Genome Sequence Analysis Research Articles

High-quality reference genome decoding and population evolution analysis of prickly Sechium edule

Sechium edule (chayote) is an important vegetable crop belonging to the Cucurbitaceae family. To decipher the chayote genome, a high-quality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis. The total length was 612.91 Mb, and 25 755 genes were detected in the chayote genome. The contig N50 was more than 20.01 Mb, and the scaffold N50 was over 47.11 Mb. Of the genome, 60.35% were composed of repetitive sequences, and 31.18% of genome sequences belonged to long-terminal repeats. A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference. Based on this genome-wide and global alignment map, researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species. Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree, population structure analysis, and principal component analysis using genome re-sequencing data. The chayote genome, re-sequencing dataset, and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.

First Detected Transmission of C. auris within a Minnesota Healthcare Facility Following Exposure in the Emergency Department

Background: Candida auris reporting and submission of confirmed or possible isolates has been mandatory in Minnesota since August 2019. On August 9, 2023, the Minnesota Department of Health (MDH) was notified of a C. auris isolate in hip tissue from a patient in acute care hospital A (ACH-A). Only 9 cases of C. auris were detected prior to August 2023, in Minnesota, and all from patients with a history of international healthcare or healthcare in endemic C. auris locations of the United States. Methods: The MDH Public Health Laboratory (MDH-PHL) confirmed identification of C. auris from the ACH-A isolate by MALDI-TOF. MDH partnered with ACH-A to review medical records, assess infection prevention and control (IPC) practices, conduct contact tracing, and identify patients for colonization screening. Screening was performed on all patients that overlapped with the index case (case A) and were admitted to a facility in the same healthcare system as ACH-A. Facilities accepting discharged patients who overlapped with case A were contacted for colonization screening. Overlapping patients, no longer admitted to a healthcare facility, were sent a notification letter, and offered outpatient screening. Composite axilla/groin swabs were screened for C. auris using real-time PCR at MDH-PHL, who also performed whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis. Results: Case A’s medical record showed only Minnesota healthcare exposures, a surgical procedure in June 2023 and indicated the case overlapped with a previous case (case B) from July 2023, who had recent international healthcare. The two cases were hospitalized at ACH-B July 12-18, on different care floors without evident links to shared services. However, the cases were in adjacent rooms in ACH-B Emergency Department (ED) on July 3 for 5 hours, when C. auris status of case B was unknown. WGS indicated both isolates were within clade I (South Asian) and separated by 2 SNPs, suggesting relatedness. Extensive colonization screening occurred among 109 potentially exposed patients, including 18 patients from the ED. No additional C. auris was detected. Conclusions: This case represents the first detected transmission of C. auris within a Minnesota healthcare facility. The role of C. auris transmission within the ED is not well understood. Medical record review in combination with WGS analysis suggests potential transmission within the ED. Clinicians should be aware of the risks for C. auris transmission in the ED and follow all IPC measures to prevent transmission of this emerging fungal pathogen.

Genomic insights of S. aureus associated with bovine mastitis in a high livestock activity region of Mexico.

Bovine mastitis, predominantly associated with gram-positive Staphylococcus aureus, poses a significant threat to dairy cows, leading to a decline in milk quality and volume with substantial economic implications. This study investigated the incidence, virulence, and antibiotic resistance of S. aureus associated with mastitis in dairy cows. Fifty milk-productive cows underwent a subclinical mastitis diagnosis, and the S. aureus strains were isolated. Genomic DNA extraction, sequencing, and bioinformatic analysis were performed, supplemented by including 124 S. aureus genomes from cows with subclinical mastitis to enhance the overall analysis. The results revealed a 42% prevalence of subclinical mastitis among the cows tested. Genomic analysis identified 26 sequence types (STs) for all isolates, with Mexican STs belonging primarily to CC1 and CC97. The analyzed genomes exhibited multidrug resistance to phenicol, fluoroquinolone, tetracycline, and cephalosporine, which are commonly used as the first line of treatment. Furthermore, a similar genomic virulence repertoire was observed across the genomes, encompassing the genes related to invasion, survival, pathogenesis, and iron uptake. In particular, the toxic shock syndrome toxin (tss-1) was found predominantly in the genomes isolated in this study, posing potential health risks, particularly in children. These findings underscore the broad capacity for antibiotic resistance and pathogenicity by S. aureus, compromising the integrity of milk and dairy products. The study emphasizes the need to evaluate the effectiveness of antibiotics in combating S. aureus infections.

