Biology subjects

Kot, W.

Publications and source records attributed to Kot, W..

At least 19 recordsLinked to original sources

bioRxiv2026

Danish profile of soft rot Pectobacteriaceae; A three-year field sampling study proving several clonal clades of soft rot isolates across diverse locations implicating a common origin

Soft rot Pectobacteriaceae (SRP) are among the most economically important plant pathogenic bacteria and are especially known to be problematic in potato production. The epidemiology of disease transmission has been investigated for almost a century, and several aspects have been highlighted as plausible infection routes. However, it is generally accepted that the major source of disease is the latently infected mother tuber, but several parameters are still influencing disease prevalence including contaminated equipment, soil water status as well as temperature. Management of the disease is limited to hygiene practices, dry storage and seed certification systems but several studies have also proven biocontrol agents such as bacteriophages (phages) as promising tools. Despite the severity of SRP on potato production, little is known about the genetic diversity of SRPs in Denmark, and since only few isolates are available, the possibility to design a broadly effective phage cocktail is limited. Here we describe a three-year field study utilizing an agri-citizen science approach where Danish farmers provided symptomatic potato plants or tubers, together with metadata such as date, location, potato variety and origin. By using whole genome sequencing (Illumina and Nanopore) together with metadata we were able to investigate and monitor the epidemiological disease spread across the country using 103 complete genomes, sampled across all three years. In this study we provide epidemiological evidence of disease origins and a suite of phages that could be used as a biocontrol tool for early disease intervention. Our results revealed several clonal clades across diverse locations (SNPs < 20) which strongly indicate common origin. A total of 17 Pectobacterium phages were tested and did target > 80% of clonal clades. Based on the clonality across the soft rot isolates we propose the possibility to set in early on using phages targeting strains relevant for soft rot development, with the possibility of a surveillance program together with customizing the phage preference.

microbiology↗

bioRxiv2025

Exploring Clinical Class 1 Integrons as Valuable Targets for the Re-sensitization of Multidrug Resistant Pathogenic Bacteria Using CRISPR-Cas

The increasing prevalence of bacteria resistant to many or all types of antibiotics poses a major health crisis. Novel classes of antibiotics are only slowly being developed and alternative strategies are needed to tackle the issue. Mobile genetic elements and class 1 integrons are important facilitators for antibiotic resistance genes, with the latter being highly conserved in human pathogens. The growing prevalence of multidrug-resistant bacteria and the paucity in the development of new antibiotics underscore the urgent need for innovative approaches in the treatment of pathogens. Among these, CRISPR-Cas nucleases can be used to cleave acquired resistance genes, leading to either plasmid curing or cell death if the target is on a chromosome. In this study, we investigate the feasibility of using class 1 integrons as a target for Cas9-based cleavage leading to re-sensitizing antibiotic-resistant bacteria. We analyze the conserved and widespread integrase gene intI1 and conclude that it is a suitable target for Cas-based re-sensitization due to its high sequence conservation and its occurrence largely limited to human pathogens, alleviating the risk of targeting benign bacteria. We developed a broad host range conjugative plasmid encoding a class 1 integron-targeting Cas9 system that leads to removal of resistance plasmids in target bacteria with subsequent re-sensitization towards antibiotics. We find that 290 distinct ARGs co-occur on int1-harboring plasmids, showing the potential for re-sensitization towards a very broad range of antibiotics.

