gut microbiota composition of the patient and can, therefore, be objectively measured. This is in contrast to th...

The intestinal microbiome continues to shift and develop throughout youth and could play a pivotal role in health and wellbeing throughout adulthood. Environmental and interpersonal determinants are strong mediators of the intestinal microbiome during the rapid growth period of preadolescence. We aim to delineate associations between the gut microb...

Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also...

Background and Aims Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD]. Methods The distribution of urease-producing bacteria in IBD was assessed using public fecal metagenomic data from various cohorts, including non-IBD cont...

Background: Primary prevention trials have demonstrated that the traditional Mediterranean diet is associated with a reduction in cardiovascular mortality and morbidity. However, this benefit has not been proven for secondary prevention after an acute coronary syndrome (ACS). We hypothesized that a high-intensity Mediterranean diet intervention aft...

Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs’ efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for sh...

Crohn's disease (CD), ulcerative colitis (UC), and pouchitis are multifactorial and chronic inflammatory bowel diseases (IBD). Pouchitis develops in former UC patients after proctocolectomy and ileal-pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbi...

A hallmark of the desert locust's ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be...

Prolonged exposure to psychiatric pharmacological agents is often associated with marked gastrointestinal phenomena, including changes in food intake, bowel motility, gastric emptying, and transit time. Those changes are reflected in the gut microbiome composition of the patient and can therefore be objectively measured. This is in contrast to the...

Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and...

The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to the host wellbeing. Spondylus spinosus is a Lessepsian invasive oyster to the eastern Mediterranean Sea that has become highly abundant, while constantly expending its range northwestward. Using 16S rRNA gene amplicon sequencing we examined how tem...

Microbial fuel cells (MFCs) can generate electricity simultaneously with wastewater treatment. For MFCs to be considered a cost-effective treatment technology, they should quickly re-establish a stable electroactive microbial community in the case of system failure. In order to shorten startup times, temporal studies of anodic biofilm development a...

Background Mediterranean diet (MED) is associated with health benefits, yet scarce data exist regarding the role of MED in inflammatory bowel diseases (IBD). Herein, we aimed to evaluate the association between MED and inflammatory markers in patients with IBD after pouch surgery. Methods Consecutive patients after pouch surgery due to ulcerative...

Crohn's disease (CD), ulcerative colitis (UC) and pouchitis are multifactorial and chronic inflammatory bowel diseases (IBD). Pouchitis develops in former patients with UC after total proctocolectomy and ileal pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. It has been shown...

As one of the world's most infamous agricultural pests, locusts have been subjected to many in-depth studies. Their ability at one end of their behavioral spectrum to live as solitary individuals under specific conditions, and at the other end of the spectrum to form swarms of biblical scale, has placed them at the focus of vast research efforts. O...

Locust plagues are an ancient phenomenon, with references going back to the Old Testament. These swarming pests are notorious for their tendency to aggregate and perform long migrations, consuming vast amounts of vegetation and decimating the cultivated fields on their path. However, when population density is low, locusts will express a solitary,...

A hallmark of the desert locust’s ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be...

Inteins are selfish genetic elements residing in open reading frames that can splice post-translationally, resulting in the ligation of an uninterrupted, functional protein. Like other inteins, the DNA polymerase B (PolB) intein of the halophilic archaeon Haloferax volcanii has an active homing endonuclease (HEN) domain, facilitating its horizontal...

Inter-subject variability in human milk microbiome is well known; however, its origins and possible relationship to the mother’s diet are still debated. We investigated associations between maternal nutrition, milk fatty acids composition and microbiomes in mother–infant dyads. Breast milk and infant fecal samples were collected across three time p...

Cheater viruses, also known as defective interfering viruses, cannot replicate on their own yet replicate faster than the wild type upon coinfection. While there is growing interest in using cheaters as antiviral therapeutics, the mechanisms underlying cheating have been rarely explored. During experimental evolution of MS2 phage, we observed the p...