Preliminary insights of the genetic diversity and invasion pathways of Cedrela odorata in the Galapagos Islands, Ecuador.

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (H e = 0.55) was lower than reported in the mainland (H e = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad-Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna.

Genome sequence analyses identify novel risk loci for multiple system atrophy.

Multiple system atrophy (MSA) is an adult-onset, sporadic synucleinopathy characterized by parkinsonism, cerebellar ataxia, and dysautonomia. The genetic architecture of MSA is poorly understood, and treatments are limited to supportive measures. Here, we performed a comprehensive analysis of whole genome sequence data from 888 European-ancestry MSA cases and 7,128 controls to systematically investigate the genetic underpinnings of this understudied neurodegenerative disease. We identified four significantly associated risk loci using a genome-wide association study approach. Transcriptome-wide association analyses prioritized USP38-DT, KCTD7, and lnc-KCTD7-2 as novel susceptibility genes for MSA within these loci, and single-nucleus RNA sequence analysis found that the associated variants acted as cis-expression quantitative trait loci for multiple genes across neuronal and glial cell types. In conclusion, this study highlights the role of genetic determinants in the pathogenesis of MSA, and the publicly available data from this study represent a valuable resource for investigating synucleinopathies.

Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage.

Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food substrates has become an emerging strategy. Bacteriophages have the potential to control Salmonella contamination.We have isolated and characterized a broad-spectrum Salmonella phage, SP154, which can lyse 9 serotypes, including S. Enteritidis, S. Typhimurium, S. Pullorum, S. Arizonae, S. Dublin, S. Cholerasuis, S. Chester, S. 1, 4, [5], 12: i: -, and S. Derby, accounting for 81.9% of 144 isolates. SP154 showed a short latent period (40min) and a high burst size (with the first rapid burst size at 107 PFUs/cell and the second rapid burst size at approximately 40 PFUs/cell). Furthermore, SP154 activity has higher survival rates across various environmental conditions, including pH 4.0-12.0 and temperatures ranging from 4 to 50°C for 60min, making it suitable for diverse food processing and storage applications. Significant reductions in live Salmonella were observed in different foods matrices such as milk and chicken meat, with a decrease of up to 1.9 log10 CFU/mL in milk contamination and a 1 log10 CFU/mL reduction in chicken meat. Whole genome sequencing analysis revealed that SP154 belongs to the genus Ithacavirus, subfamily Humphriesvirinae, within the family Schitoviridae. Phylogenetic analysis based on the terminase large subunit supported this classification, although an alternate tree using the tail spike protein gene suggested affiliation with the genus Kuttervirus, underscoring the limitations of relying on a single gene for phylogenetic inference. Importantly, no virulence or antibiotic resistance genes were detected in SP154. Our research highlights the potential of using SP154 for biocontrol of Salmonella in the food industry.

Sustainable improvement of rice growth under salinity stress using an endophytic fungus-based biofertilizer