microbiology↗

bioRxiv2025

Schistosoma mansoni-induced host immunopathology is gut microbiota dependent

Despite progress in schistosomiasis control during recent decades in endemic areas, this parasitic blood-fluke infection continues to pose a substantial public health burden. In depth understanding of the mechanisms behind the complex immunopathology and drivers of morbidity in schistosomiasis is urgently needed. Chronic infection with the parasitic blood fluke Schistosoma mansoni manifests the most severe pathology in relation to egg-induced host immune responses and fibrosis development. Host immune homeostasis is influenced by the commensal gut microbiota, which may therefore also affect systemic immunopathology induced by S. mansoni. Both humans and experimental animal models show metabolomic changes related to gut microbial and liver metabolism during S. mansoni infection, further supporting a link between gut microbiota and regulation of S. mansoni pathology. To investigate whether a radically changed gut microbiota composition would result in changed S. mansoni egg-induced pathology, a mouse model combining antibiotic treatment and infection was established. In the model, the commensal gut microbial composition of female C57BL/6-NTac mice was altered by oral administration of a broad-spectrum ampicillin-vancomycin cocktail prior to infection with S. mansoni and throughout the experiment. An ecosystem view of the host immune milieu was collated by measuring a wide range of parameters: gut microbiome characterisation, immune profiling on the transcriptional level (ileum and liver) supported by flow cytometry of cells (spleen and mesenteric lymph nodes) and bead-based measurements of immune parameters in sera, short-chain fatty acid measurements in sera and caecal content, intestinal permeability assessment, liver enzyme levels in sera, and histology and stereology to characterise immunopathology (ileum and liver). The application of stereological principles to address the non-spherical nature of egg-induced liver granulomas and ileum inflammation supported by liver enzyme levels, collagen deposition, and immune parameters, enabled demonstration of significantly less granuloma formation in livers from antibiotics treated mice compared to controls. The observed difference in the degree of egg-induced inflammatory response in livers from infected mice mediated by antibiotics treatment, was not observed in ileum tissue and could not be explained by infection burden. Our mouse model results demonstrate a role for the gut microbiota and intestinal immune milieu in regulation of systemic S. mansoni infection-driven liver pathology and, hence, potential morbidity. In translational context, these findings warrant that drivers of gut microbial changes and intestinal immune milieu must be considered when pursuing novel holistic interventions for treatment or alleviation of persistent schistosomiasis.

immunology↗

bioRxiv2023

Activity and diversity of prophages harbored by wheat phyllosphere bacteria

1.The plant microbiome harbors an enormous diversity of fungi, bacteria, and viruses, but little is known on the diversity and function of prophages harbored within plant-associated bacteria. Using "VIP-Seq", a novel method based on supernatant sequencing, we identified and quantified the activity of 120 spontaneously induced prophages in a collection of 63 Erwinia and Pseudomonas strains isolated from wheat flag leaves collected from the same field. These bacterial strains exhibited high levels of spontaneous prophage induction, with some producing > 108 virions/mL in overnight culture. Significant induction in planta also occurred from a lysogenic Erwinia strain inoculated on wheat seedlings. The potential of these active prophages in bacterial warfare was exhibited by their widespread killing of rival bacterial strains. Evidence of transduction was observed, and the prophages were shown to contribute a majority of the non-core genome of E. aphidicola isolates. Many additional prophages were predicted by bioinformatic tools, and we found that the predicted prophages that were not spontaneously induced had a significantly higher number of IS elements. Our results suggest that spontaneous induction of prophages may represent an unknown but wide-spread competition mechanism involved in phyllosphere microbiome assembly and function. This may also have implications for the design and resilience of synthetic bacterial communities used as biocontrol for certain plant diseases.

microbiology↗

bioRxiv2021

Parasite-probiotic interactions in the gut: Bacillus sp. and Enterococcus faecium regulate type-2 inflammatory responses and modify the gut microbiota of pigs during helminth infection

