Versatile genome assembly evaluation with QUAST-LG

Complete genome sequence of Streptococcus suis isolated from an aborted bovine fetus and placenta in British Columbia, Canada

We present the complete genome of Streptococcus suis KKAHC02 isolated from an aborted bovine fetus and placenta in British Columbia, Canada. The genome consists of a circular chromosome of 2,340,488 bp long and five circular plasmids of 5,796, 4,273, 3,973, 3,964, and 2,832 bp, respectively.

Comparative genome analysis of the immunomodulatory ability of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus from Japanese pickles

Lactic acid bacteria (LAB) are pivotal in food preservation and exhibit immunomodulatory effects on interleukin-10 (IL-10) and interleukin-12 (IL-12) production. Lactiplantibacillus plantarum (L. plantarum) and Lactiplantibacillus pentosus (L. pentosus) from fermented food are known for their effect; however, a comprehensive comparative genome analysis is needed to identify the linked genes. Here, we investigated the immunomodulatory capability at the genome level of L. plantarum and L. pentosus strains isolated from Japanese pickles at the genome level, and we further identified their immunomodulation-associated genes using the potential-gene (PG) index derived from the Calinski-Harabasz (CH) index. The results revealed an immunostimulatory clade with strain-specific IL-10 and IL-12 induction and identified key genes via the PG index. Both genes across two species were shown to encode the enzyme TagF2, which is crucial for synthesizing poly-glycerol-3-phosphate type wall teichoic acid (poly-GroP WTA), indicating that TagF2 plays a potential role as an effective microbe-associated-molecular-pattern. In vivo analyses confirmed the IL-10-inducing ability of one strain, reinforcing the IL-10-stimulating capacity of its poly-GroP WTA. Subpotential genes in L. plantarum TagF2-possessing strains were linked to host‒cell interactions, suggesting that such strains play potential probiotic roles. Collectively, the PG index effectively identified immunomodulation-related genes, thus paving the way for the use of the PG index to detect potential health benefit-associated genes in other LAB species.

IMPORTANCE

Lactic acid bacteria are pivotal in food preservation and exhibit immunomodulatory effects on interleukin-10 (IL-10) and interleukin-12 (IL-12) production. Lactiplantibacillus plantarum and Lactiplantibacillus pentosus from fermented food are known for such effect, yet comprehensive comparative genome analysis is needed to elucidate the linked genes of the two species. The significance of our research is in observing the immunostimulatory clade with strain-specific cytokine induction and identifying key immunostimulation-related genes encoding enzymes that are crucial for synthesizing a potentially effective microbe-associated-molecular-pattern using the potential-gene index across two species. The further in vivo validation reinforced the interleukin-10-stimulating capacity of the identified pattern, and the detected sub-potential genes in Lactiplantibacillus plantarum key-gene possessing strains implied the utility of potential-gene index in detecting potential health-benefit-associated genes in other lactic acid bacteria species.

Draft genome of Paenibacillus ottowii LIS04 and Bacillus velezensis IM14: dual biocontrol bacterial strains with broad-spectrum antifungal activity

Paenibacillus and Bacillus are gram-positive bacteria known for promoting plant growth and controlling agriculturally important phytopathogens. This study highlights the genomic traits of Paenibacillus ottowii LIS04 and Bacillus velezensis IM14, isolated from sorghum seeds and maize stigmas, respectively, with potential applications in developing innovative agricultural bioproducts.

Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka

BACKGROUND

Antimicrobial resistance (AMR) is a major global challenge that disproportionately affects low- and middle-income countries (LMICs). Environmental contamination by resistant bacteria from animal production facilities is a major driver of the spread of AMR through the food chain, requiring a robust one-health control approach. Traditional culture-based AMR surveillance is time-consuming and less sensitive, and fails to fully capture the spectrum of AMR, evolutionary trends, and epidemiological patterns of AMR spread. Whole-genome sequencing (WGS) has revolutionized AMR surveillance capabilities. Rapid WGS captures the full AMR spectrum with minimum samples, aids source attribution, and provides insights into trends in AMR spread. The portable Oxford Nanopore® Technology (ONT) platform, coupled with open-source software such as Galaxy and Konstanz Information Miner (KNIME), enables the establishment of a potentially portable, transferable workflow for low-resource settings. This study aimed to assess the AMR burden on four dairy farms in Kandy, Sri Lanka, via a resource-limited LMIC using a low-cost high-throughput screening assay and rapid WGS via ONT with Galaxy and KNIME processing to obtain full antibiotic resistomes.