Salinity stress adversely affects rice (Oryza sativa L.) growth, development and overall productivity. Multiple strategies have been implemented to enhance the resilience of rice plants, enabling them to grow better in saline environments. Use of biofertilizers, a sustainable alternative to chemical fertilizers, has gained significant attention in modern agriculture due to their potential to improve soil fertility, enhance crop productivity, and mitigate environmental concerns. Biofertilizers encompass a diverse group of microorganisms, including bacteria, fungi, and algae, which interact with plants through various mechanisms. These beneficial microbes have been reported to convert atmospheric nitrogen into plant-available forms and break down insoluble phosphates and zinc complexes in the soil. Additionally, they can also produce growth regulators, enhance nutrient availability, and protect plants against pathogens. In our previous study, a salt-tolerant endophytic fungus isolated from the halophytic wild rice, Oryza coarctata, was identified as Aspergillus welwitschiae Ocstreb1 by whole genome sequence analysis. During the in-vitro experiments, the endophyte showed several plant growth promoting activities such as, zinc and phosphate solubilization, siderophore, IAA, and ACC-deaminase production, nitrogen fixation, etc. in both normal and 900 mM salt stress. In this study, the endophyte was used to formulate a biofertilizer in combination with talcum powder to enhance the growth and yield of rice plants under salinity stress. This research investigated the effectiveness of the biofertilizer in four distinct salinity tanks under both non-saline and 6 dS/m saline conditions, each containing three different varieties of rice. Treatment of BRRI dhan28 (BD-28), BRRI dhan67 (BD-67) and BRRI dhan87 (BD-87) rice plants with the formulated biofertilizer significantly enhanced their yield in both non-saline and saline conditions. Among the three rice varieties, BD-28 showed the highest significant (p<0.05) yield increase, with 104.20% under normal conditions and 3080.56% under salt stress. BD-67 exhibited a 45.15% increase in normal conditions and 153.64% under salt stress (P<0.05). BD-87 showed a significant yield increase only under salt stress, at 293.63% (p<0.05). From the results of the study, it can be proposed that the formulated biofertilizer is a potential eco-friendly and cost-effective solution to improve cultivation and yield of rice in the highly saline coastal regions of Bangladesh. Bioresearch Commu. 10(2): 1474-1481, 2024 (July)

Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.

In silico comparative analysis of the complete chloroplast genome sequences in the mulberry family (Moraceae)

The mulberry family (Moraceae) encompasses a wide range of angiosperms and includes several important fruit plants, such as jackfruit, breadfruit, and figs, among others. While there have been multiple published complete chloroplast (cp) genomes within this family, there has been no comprehensive study that summarizes the characteristics of these sequences. In the current study, a comprehensive analysis was conducted using a dataset consisting of 32 cp genomes obtained from NCBI GenBank. These genomes belong to 32 species, encompassing 12 genera within the mulberry family. The collected data were used to conduct genomic comparisons and phylogenetic analyses, employing a range of bioinformatics tools. The findings revealed length variations among the cp genomes of different species, ranging from 158,459 bp in Morus mongolica to 162,594 bp in Broussonetia luzonica. Additionally, the study detected structural variations in simple sequence repeat motifs including gene losses. Overall, the phylogenetic results in this study generally supported the existing taxonomy of species within this family, with the exception that Malaisia scandens and Trophis scandens are clustered in the clade of the Broussonetia genus. This investigation provides further evidence of the effectiveness of characterizing the entire cp genome when classifying species and genera within the mulberry family.

Secondary findings in genes related to cancer phenotypes in Turkish exome sequencing data from 2020 individuals.

Big data generated from exome sequencing (ES) and genome sequencing (GS) analyses can be used to detect actionable and high-penetrance variants that are not directly associated with the primary diagnosis of patients but can guide their clinical follow-up and treatment. Variants that are classified as pathogenic/likely pathogenic and are clinically significant but not directly associated with the primary diagnosis of patients are defined as secondary findings (SF). The aim of this study was to examine the frequency and variant spectrum of cancer-related SF in 2020 Turkish ES data and to discuss the importance of the presence of cancer-related SF in at-risk family members in terms of genetic counseling and follow-up. A total of 2020 patients from 2020 different families were evaluated by ES. SF were detected in 28 unrelated cases (1.38%), and variants in BRCA2 (11 patients) and MLH1 (4 patients) genes were observed most frequently. A total of 21 different variants were identified, with 4 of them (c.9919_9932del and c.3653del in the BRCA2 gene, c.2002A>G in the MSH2 gene, c.26_29del in the TMEM127 gene) being novel variations. In three different families, c.1189C>T (p.Gln397*) variation in BRCA2 gene was detected, suggesting that this may be a common variant in the Turkish population. This study represents the largest cohort conducted in the Turkish population, examining the frequency and variant spectrum of cancer-related SF. With the identification of frequent variations and the detection of novel variations, the findings of this study have contributed to the variant spectrum. Genetic testing conducted in family members is presented as real-life data, showcasing the implications in terms of counseling, monitoring, and treatment through case examples.