Dietary probiotics may enhance gut health by directly competing with pathogenic agents and through immunostimulatory effects. These properties are recognized in the context of bacterial and viral pathogens, but less is known about interactions with eukaryotic pathogens such as parasitic worms (helminths). In this study we investigated whether two probiotic mixtures (comprised of Bacillus amyloliquefaciens, B. subtilis, and Enterococcus faecium [BBE], or Lactobacillus rhamnosus LGG and Bifidobacterium animalis subspecies Lactis Bb12 [LB]) could modulate helminth infection kinetics as well as the gut microbiome and intestinal immune responses in pigs infected with the nodular worm Oesophagostomum dentatum. We observed that neither probiotic mixture influenced helminth infection levels. BBE, and to a lesser extent LB, changed the alpha- and beta-diversity indices of the colon and faecal microbiota, notably including an enrichment of faecal Bifidobacterium spp. by BBE. However, these effects were muted by concurrent O. dentatum infection. BBE (but not LB) significantly attenuated the O. dentatum-induced upregulation of genes involved in type-2 inflammation and restored normal lymphocyte ratios in the ileo-caecal lymph nodes that were altered by infection. Moreover, inflammatory cytokine release from blood mononuclear cells and intestinal lymphocytes was diminished by BBE. Collectively, our data suggest that selected probiotic mixtures can play a role in maintaining immune homeostasis during type 2-biased inflammation. In addition, potentially beneficial changes in the microbiome induced by dietary probiotics may be counteracted by helminths, highlighting the complex inter-relationships that potentially exist between probiotic bacteria and intestinal parasites.

microbiology↗

bioRxiv2021

Viruses roam the wheat phyllosphere

The phyllosphere comprises all the above-ground sections of plants. This niche is colonised by complex microbial communities, including algae, fungi, archaea, and bacteria1-3. They are known to induce plant growth and promote health4,5 or act as causative agents of plant diseases6-8. It is thought that the most abundant organisms are phyllobacteria2, with an estimate between 106 to 107 cells per cm2. Viruses are highly abundant across many environments, often outnumbering bacteria 10 to 19. However, not much is known about their abundance and composition in the phyllosphere, a harsh environment for viruses due to environmental variability and high UV exposure. To investigate this niche in detail, we extracted, sequenced and analysed phyllosphere virome. Using leaf samples from winter wheat (Triticum aestivum), we identified a total of 876 viral populations (vOTUs), mostly belonging to the Caudovirales order. Most of these were predicted to be lytic. Remarkably, 810 of these viral populations correspond to new viral species with no matches to known sequences. We estimate a minimum of 2.0 x106 viral particles per leaf. Overall, these findings suggest that the phyllosphere ecosystem harbours an abundant and active community of novel viruses that play essential roles in shaping this habitat.

microbiology↗

bioRxiv2021

Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in envi-ronmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage communitys shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media corresponds to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum 2-fold change above 0 in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, was highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlights how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.

microbiology↗

bioRxiv2021

The phytonutrient cinnamaldehyde limits intestinal inflammation and enteric parasite infection

Phytonutrients such as cinnamaldehyde (CA) have been studied for their effects on metabolic diseases, but their influence on mucosal inflammation and immunity to enteric infection are not well documented. Here, we show that consumption of CA significantly down-regulates transcriptional pathways connected to inflammation in the small intestine of mice. During infection with the enteric helminth Heligomosomoides polygyrus, CA-treated mice displayed higher growth rates and less worms, concomitant with altered T-cell populations in mesenteric lymph nodes. Furthermore, infection-induced changes in gene pathways connected to cell cycle and mitotic activity were counteracted by CA. Mechanically, CA did not appear to exert activity through a prebiotic effect, as CA treatment did not significantly change the composition of the gut microbiota. Instead, in vitro experiments showed that CA directly induced xenobiotic metabolizing pathways in intestinal epithelial cells and suppressed endotoxin-induced inflammatory responses in macrophages. Thus, CA down-regulates inflammatory pathways in the intestinal mucosa and regulates host responses to enteric infection. These properties appear to be largely independent of the gut microbiota and instead connected to CAs ability to induce antioxidant pathways in intestinal cells. Our results encourage further investigation into the use of CA and related phytonutrients as functional food components to promote intestinal health in humans and animals.

immunology↗

bioRxiv2020

Necrotizing enterocolitis-induced systemic immune suppression in neonatal preterm pigs