RESULTS

The four isolates exhibiting the highest minimum inhibitory concentrations for amoxicillin were identified as Enterobacter cloacae and E. hormaechei by WGS. Chromosomes (4.8 to 4.9 Mb) carry the strain-specific resistance genes blaCMH-1, blaACT-25, fosA_7, and ramA, which are associated with diverse antibiotic classes. Plasmids, including IncFIB (pECLA), IncFII (pECLA), and IncX3, carry multiple resistance genes, including AAC(3)-IIe, AAC(6')-Ib-cr, APH(3″)-Ib, APH(6)-Id, blaCTX-M-15, blaNDM, blaOXA-1, blaTEM-1, dfrA14, QnrB17, catII, determinant-of-bleomycin-resistance, and sul2. Novel arrangements of insertion sequences were observed in E. hormaechei plasmids. The phenotypic resistance of all the isolates matched the genotypic MDR profiles, including resistance to chloramphenicol, gentamicin, tetracycline, and cotrimoxazole.

CONCLUSIONS

ONT WGS with Galaxy and KNIME processing may be a feasible option for AMR surveillance in resource-limited LMICs. To the best of our knowledge, this is the first in-house whole-genome analysis workflow in the country tailored for AMR surveillance. The presence of potentially pathogenic high-MIC, MDR Enterobacter spp. with wide resistomes, including the blaNDM gene, emphasizes the urgent need to address AMR in animal production facilities within a one-health framework.

Whole genome sequencing and annotation of Pseudocercospora abelmoschi, a causal agent of black leaf mould of okra

Pseudocercospora abelmoschi causes black mould on the leaves of okra. The disease is prevalent post-rainy season when high moisture and warm temperatures prevail. Severe defoliation is observed during favourable environments, leading to a significant loss in productivity. Based on the importance of the pathogen agriculturally, the P. abelmoschi isolate Cer 86 - 18 (MCC:9491) was selected for genome sequencing. The genome assembly of P. abelmoschi resulted in a genome of 31.90 Mb with an overall GC content of 54.26%. Quantitative genome assessment using BUSCO (Benchmarking Universal Single-Copy Orthologs) identified 1,664 (97.53%) complete BUSCOs, reflecting a high representation of conserved genes with minimal duplication and strong orthologous uniqueness. Gene prediction analysis identified 11,325 protein-coding genes, of which 3,857 were annotated using the KEGG database. As per analyses, 410 genes were predicted to encode carbohydrate-active enzymes, whereas 369 genes were predicted to encode peptidases. Eighteen gene clusters involved in secondary metabolite biosynthesis were also identified. A total of 143 proteins were predicted to be effectors using the in-silico pipeline. This is the first report on the genome organisation of P. abelmoschi. This study was designed to address this gap by enhancing our understanding of the genome organisation of P. abelmoschi and gene annotation, thereby paving the way for functional genomics studies, such as identifying virulence genes to aid in resistance breeding. Also, this genome could be another addition to the available genomic resources of the genus Pseudocercospora and can provide valuable insights into host-pathogen interactions and evolutionary relationships.

Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis

Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying "bitterness" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.

Chromosome-scale assembly of Artemia tibetiana genome, first aquatic invertebrate genome from Tibet Plateau

Genomic-level studies on the adaptive evolution of animals in the Qinghai-Tibet Plateau have been rapidly increasing. However, most studies are concentrated on vertebrates, and there are few reports on invertebrates. Here, we report the chromosome-level genome assembly for the brine shrimp Artemia tibetiana from Kyêbxang Co, a high-altitude (4620 m above sea level) salt lake on the plateau, based on the combination of Illumina, Nanopore long-reads and Hi-C sequencing data. The assembled genome is 1.69 Gb, and 94.83% of the assembled sequences are anchored to 21 pseudo-chromosomes. Approximately 75% of the genome was identified as repetitive sequences, which is higher than most crustaceans documented so far. A total of 17,988 protein-coding genes were identified, among them 14,388 were functionally annotated. This genomic resource provides the foundation for whole-genome level investigation on the genetic adaptation of Artemia to the harsh conditions in the Qinghai-Tibet Plateau.

The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting

Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.