Characterization of Degraded Konjac Glucomannan from an Isolated Bacillus licheniformis Strain with Multi-Enzyme Synergetic Action.

The large molecular weight and high viscosity of natural konjac glucomannan (KGM) limit its industrial application. Microbial degradation of low-molecular-weight KGM has health benefits and various biological functions; however, the available KGM strains used in the industry have microbial contamination and low degradation efficiencies. Therefore, exploring novelly adaptable strains is critical for industrial processes. Here, the Bacillus licheniformis Z7-1 strain isolated from decaying konjac showed high efficiency for KGM degradation. The monosaccharide composition of the degradation products had a reduced molar ratio of mannose to glucose, indicating that Z7-1 preferentially degraded glucose in KGM. The degraded component was further characterized by ESI-MS, Fourier-transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM), and it also exhibited good antibacterial activity against various food-spoilage bacteria. Genome sequencing and zymolytic analysis revealed that abundant carbohydrate-active enzymes exist in the Z7-1 genome, with at least five types of extracellular enzymes responsible for KGM degradation, manifesting multi-enzyme synergetic action. The extracellular enzymes had significant thermal stability, indicating their potential application in industry. This study provides an alternative method for obtaining low-molecular-weight KGM with antibacterial functions and supports foundational knowledge for its development as a biocatalyst for the direct conversion of biomass polysaccharides into functional components.

Characterization of Mice Carrying a Neurodevelopmental Disease-Associated GluN2B(L825V) Variant.

N-Methyl-d-aspartate receptors (NMDARs), encoded by GRIN genes, are ionotropic glutamate receptors playing a critical role in synaptic transmission, plasticity, and synapse development. Genome sequence analyses have identified variants in GRIN genes in patients with neurodevelopmental disorders, but the underlying disease mechanisms are not well understood. Here, we have created and evaluated a transgenic mouse line carrying a missense variant Grin2bL825V , corresponding to a de novo GRIN2B variant encoding GluN2B(L825V) found in a patient with intellectual disability (ID) and autism spectrum disorder (ASD). We used HEK293T cells expressing recombinant receptors and primary hippocampal neurons prepared from heterozygous Grin2bL825V/+ (L825V/+) and wild-type (WT) Grin2b+/+ (+/+) male and female mice to assess the functional impact of the variant. Whole-cell NMDAR currents were reduced in neurons from L825V/+ compared with +/+ mice. The peak amplitude of NMDAR-mediated evoked excitatory postsynaptic currents (NMDAR-eEPSCs) was unchanged, but NMDAR-eEPSCs in L825V/+ neurons had faster deactivation compared with +/+ neurons and were less sensitive to a GluN2B-selective antagonist ifenprodil. Together, these results suggest a decreased functional contribution of GluN2B subunits to synaptic NMDAR currents in hippocampal neurons from L825V/+ mice. The analysis of the GluN2B(L825V) subunit surface expression and synaptic localization revealed no differences compared with WT GluN2B. Behavioral testing of mice of both sexes demonstrated hypoactivity, anxiety, and impaired sensorimotor gating in the L825V/+ strain, particularly affecting males, as well as cognitive symptoms. The heterozygous L825V/+ mouse offers a clinically relevant model of GRIN2B-related ID/ASD, and our results suggest synaptic-level functional changes that may contribute to neurodevelopmental pathology.