ObjectivesPreterm infants are at high risks of sepsis and necrotising enterocolitis (NEC). Some develop sepsis shortly after suspected or confirmed NEC, implying that NEC may predispose to sepsis but the underlying mechanisms are unknown. Using NEC-sensitive preterm pigs as models, we investigated the immune status in animals with and without NEC. MethodsPreterm pigs (n=113, caesarean delivered at day 106) were reared until day 5 or 9. Blood was analyzed for T cell subsets, neutrophil phagocytosis, trans criptomics and immune responses to LPS challenge. Gut tissues were used for histology and cytokine analyses. Pigs with/without macroscopic NEC lesions were scored as healthy, mild or severe NEC. ResultsOverall NEC incidence was similar on days 5 and 9 (61-62%) with less severe lesions on day 9, implying gradual mucosal repair following the early phase of NEC on day 5. Pigs with NEC, especially severe NEC, showed decreased goblet cell density and increased MPO+ and CD3+ cell density in the distal intestine or colon. Circulating parameters were minimally affected by NEC on day 5, but widely altered on day 9 in pigs with NEC, especially severe NEC, to the direction of immune suppression. These included elevated Treg frequency, impaired neutrophil phagocytosis, diminished LPS-induced cytokine secretions and immune gene responses, and consistently low expressions of genes related to innate immune signalling and Th1 polarization. ConclusionWe shows evidence for NEC-induced systemic immune suppression, even with mild and sub-clinical NEC lesions, thereby suggesting mechanisms for increased secondary infections in infants with previous NEC diagnosis.

pathology↗

bioRxiv2020

Fecal filtrate transfer protects against necrotizing enterocolitis in preterm pigs

Background and aimsNecrotizing enterocolitis (NEC) is an acute and life-threatening gastrointestinal disorder afflicting preterm infants, which is currently unpreventable. Fecal microbiota transplantation (FMT) is a promising preventative therapy, but potential side effects raise concern. Removal of bacteria from donor fecal water may reduce side effects while maintaining wanted effects. We aimed to assess preclinical efficacy and safety of bacteria-free fecal filtrate transfer (FFT). MethodsUsing fecal material from healthy suckling piglets, we administered rectal FMT or cognate FFT by either rectal or oro-gastric administration to formula-fed preterm, cesarean piglets, and compared gut pathology and related safety parameters with saline controls. We then analyzed mucosa and luminal bacterial and viral composition using 16S rRNA gene amplicon and metavirome sequencing, respectively. Finally, we used isolated ileal mucosa, coupled with RNA-Seq, to gauge the host response to the different treatments. ResultsOro-gastric FFT eliminated NEC, which was confirmed by microscopy, whereas FMT did not perform better than control. Moreover, FFT but not FMT reduced intestinal permeability, whereas FMT animals had reduced body weight increase and intestinal growth. Oro-gastric FFT increased viral diversity and reduced Proteobacteria abundance in ileal mucosa relative to control. Global gene expression of host mucosa responded to FMT but not FFT with increased and decreased bacterial and viral defense mechanisms, respectively. ConclusionsAs preterm infants are extremely vulnerable, rational therapies need incontestable safety profiles. Here we show in a clinically relevant animal model that FFT, as opposed to FMT, efficiently prevents NEC without any recognizable side effects. If translatable to preterm infants, this could lead to a change of practice and in turn a reduction in NEC burden.

microbiology↗

bioRxiv2020

Gut Mycobiome Dysbiosis Is Linked to Hypertriglyceridemia among Home Dwelling Elderly Danes

