Biology subjects

Korneev, D.

Publications and source records attributed to Korneev, D..

7 recordsLinked to original sources

bioRxiv2026

Predictable induction responses of gut prophages

Temperate bacteriophages are dominant members of the human gut microbiome that can infect and lyse their bacterial hosts or integrate as prophages. During this integrated state, prophages exhibit extensive control over host physiology and lysis via induction. Here, we studied a diverse collection of Bacteroidales isolates, which are amongst the most abundant bacterial orders within the human gut, identifying 902 high-quality prophage genomes present within 305 isolates, 240 of which were poly-lysogens. Despite their prevalence, our understanding of the function and induction triggers of prophages is limited. To predict prophage induction, we employed an iterative profile Hidden Markov Model search across divergent bacterial hosts to identify prophage regulatory components. We found 197 Bacteroidales prophages encoding complete CI-like repressor proteins, which initiate induction upon DNA damage. We selected Bacteroides thetaiotaomicron strain Bt_806 to characterise further as it harboured six diverse prophages, including the prevalent and abundant prophage LoVE, which was the only integrated prophage encoding a complete CI-like repressor. Transcriptomics revealed phage LoVE was routinely induced upon DNA damage, while the five co-habiting prophages remained stably integrated yet exhibited transcriptionally active genes associated with regulation, prophage maintenance, and uncharacterised functions. Finally, we selected an additional eleven Bacteroidales poly-lysogens, confirming that integrated prophages encoding complete CI-like repressors were reliably induced upon DNA damage. Together, we demonstrate that mechanistic understanding of prophage induction linked with identification of regulatory genes enables selective and predictable induction of gut prophage species as a potential tool to modulate the microbiome.

microbiology↗

bioRxiv2025

Mechanistic insights and clinical implications of cross-reactive anti-prophage antibodies and bacterial heteroresistance on phage therapeutic failure

Phage therapy is an exciting strategy against antimicrobial-resistant bacterial infections, but critical knowledge gaps regarding its clinical application persist. Studying a patient with a life-threatening, chronic bacterial infection who failed phage therapy, we uncovered important biological concepts with direct translational impact. Using longitudinal clinical samples, we found that patients can harbour pre-existing antibodies against active prophages induced from the genome of the causative pathogen. Notably, these antibodies can contribute to clinical failure by cross-reacting with and effectively neutralising therapeutic phage. We also uncovered bacterial heteroresistance, characterised by bacterial subpopulations from the initial infection with reduced phage susceptibility, as a further contributor to treatment failure. These findings highlight the intricate interplay between host immunology, bacterial genetic diversity and phage biology, bearing broad significance for clinical phage therapy. Future phage therapy patients, especially those with chronic infections, should be screened for antiphage immunity and bacterial heteroresistance prior to phage treatment.

microbiology↗

bioRxiv2024

A novel CCDC112-dependent process of sperm midpiece formation and epididymal maturation

The sperm mitochondrial sheath has proposed functions in structural support and energy production for motility. Here we define coiled coil domain containing protein 112, CCDC112, as crucial for male fertility, specifically in the assembly and function of the mitochondrial sheath. We unveiled a previously unrecognised process of epididymal mitochondrial sheath maturation. Sperm mitochondrial sheaths are structurally immature upon exiting the testis and continue to mature as they transit from the caput to the cauda epididymis. Data reveal the critical role of CCDC112 in mitochondrial morphogenesis during sheath formation. A lack of CCDC112 lead to significantly reduced mitochondrial respiration capacity, irregular flagellar waveforms, diminished progressive motility and a failure of sperm to traverse the female reproductive tract to the site of fertilisation and penetrate the zonae pellucidae of oocytes. Finally, we identify CCDC112 as a component of the distal appendages of the mother centriole and identify a facilitative role in core tail assembly. Collectively, CCDC112 is a key regulator of sperm mitochondrial sheath assembly while further expanding the understanding of spermatogenesis, energy generation and flagella kinematics.