Isolation and complete genome sequence analysis of Vibrio rotiferianus strain TO-01 from Trachinotus ovatus to reveal its pathogenicity and drug resistance

Vibrio rotiferianus is a pathogenic bacterium that is widely distributed in the ocean and can cause diseases in a variety of marine animals, including fish, shrimp and shellfish. In this study, we isolated and identified V. rotiferianus strain TO-01 from diseased Trachinotus ovatus. Infected fish exhibited a range of pathological symptoms, including lethargy in swimming, blackened body coloration, skin ulceration and erratic side swimming. Tissue section examination revealed pronounced damage to the liver, spleen and gills of the infected fish. An analysis of immune factor expression revealed a significant increase in the expression of inflammatory factors, including interleukin (IL)-1, IL-2, IL-6 receptor and IL-21, in the spleen and kidney of fish infected with TO-01 at 6 h post-infection. To gain a more in-depth comprehension of the pathogenicity and drug resistance of V. rotiferianus, we conducted whole genome sequencing. The total genome length of V. rotiferianus was 4734,075 bp, and 74 virulence factors were predicted within the genome. Most of these virulence genes were associated with bacterial adhesion and flagellar motility. A gene associated with group sensing, cqsA, and a gene associated with hemolysin, tlh, were also identified. The prediction of drug resistance genes was in agreement with the results of drug sensitivity assays, both of which indicated that TO-01 has significant resistance to β-lactams. The findings of this study significantly enhance our understanding of the pathogenic mechanism of V. rotiferianus and give crucial insights into disease prevention and control in the management of T. ovatus.

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile.

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was isolated from a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 to 9.0, with the best growth occurring at 6.8. Under optimal conditions in a glucose-containing medium, the cells were predominantly observed singly, in pairs, or less frequently in chains, and did not form endospores. However, under conditions involving growth with merino wool or feathers, or under suboptimal conditions, the cells of strain KAk exhibited a notably elongated and thinner morphology, with lengths ranging from 5 to 8 µm, and spores were observed. The KAk strain exhibited efficient degradation of feather keratin and merino wool at temperatures ranging from 65 to 70 °C. Analysis of the 16S rRNA gene sequence placed KAk within the genus Caldanaerobacter, family Thermoanaerobacteraceae, with the highest similarity to C. subterraneus subsp. tengcongensis MB4T (98.84% sequence identity). Furthermore, our analysis of the draft genome sequence indicated a genome size of 2.4 Mbp, accompanied by a G+C value of 37.6 mol%. This study elucidated the physiological and genomic characteristics of strain KAk, highlighting its keratinolytic capabilities and distinctiveness compared to other members of the genus Caldanaerobacter.

Ethylene glycol is metabolized to ethanol and acetate and induces expression of bacterial microcompartments in Propionibacterium freudenreichii

Ethylene glycol (EG, 1,2-ethanediol) is a two-carbon dihydroxy alcohol that can be derived from fermentation of plant-derived xylose and arabinose and which can be formed during food fermentations. Here we show that Propionibacterium freudenreichii DSM 20271 is able to convert EG in anaerobic conditions to ethanol and acetate in almost equimolar amounts. The metabolism of EG led to a moderate increase of biomass, indicating its metabolism is energetically favourable. A proteomic analysis revealed EG induced expression of the pdu-cluster, which encodes a functional bacterial microcompartment (BMC) involved in the degradation of 1,2-propanediol, with the presence of BMCs confirmed using transmission electron microscopy. Cross-examination of the proteomes of 1,2-propanediol and EG grown cells revealed PDU BMC-expressing cells have elevated levels of DNA repair proteins and cysteine biosynthesis proteins. Cells grown in 1,2-propanediol and EG also showed enhanced resistance against acid and bile salt-induced stresses compared to lactate-grown cells. Our analysis of whole genome sequences of selected genomes of BMC-encoding microorganisms able to metabolize EG with acetaldehyde as intermediate indicate a potentially broad-distributed role of the pdu operon in metabolism of EG. Based on our results we conclude EG is metabolized to acetate and ethanol with acetaldehyde as intermediate within BMCs in P. freudenreichii.

Transfection of a Molecular Clone of Naegleria gruberi rDNA into N. gruberi Trophozoites.