Gut microbial dysbiosis have been linked to frailty in elderly, yet the presence of fungal communities and their possible association with host health are little understood. This study attempts to identify gut microbial fungal associations with the progression of atherogenic dyslipidemia in a population of older adults by investigating the interplay between dietary intake, gut mycobiome composition, plasma and fecal metabolome and anthropometric/body-composition measurements of 99 Danes aged 65 to 81 (69.57 {+/-} 3.64) years. The gut mycobiome composition were determined by high-throughput sequencing of internal transcribed spacer (ITS2) gene amplicons, while the plasma and fecal metabolome was determined by GC-MS. The gut microbiome of the subjects investigated is home to three main eukaryotic phyla, namely Ascomyco-ta, Basidiomycota and Zygomycota, with genera Penicillium, Candida, and Aspergillus being particularly common. Hypertriglyceridemia was associated with fewer observed fungal species, and Bray-Curtis dissimilarity matrix-based analysis showed significant (p < 0.05) clustering according to fasting levels of circulating plasma triglycerides (Tg) and very low-density lipoprotein (VLDL) cholesterol fasting levels, respectively. Higher levels of Tg and VLDL cholesterol significantly associates with increased relative abundance of genus Penicillium, and Saccha:ramyces likely mediated by a higher dietary fatty acids intake (p < 0.05), and Sac-charomyces, Debaryomyces, Candida, Agaricus and Starmerella were moderately associated with SCF As groups. Collectively, these findings suggest that gut mycobiome dysbiosis on older adults is associated with hypertriglyceridemia, a known risk factor for development of cardiovascular disease.

microbiology↗

bioRxiv2020

A New High-throughput Screening (HiTS) Method for Phages - Enabling Crude Isolation and Fast Identification of Diverse Phages with Therapeutic Potential

Bacteriophage therapy and application of phages as biocontrol in plant production and food processing, all necessitates acquisition of suitable phages. Depending on purpose, the selection criteria of phage characteristics include lifestyle (lytic/lysogenic), host range, physical stability and absence of unwanted genetic traits such as integrases, antibiotic resistance or bacterial virulence factors. The exclusivity of antibiotic resistant clinical infections and possible development of phage-resistance instigates a need to continually build sizeable phage libraries and also be able to rapidly isolate and characterise novel phages of specified bacterial hosts. Current methods for phage isolation are both laborious and time consuming, suitable only for the isolation of a limited number of phages. Thus, we developed the High-Throughput Screening (HITS) method for phages for fast isolation and identification of potentially hundreds of distinct phages against single hosts. This scalable method enables screening of hundreds of samples, in multiple simultaneous setups with varying parameters increasing the likelihood of isolating multiple distinct phages specific for the given conditions. The efficiency of the method is emphasised by our screening of 200 environmental samples, resulting in the identification of an abundance of unique phage species lytic to Escherichia coli, Salmonella Enterica, Enterococcus faecalis and Pseudomonas aeruginosa.

microbiology↗

bioRxiv2020

Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Phages drive bacterial diversity - profoundly influencing diverse microbial communities, from microbiomes to the drivers of global biogeochemical cycling. The vast genomic diversity of phages is gradually being uncovered as >8000 phage genomes have now been sequenced. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples (0.5 ml) and identified 136 phages of which 104 are unique phage species and 91 represent novel species, including several novel lineages. These phages are estimated to represent roughly a third of the true diversity of Escherichia phages in Danish wastewater. The novel phages are remarkably diverse and represent four different families Myoviridae, Siphoviridae, Podoviridae and Microviridae. They group into 14 distinct clusters and nine singletons without any substantial similarity to other phages in the dataset. Their genomes vary drastically in length from merely 5 342 bp to 170 817 kb, with an impressive span of GC contents ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, in the go-to source for phages, substantial diversity remains to be uncovered. These results expand and underlines the range of Escherichia phage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.

microbiology↗

bioRxiv2020

Isolation and complete genome sequencing of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae

Pectobacterium carotovorum is the causative agent of bacterial soft rot on various plant species. The use of phages for plant disease control have gained increased awareness over the past years. We here describe the isolation and characterization of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames (ORFs). Gene synteny and products seem to be somewhat conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the subfamily Autographivirinae. We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the subfamily Autographivirinae.