IMPORTANCE

Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily focus on clonal transmission of multidrug-resistant bacteria, until today, AMR plasmid transmission routes are neither understood nor analyzed in the hospital setting. In our study, we simultaneously determined both clonal, that is, based on chromosomes, and AMR plasmid transmissions during routine molecular surveillance by combining long-read sequencing with a novel real-time applicable software tool and validated all potential transmission events with epidemiological data. Our analysis determined not only the yet unknown plasmid transmissions within healthcare facilities or within the community but also resulted, in addition to the clonal transmissions, in at least a third more transmissions due to AMR plasmids.

Longitudinal and cross-sectional sampling and whole genome sequencing of Campylobacter in a chicken abattoir reveal highly dynamic population structure

Campylobacter is a leading cause of human gastroenteritis worldwide and is commonly identified in poultry products. Current knowledge of its dissemination patterns in poultry production largely relies on the less sensitive traditional genotyping methods. In this study, whole-genome sequencing was applied to 324 Campylobacter isolates sampled from a chicken abattoir in the Greater Vancouver area throughout 2020. Core genome multi-locus sequence typing analysis revealed a highly diverse and dynamic Campylobacter population containing 27 distinct lineages. A wide range of plasmids was characterized, and a high prevalence of antibiotic resistance was observed among these isolates. Distinct subpopulations were identified in 10 lineages, suggesting that some Campylobacter populations may have diversified within the local agricultural environment. Some lineages were frequently reintroduced to the abattoir, suggesting the potential presence of hidden Campylobacter reservoirs upstream of slaughter. Comparisons between biological and environmental samples suggest a high probability of between-batch cross-contamination. Locally sourced public Campylobacter isolates showed strong genomic correlations with the lineages identified in this study. Notably, lineages 1629a and 1629b were identified to have persisted within the local poultry production ecosystem for several years, explaining their recurrent detection. In conclusion, this study enhances our understanding of Campylobacter population dynamics in the chicken abattoir environment, providing insights for controlling this foodborne pathogen in poultry production systems.IMPORTANCEUsing whole-genome sequencing, this study revealed a highly diverse and dynamic Campylobacter population within the chicken abattoir. The high prevalence of antibiotic resistance marked the critical need for surveillance in this region. The findings highlighted the likely existence of a hidden common source of Campylobacter upstream in the poultry production chain, which significantly contributes to the repeated introduction of the same lineages into the abattoir. Given the frequent reintroductions, the current understanding of Campylobacter persistence in the abattoir environment (up to 21 days) may require revision. Additionally, batch-to-batch dissemination of Campylobacter strains during processing is highly possible. A robust geographic association was also observed between the Campylobacter population in the abattoir and the local community. In sum, this study provides insights into the dynamics of Campylobacter contamination in the poultry production chain, offering guidance for improving prevention and control strategies.

Draft genome sequence and annotation of Priestia aryabhattai MS3, a salt-tolerant plant growth-promoting rhizobacteria

Priestia aryabhattai strain MS3, a salt-tolerant, plant growth-promoting rhizobacterium, was isolated from saline soil in Kalapara, Patuakhali, Bangladesh. This study presents the whole-genome sequencing of strain MS3, revealing a 5.296 Mb genome comprising 5,369 predicted protein-coding sequences and 46 RNA genes.

Complete genome sequence of the environmental Burkholderia pseudomallei strain 22-10884_313#20 from Guadeloupe, French West Indies

Burkholderia pseudomallei is the causative agent of melioidosis. Here, we present the complete genome sequence of the strain 22-10884_313#20, isolated from a soil sample in Guadeloupe (French West Indies).

Whole-genome sequencing analysis to identify antimicrobial resistance regions and virulence factors in Mycobacterium tuberculosis isolates from the Amhara Region, Ethiopia