All ribosomal genes of Naegleria trophozoites are maintained in a closed circular extrachromosomal ribosomal DNA (rDNA) containing element (CERE). While little is known about the CERE, a complete genome sequence analysis of three Naegleria species clearly demonstrates that there are no rDNA cistrons in the nuclear genome. Furthermore, a single DNA origin of replication has been mapped in the N. gruberi CERE, supporting the hypothesis that CERE replicates independently of the nuclear genome. This CERE characteristic suggests that it may be possible to use engineered CERE to introduce foreign proteins into Naegleria trophozoites. As the first step in exploring the use of a CERE as a vector in Naegleria, we developed a protocol to transfect N. gruberi with a molecular clone of the N. gruberi CERE cloned into pGEM7zf+ (pGRUB). Following transfection, pGRUB was readily detected in N. gruberi trophozoites for at least seven passages, as well as through encystment and excystment. As a control, trophozoites were transfected with the backbone vector, pGEM7zf+, without the N. gruberi sequences (pGEM). pGEM was not detected after the first passage following transfection into N. gruberi, indicating its inability to replicate in a eukaryotic organism. These studies describe a transfection protocol for Naegleria trophozoites and demonstrate that the bacterial plasmid sequence in pGRUB does not inhibit successful transfection and replication of the transfected CERE clone. Furthermore, this transfection protocol will be critical in understanding the minimal sequence of the CERE that drives its replication in trophozoites, as well as identifying regulatory regions in the non-ribosomal sequence (NRS).

Dietary Supplementation of Lactococcus lactis subsp. lactis BIONCL17752 on Growth Performance, and Gut Microbiota of Broiler Chickens.

The rapid rise of antimicrobial resistance (AMR) is a global concern, being triggered by the overuse or misuse of antibiotics in poultry farming sector. We evaluated Lactococcus lactis subsp. lactis BIONCL17752 strain, and characterized its probiotic potential to endure hostile gastrointestinal conditions. Genome sequencing analysis revealed probiotics traits, and gene clusters involved in bacteriocins, lactococcin A, and sactipeptides production. The absence of genes for antibiotic resistance, virulence, and biogenic amine production indicates the potential of probiotic strain. The BIONCL17752 strain was explored for antibiotic-free feed supplement for growth promotor in broiler chicken. The feed supplemented with 4 × 109CFU/kg of probiotic strain, in combination with various concentrations of fructooligosaccharides (FOS) 1.0, 2.5, and 5.0kg/tonne in starter, grower, and finisher diets, respectively. A significant improvement of body weight 152 to 171g/bird (p < 0.05), and a low feed conversion ratio (FCR) of 1.62, was achieved without using synthetic antibiotics for growth promotion. The results of biochemical, hematological, and histological examinations showed normal features, indicating that the treatment had no harmful effects on the bird's health. Reduced levels of cholesterol, triglycerides, high-density lipoprotein(HDL), and low-density lipoprotein (LDL) in serum are an indication of the health benefits for the treated birds. Microbial community analysis of fecal samples of poultry birds exhibited a higher abundance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria. Probiotic treatment resulted in reduced Firmicutes and increased Bacteroidetes (F/B ratio) in the broiler's gut which highlights the benefits of probiotic dietary supplements. Importantly, the probiotic-fed group exhibited a high abundance of carbohydrate-active enzymes (CAZyme) such as glycoside hydrolases (GH), glycoside transferases (GT), and carbohydrate-binding module (CBM) hydrolases which are essential for the degradation of complex sugar molecules. The probiotic potential of the BIONCL17752 strain contributes to broilers' health by positively affecting intestinal microbiota, achieving optimal growth, and lowering mortality, demonstrating the economic benefits of probiotic treatment in organic poultry farming.