developmental biology↗

bioRxiv2024

Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections

Phage therapy is a promising strategy to treat antimicrobial-resistant infections. Currently, phage therapy applications span personalised treatments that are tailored for a given patients infection, through to the use of pre-established cocktails of virulent phages against clinically relevant pathogens. However, both approaches face challenges, with personalised phage therapy being time-consuming and requiring a phage match to a patients infection, while phage cocktails may not be effective against a patients specific strain. The Alfred Hospital in Melbourne, Australia has reported an ongoing outbreak of infections by the Enterobacter cloacae complex (ECC), a group of emerging multidrug-resistant pathogens responsible for considerable morbidity and mortality. Utilising the hospitals strain collection, built over the last decade, we established an initial three-phage product with 54% ECC coverage that effectively reduced bacterial loads (>99%) in septicaemic mice. We then iteratively improved this product by enhancing phage killing efficiency using phage training and expanded host range through targeted phage isolation against low-coverage ECC strains. This iterative optimisation led to the creation of the product Entelli-02, containing five well characterised virulent phages that target clinical ECC strains through distinct bacterial cell surface receptors. Importantly, Entelli-02 exhibits broad host coverage (99%) and efficacy (92%) against The Alfred Hospitals ECC strain collection (n = 156). We produced this as a therapeutic-grade product, verified and endotoxin unit compliant, ready for use. This approach integrated academic phage research with clinical insights to produce the phage product Entelli-02 as an institution-specific phage cocktail with frontline efficacy and on-demand availability. SUMMARYO_ST_ABSIn briefC_ST_ABSWe developed a phage product containing five phages with frontline potential to address infections caused by multidrug-resistant Enterobacter cloacae complex.

microbiology↗

bioRxiv2020

New insights into sperm ultrastructure through enhanced scanning electron microscopy

The analysis of spermatozoa morphology is fundamental to understand male fertility and the aetiology of infertility. Traditionally scanning electron microscopy (SEM) has been used to define surface topology. Recently, however, it has become a critical tool for three-dimensionally analyse of internal cellular ultrastructure. Modern SEM provides nanometer-scale resolution, but the meaningfulness of such information is proportional to the quality of the sample preservation. In this study, we demonstrate that sperm quickly and robustly adhere to gold-coated surfaces. Leveraging this property, we developed three step-by-step protocols fulfilling different needs for sperm imaging: chemically fixed monolayers for SEM examination of the external morphology, and two high-pressure freezing-based protocols for fast SEM examination of full cell internal morphology and focused ion-beam SEM (FIB-SEM) tomography. These analyses allow previously unappreciated insights into mouse sperm ultrastructure, including the identification of novel structures within the fibrous sheath and domain-specific interactions between the plasma membrane and exosome-like structures.

cell biology↗

bioRxiv2020

Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization

Carbapenem-resistant Acinetobacter baumannii is responsible for frequent, hard-to-treat and often fatal healthcare-associated infections. Phage therapy, the use of viruses that infect and kill bacteria, is an approach gaining significant clinical interest to combat antibiotic-resistant infections. However, a major limitation is that bacteria can develop resistance against phages. Here, we isolated phages with activity against a panel of A. baumannii strains and focused on clinical isolates AB900 and A9844 and their phages for detailed characterization. As expected, coincubation of the phages with their hosts in vitro resulted in the emergence of phage-resistant bacterial mutants. Genome sequence analysis revealed that phage-resistant mutants harbored loss-of-function mutations in genes from the K locus, responsible for the biosynthesis of the bacterial capsule. Using molecular biology techniques, phage adsorption assays, and quantitative evaluation of capsule production, we established that the bacterial capsule serves as the primary receptor for these phages. As a collateral phenotype of impaired capsule production, the phage-resistant strains could not form biofilms, became fully sensitized to the human complement system, showed increased susceptibility to beta-lactam antibiotics, and became vulnerable to additional phages. Finally, in a murine model of bacteremia, the phage-resistant A. baumannii demonstrated a diminished capacity to colonize blood and solid tissues. This study demonstrates that phages can be used not only for their lytic activity but, if combined with a posteriori knowledge of their receptors and the mechanism of bacterial resistance, for their potential synergy with other antimicrobial agents, thus providing even broader clinical options for phage therapy.

microbiology↗

bioRxiv2018

Oxygen plasma focused ion beam scanning electron microscopy for biological samples

Over the past decade, gallium Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) has been established as a key technology for cellular tomography. The utility of this approach, however, is severely limited both by throughput and the limited selection of compatible sample preparation protocols. Here, we address these limitations and present oxygen plasma FIB (O-PFIB) as a new and versatile tool for cellular FIB-SEM tomography. Oxygen displays superior resin compatibility to other ion beams and produces curtain-free surfaces with minimal polishing. Our novel approach permits more flexible sample preparation and 30% faster data collection when compared to using gallium ion sources. We demonstrate this alternative FIB is applicable to a variety of embedding procedures and biological samples including brain tissue and whole organisms. Finally, we demonstrate the use of O-PFIB to produce targeted FIB-SEM tomograms through fiducial free en-block correlative light and electron microscopy.

cell biology↗