Tuberculosis caused by Mycobacterium tuberculosis complex is a significant global health burden, with drug-resistant TB, especially multidrug-resistant TB, causing severe challenges to treatment. In Ethiopia, a high TB-burden country, drug resistance has continued spreading. However, some studies indicate genetic diversity, transmission dynamics, and resistance-conferring mutations by using targeted amplification, there are limited reports of whole genome sequencing analysis to uncover the antimicrobial resistance and virulent genes. Based on that, the objective of this project was to identify antimicrobial resistance regions and characterize virulence factors in M. tuberculosis isolates through in silico whole-genome sequence analysis. A FASTQ file of 45 M. tuberculosis isolates whole genome sequence was downloaded from the SAR database. Following quality control using FASTQC coupled with MultiQC and trimming with Trimmomatic, de novo assembly was conducted using SPAdes. The Burrows-Wheeler Aligner was used for mapping against the M. tuberculosis H37Rv reference genome, followed by variant calling with FreeBayes. In silico spoligotyping was performed using SpoTyping, and drug resistance mutations were identified with TB-Profiler and validated using Mykrobe. Virulence factors were detected through ABRicate and the Virulence Factor Database. STRING was used to network the virulent genes. All statistical analyses were performed using R software. This study revealed the most prevalent TB-lineage in the Amhara region was L4 (58.53%), followed by L3 (34.15%), and L1 (4.88%), and in silico spoligotyping classified 90.24% of the isolates into 12 shared types, with SIT 149 (41.46%) and SIT 21 (14.63%) as the most frequent spoligotypes. Seven major genotypic families were identified, with T3-ETH being the dominant family (48.78%). Drug resistance analysis revealed that 38 isolates (92.7%) were multidrug-resistant, and 1 (2.4%) was pre-extensively drug-resistant. Lineage 4 (59%) and its sub-lineage 4.2.2 (51.3%) show the highest resistance. The most frequent mutations to rifampicin, isoniazid, pyrazinamide, ethambutol, streptomycin, ethionamide, fluoroquinolone, and 2nd-line injectable drugs occurred at rpoB Ser450Leu, katG Ser315Thr, pncA c.-11A > G, embB Gly406Ala, rpsL Lys43Arg, Lys88Thr, ethA Met1, gyrA Ala90Val, Asp94Asn, and rrs 1401A > G, respectively. Additionally, a mutation at the mmpR5 gene for bedaquiline and clofazimine resistance occurred in one isolate. A total of 67 virulence genes were identified and 63 of them occurred in all isolates. The high prevalence of MDR-TB and the detection of resistance to both first- and second-line drugs in this study underscore the urgent need for enhanced TB control measures in the Amhara region.

Complete genome sequence of Planococcus koreensis isolated from soil in Fort Collins, Colorado

The complete genome of Planococcus koreensis was obtained using Nanopore MinION sequencing after isolation from soil in Colorado. The assembled genome contains one circular contig with 3,519,105 bp, 3,606 genes, 419 pseudogenes, and 47.62% guanine-cytosine content. This discovery provides a fully assembled P. koreensis genome available at the National Center for Biotechnology Information.

Draft genome of the endophytic Bacillus velezensis CNPMS-22 isolated from maize leaves

Bacillus velezensis has been widely used as a biocontrol agent and plant growth promoter in agricultural bio-inputs. The genome of the endophytic bacterial strain CNPMS-22 isolated from maize leaves was sequenced, and the results showed that the strain is a Bacillus velezensis species.

Genome sequencing and de novo assembly of Photobacterium arenosum isolate from coastal sediment

Genomic analyses have led to the discovery of novel chitinases with emerging applications as environmentally friendly alternatives to synthetic chemical pesticides and for processing renewable resources in various industries. Here, we report the sequencing and assembly of the chitinolytic marine bacterium Photobacterium arenosum isolated from coastal sediment from Oostende, Belgium.

Draft genome sequence of Bradyrhizobium sp. strain RDM4, a microsymbiont bacterium isolated from the root nodules of Retama dasycarpa in soils of Maâmora forest, Morocco

Bradyrhizobium sp. RDM4 is a symbiotic nitrogen-fixing bacterium, isolated from root nodules of the Moroccan endemic shrub Retama dasycarpa grown in Moroccan forest soils. In this work, we present the 8.4 Mb draft genome of this strain, characterized by a GC content of 63% and the presence of 8,141 total genes, with 7,032 protein-coding.

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly

MOTIVATION

De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow.

RESULTS

Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies.

AVAILABILITY AND IMPLEMENTATION

The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).