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Bacillus velezensis is a member of the genus Bacillus, which harbours useful, novel, and efficient secondary metabolites that can be utilized in the disruption of xenobiotics. Although a few strains of B. velezensis and related species are reported every year as having xenobiotic metabolism potential, several novel gene clusters are still unexplored, which could be more potent than those already discovered. The current B. velezensis strain was isolated from gills of healthy Oreochromis niloticus and the novelty of the strain was assessed through whole genome sequence analysis. Prokka, DFAST, BAKTA, and RASTtk were computational tools utilized for genome elucidation following the genome assembly. Protein and protein pathway prediction was achieved through the PATRIC database. Additionally, the resistance genes against microorganisms were examined through CARD (via Proksee), bacteriocin, and RiPPs using BAGEL4, and forecast of virulence factors using VFDB in PATRIC. The analysis led to identification of indicator genes for xenobiotic breakdown. The results were compared to pre-existing strains of B. velezensis and it was compelling to conclude the high biotechnological potential and the candidacy of the strain in xenobiotic degradation.

Genomic and immunocyte characterisation of bloodstream infection caused by Klebsiella pneumoniae

ObjectivesThe aim of this study was to evaluate the characteristics of immunocyte associated with bloodstream infection (BSI) caused by Klebsiella pneumoniae (Kpn).MethodsPatients with BSI-Kpn were included from 2015 to 2022 in our hospital. Immunocyte subpopulations of enrolled BSI-Kpn patients were tested on the same day of blood culture using multicolor flow cytometry analysis. Antibiotic susceptibility test was determined by agar dilution or broth dilution method. All included isolates were subjected to whole genome sequencing and comparative genomics analysis. Clinical and genetic data were integrated to investigate the risk factors associated with clinical outcome.ResultsThere were 173 patients with non-duplicate BSI-Kpn, including 81 carbapenem-resistant Kpn (CRKP), 30 extended-spectrum β-lactamases producing Kpn (ESBL-Kpn), 62 none CRKP or ESBL-Kpn (S-Kpn). Among 68 ST11-CRKP isolates, ST11-O2v1:KL64 was the most common serotypes cluster (77.9%, 53/68), followed by ST11-OL101: KL47 (13.2%, 9/68). Compared with CSKP group, subpopulations of immunocyte in patients with CRKP were significantly lower (P < 0.01). In patients with ST11-O2v1:KL64 BSI-Kpn, the level of cytotoxic T lymphocytes (CD3 + CD8 +) is the highest, while the B lymphocytes (CD3-CD19 +) was the least. In addition, the level of immunocyte in patients with Kpn co-harbored clpV-ybtQ-qacE were lower than that in patients with Kpn harbored one of clpV, ybtQ or qacE and without these three genes. Furthermore, co-existence of clpV-ybtQ-qacE was independently associated with a higher risk for 30-day mortality.ConclusionsThe results demonstrate that patients with BSI-CRKP, especially for ST11-O2v1:KL64, exhibit lower leukomonocyte counts. In addition, BSI-Kpn co-harbored clpV-ybtQ-qacE is correlated to higher 30-day mortality.

Complete genome sequence and phylogenetic analysis of a newly discovered fusagra-like virus infecting Carica papaya in Ecuador.

A new fusagra-like virus infecting papaya (Carica papaya L.) was genetically characterized. The genome of the virus, provisionally named "papaya sticky fruit-associated virus" (PSFaV), is a single molecule of double-stranded RNA, 9,199 nucleotides (nt) in length, containing two discontinuous open reading frames. Pairwise sequence comparisons based on complete RNA-dependent-RNA-polymerase (RdRp) sequences revealed identity of 79.4% and 83.3% at the nt and amino acid (aa) level, respectively, to babaco meleira-like virus (BabMelV), an uncharacterized virus sequence discovered in babaco (Vasconcellea x heilbornii) in Ecuador. Additional plant-associated viruses with sequence identity in the 50% range included papaya meleira virus (PMeV) isolates from Brazil. Phylogenetic analysis based on the amino acid sequences of the capsid protein (CP), RdRp, and CP-RdRp fusion protein genes placed PSFaV in a group within a well-supported clade that shares a recent ancestor with Sclerotium rolfsii RNA virus 2 and Phlebiopsis gigantea mycovirus dsRNA 2, two fungus-associated fusagraviruses. Genomic features and phylogenetic relatedness suggest that PSFaV, along with its closest relative BabMelV, represent a species of novel plant-associated virus classified within the recently established family Fusagraviridae.