microbiology↗

bioRxiv2019

Physical fitness in community dwelling older adults is linked to dietary intake, gut microbiota and metabolomic signatures

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.

cell biology↗

bioRxiv2019

Faecal virome transplantation decrease symptoms of type-2-diabetes and obesity in a murine model

ObjectiveDevelopment of obesity and type-2-diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. As a proof-of-concept we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice.\n\nDesignThe FVT consisted of viromes extracted from the caecal content of mice fed a low-fat (LF) diet for fourteen weeks. Male C57BL/6NTac mice were divided into five groups: LF (as control), high-fat diet (HF), HF+Ampicillin (Amp), HF+Amp+FVT and HF+FVT. At week six and seven of the study the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with ampicillin 24 h prior to first FVT treatment.\n\nResultsSix weeks after first FVT the HF+FVT mice showed a significant decrease in weight gain compared to the HF group. Further, glucose tolerance was comparable between the lean LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome, and expression levels of genes involved in obesity and T2D development.\n\nConclusionsTransfer of gut viral communities from mice with a lean phenotype into those with an obese phenotype reduce weight gain and normalise blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes.\n\nSignificance of this studyWhat is already known about this subject?\n\nO_LIObesity and type-2-diabetes (T2D) are associated with gut microbiota (GM) dysbiosis.\nC_LIO_LIFaecal microbiota transplant from lean donors has previously shown potential in treating obesity and T2D.\nC_LIO_LIPatients suffering from recurrent Clostridium difficile infections (rCDI) have been cured with sterile filtered donor faeces (containing enteric viruses and no bacteria), here defined as faecal virome transplantation (FVT).\nC_LI\n\nWhat are the new findings?\n\nO_LIFVT from lean donors lead to decreased weight gain and normalised blood sugar tolerance in a diet-induced obesity (DIO) mouse model.\nC_LIO_LIFVT significantly changed the bacterial and viral GM component, as well as the plasma metabolome and the expression profiles of obesity and T2D associated genes.\nC_LIO_LIInitial treatment with ampicillin prior FVT seems to counteract the beneficial effects associated with FVT.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future?\n\nO_LIWe here show a proof-of-concept, providing a solid base for designing a clinical study of FVT targeting obesity and T2D in humans. This is further augmented by the increased safety related to FVT, since bacteria and other microorganisms are removed from the donor faeces, and therefore minimises the risk of disease transmission.\nC_LIO_LIThese findings highlight the potential application of FVT treatment of various diseases related to GM dysbiosis and further support the vital role of the viral community in maintaining and shaping the GM.\nC_LI

microbiology↗

bioRxiv2019

Characterization of the vaginal DNA virome in health and dysbiosis: an opening study in patients with non-female factor infertility

BackgroundBacterial vaginosis (BV) is characterised by a reduction in Lactobacillus spp. abundance and increased abundance of facultative anaerobes, like Gardnerella vaginalis. BV aetiology is not fully understood, but bacteriophages could play a pivotal role causing perturbation of the vaginal bacterial community. Here we investigate the vaginal viral community, including bacteriophages, and its association to the bacterial community and BV-status.\n\nMethodsVaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with BV-status, bacterial community structure and presence of key vaginal bacterial species.\n\nResultsThe majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of total reads. Clear links between viral community composition and BV (q = 0.006, R = 0.26) as well as presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella vaginalis and Atopobium vaginae were found (q < 0.002, R > 0.15). Interestingly, also the eukaryotic viral community was correlated with BV-status (q = 0.018, R = 0.20).\n\nConclusionsThe vaginal virome is clearly linked with bacterial community structure and BV-status.\n\nClinical Trials RegistrationNCT02042352.

microbiology↗

bioRxiv2019

Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, \"Silenusvirus\".

Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \"Silenusvirus\".

microbiology↗