HiBC: a publicly available collection of bacterial strains isolated from the human gut

Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains are accessible to the scientific community. We have therefore created a publicly available collection of bacterial strains isolated from the human gut. The Human intestinal Bacteria Collection (HiBC) ( https://www.hibc.rwth-aachen.de ) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

Comprehensive genome analysis of two Cytospora (Cytosporaceae, Diaporthales) species associated with canker disease of spruce: C.piceae and C.piceicola sp. nov

Cytospora canker (CC) is among the most important diseases in conifer trees (Picea spp., mainly). This disease poses a significant risk factor for forest health, potentially leading to economic losses for wood producers. To provide a genomic basis of the CC pathogenesis, the genomes of two Cytospora species associated with the disease were sequenced and further analyzed within a set of Diaporthales species. The first species was identified as C.piceae. The second was described as C.piceicola sp. nov. based on morphological characteristics and multi-gene phylogenetic analysis. The novel species is sister to other Cytospora species isolated from conifers. Here, we report 39.7 and 43.8 Mb highly contiguous genome assemblies of C.piceae EI-19(A) and C.piceicola EI-20, respectively, obtained using Illumina sequencing technology. Despite notably different genome sizes, these species share the main genome characteristics, such as predicted gene number (10,862 and 10,742) and assembly completeness (97.6% and 98.1%). A wide range of genes encoding carbohydrate-active enzymes, secondary metabolite biosynthesis clusters, and secreted effectors were found. Multiple experimentally validated virulence genes were also identified in the studied species. The defined arsenals of enzymes and effectors generally relate to the hemibiotrophic lifestyle with a capability to switch to biotrophy. The obtained evidence also supports that C.piceae EI-19(A) and C.piceicola EI-20 can cause severe canker disease symptoms in Picea spp. specifically. It was additionally observed that the strains of C.piceae may have different pathogenicity and virulence characteristics based on the analyses of predicted secondary metabolite complements, effectomes, and virulence-related genes. Phylogenomic analysis and timetree estimations indicated that divergence of the studied species may have occurred relatively late, 11-10 million years ago. Compared to other members of Diaporthales, C.piceae EI-19(A) and C.piceicola EI-20 implied a moderate rate of gene contraction, but the latter experienced significant gene loss that can additionally support host specificity attributed to these species. But uncovered gene contraction events may point out potential lifestyle differentiation and host shift of the studied species. It was revealed that EI-19(A) and C.piceicola EI-20 carry distinct secretomes and effectomes among Diaporthales species. This feature can indicate a species lifestyle and pathogenicity potential. These findings highlight potential targets for identification and/or detection of pathogenic Cytospora in conifers. The introduced draft genome sequences of C.piceae and C.piceicola can be employed as tools to understand basic genetics and pathogenicity mechanisms of fungal species causing canker disease in woody plants. The identified pathogenicity and virulence-related genes would serve as potential candidates for host-induced gene silencing aimed at making plant hosts more resistant to pathogenic species. Furthermore, the comparative genomics component of the study will facilitate the functional analysis of the genes of unknown function in all fungal pathogens.

Genomic and antimicrobial resistance profiles of Clostridium perfringens isolated from pets in China

Clostridium perfringens is a notable pathogen causing diarrhea in domestic animals. However, data on this pathogen's prevalence and genomic characteristics in pets are limited. We collected 300 fecal samples from companion animals across two cities in China and isolated 150 strains for genomic sequencing and antimicrobial susceptibility testing (AST). Our findings showed a high prevalence of two key virulence genes (VGs), pfoA (77.33 %, 116/150) and cpb2 (60.67 %, 91/150). Moreover, for the first time in China, we identified a strain carrying netF. The analysis of AST and genomic antimicrobial resistance genes (ARGs) highlighted the resistance patterns of pet-derived C. perfringens strains in China. Particularly, we observed a high resistance rate to erythromycin, primarily associated with erm(Q), which was found in 88.67 % (133/150) of all isolates. This resistance rate was higher than that reported in previous studies. Genetic context analysis identified a novel plasmid group harboring the erm(Q) gene. In summary, this study revealed the antibiotic resistance and genomic characteristics of C. perfringens strains derived from pets in China, providing a reference for the prevention of related diseases and further research. Notably, these findings underscore the need for continuous monitoring of resistance trends, particularly concerning the spread of erm(Q), to lessen the impact of antimicrobial resistance in veterinary medicine.