Haloferax volcanii is to our knowledge the only prokaryote known to tolerate CRISPR-Cas mediated damage to its genome in the wild type background; the resulting cleavage of the genome is repaired by homologous recombination restoring the wild type version. In mutant Haloferax strains with enhanced self-targeting, cell fitness decreases and microhom...

Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and...

Halobacteria have been observed to be highly recombinogenic, frequently exchanging genetic material. Several barriers to mating in the Halobacteria have been examined, such as CRISPR-Cas, glycosylation, and archaeosortases, but these are low barriers that do not drastically reduce the recombination frequency. Another potential barrier could be rest...

Colibactin is a genotoxic molecule, produced primarily by Escherichia coli. Colibactin causes DNA damage that may lead to colorectal cancer. Here we review recent advances in the study of colibactin and propose a focus on patients with inflammatory bowel diseases (IBD) who have higher levels of colibactin-producing bacteria in their intestines.

The important role that locust gut bacteria play in their host biology is well accepted. Among other, gut bacteria were suggested to be involved in the locust swarming phenomenon. In addition, in many insect orders, the reproductive system was reported to serve as a vector for trans-generation bacterial inoculation. Knowledge of the bacterial fauna...

Microbial fuel cells (MFCs) are devices that can generate energy while aiding biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is considered essential for MFCs’ efficiency, especially during early-anode colonization. Yet, the specific ecological processes that drive the assembly of an optimized a...

Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this...

Background: Mycoplasma bovis is an important etiologic agent of bovine mycoplasmosis affecting cattle production and animal welfare. In the past in Israel, M. bovis has been most frequently associated with bovine respiratory disease (BRD) and was rarely isolated from mastitis. This situation changed in 2008 when M. bovis-associated mastitis emerge...

Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also...

Background: Alterations in the microbiome have been postulated to drive inflammation in IBD. In this pilot randomized controlled trial, we evaluated the effectiveness of quadruple antibiotic cocktail in addition to intravenous-corticosteroids (IVCSs) in acute severe colitis (ASC). Methods: Hospitalized children with ASC (pediatric ulcerative col...

Pancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiot...

One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, renderin...

BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial f...

Biogas is a sustainable, renewable energy source generated from organic waste degradation during anaerobic digestion (AD). AD is applied for treating different types of wastewater, mostly containing high organic load. However, AD practice is still limited due to the low quality of the produced biogas. Upgrading biogas to natural gas quality (>90% C...

Background: Dysregulated mucosal immune response to gut microbiota is thought to play a role in the pathogenesis of Crohn's disease (CD). Alterations in eukaryotic microbiota in CD were also reported as potential triggers for perpetuating inflammatory processes. Data on eukaryotic dysbiosis in IBD are scares and its potential contribution to CD pat...

One of the key challenges in the field of RNA virus genetics is the inference of full haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing very long reads, with the potential of sequencing the complete genomes of RNA viruses in individual reads. However, MinION suffers from high error rates, render...

Probiotics have been effectively used for treating and managing several inflammatory bowel diseases including pouchitis and ulcerative colitis by maintaining remission or decreasing disease activity indices. However, the routine use of probiotics for the induction and maintenance of remission in patients with pouchitis remains controversial due to...

Background: Patients with ulcerative colitis (UC) that undergo proctocolectomy with an ileal pouch-anal anastomosis commonly develop pouch inflammation (pouchitis). Pouchitis develops in a previously normal small intestine and may involve environmental factors. We explored whether diet and microbiota alterations contributed to the pathogenesis of...

Background Diet may play a role in the pathophysiology of inflammatory bowel diseases (IBD) via several mechanisms including metabolome alteration. We conducted an interventional cross-over study aiming to evaluate the short-term effect of two dietary regimens, the Mediterranean diet (MED) and the specific carbohydrate diet (SCD) on multiple biomar...

The desert locust demonstrates density-dependent phase polyphenism: For extended periods it appears in a non-aggregating, non-migrating phenotype, known as the solitary phase. When circumstances change, solitary individuals may aggregate and transform to the gregarious phenotype, which have a strong propensity for generating large swarms. Previous...