Effects of cyanobacterium Phormidium nigroviride K3 on zebrafish embryos and genomic insights into its toxic potential

Cyanobacterial blooms in freshwater systems pose significant environmental and public health risks, largely due to their production of toxic secondary metabolites. This study investigated the effects of Phormidium nigroviride K3 extracts on early zebrafish development, focusing on organismal toxicity and gene expression changes. Acute toxicity was assessed by monitoring developmental deformities and evaluating relative changes in the expression of six genes associated with xenobiotic metabolism, apoptosis, endoplasmic reticulum stress, and endocrine processes. Whole-genome sequencing, in silico genome annotation and mining were conducted to identify biosynthetic gene clusters involved in toxin production. Zebrafish embryos exposed to P. nigroviride K3 extracts developed spinal deformities, pericardial edema, yolk sac edema and reduced eye size, with spinal deformities being the most prevalent malformation (EC50 of 215.6 µg d.w. mL⁻¹). Significant alterations in the expression of genes involved in xenobiotic metabolism were detected, including a dose-dependent 4.6-fold induction of cyp1a1 and a 4.47-fold increase in abcb4 expression at the highest extract concentration. Genome analysis of P. nigroviride K3 revealed 15 biosynthetic gene clusters for secondary metabolites, including a match with the Cylindrospermopsis raciborskii AWT205 cluster, responsible for the cyanotoxin cylindrospermopsin biosynthesis. The LC-MS/MS analysis confirmed the production of cylindrospermopsin in P. nigroviride K3, providing new insights into cyanotoxin biosynthesis in Phormidium species, a genus that has been underexplored in the context of toxin production. These findings expand cyanobacterial genomic databases, enhancing our understanding of cyanobacterial toxic potential. Such knowledge is crucial for predicting and mitigating the risks associated with cyanotoxins in aquatic ecosystems.

Genetic Diversity of Chinese Giant Salamanders Under the Context of Translocation Using Novel Development of Genomic SSR Markers

Genetic diversity is crucial for assessing biodiversity and understanding the evolutionary potential of threatened species like the Chinese giant salamanders (Andrias spp., CGS), which are among the most endangered amphibians globally. With extensive translocation efforts aimed at conservation, it is essential to assess genetic diversity using molecular markers to gauge potential impacts on the original populations. In this study, 15,140,972 genomic scaffold sequences of CGS were assembled using next-generation sequencing, revealing 316,313 simple sequence repeat (SSR) loci, predominantly dinucleotide repeats. From 200 randomly synthesized SSR primer pairs, 19 markers with moderate to high polymorphisms were validated and selected to evaluate the genetic diversity of CGS based on 60 wild individuals from six sampling sites in the Hunan Zhangjiajie Giant Salamander National Nature Reserve. Results highlighted the highest diversity in the Jinbianxi population, a long-term reinforcement site, and the lowest in the Wumuyu population, a historically natural site. Genetic differentiation was most pronounced between the populations of Wumuyu and another historically natural site, Yuanzi, contrasting with lower differentiation between two recently reintroduced sites, Xixiping and Xiangshi. The genetic structure of the Jinbianxi population suggests potential hybridization events between distinct genetic lineages or species, along with long-term translocation practices. This study introduces a large set of genomic SSR markers of CGS, highlighting the significance of reliable markers for evaluating its genetic dynamics. It also stresses the necessity of continuous monitoring, assessment, and management of genetic diversity to enhance conservation strategies effectively.

Surveillance and Genomic Characterisation of Colistin-Resistant Gram-Negative Bacteria in the Drains of High-Risk Hospital Units

OBJECTIVE

The health care water environment, including sinks and drainage systems, can be a long-term reservoir of nosocomial pathogens. In this study, we aimed to investigate the presence of colistin-resistant Gram-negative (ColR-GN) bacteria in humid compartments of high-risk hospital units at the University Medical Center Groningen, The Netherlands.

METHODS

Environmental sampling was conducted in sink and shower drains of high-risk hospital units, and colistin MICs were determined using broth microdilution. Whole-genome sequencing was performed to investigate the presence of mobile colistin resistance (mcr) genes, chromosomal point mutations and gene alterations linked to colistin resistance.

RESULTS

ColR-GN bacteria were detected in all investigated units, with Enterobacter spp. being the most abundant genus. Twelve isolates exhibited colistin resistance (MIC >2 mg/L), including Enterobacter cloacae complex (n = 11) and Klebsiella pneumoniae (n = 1). Chromosomal mutations in genes involved in lipopolysaccharide structure modifications were the main mechanisms contributing to colistin resistance in Enterobacter spp. and Klebsiella spp. (91.6%, 11/12). Additionally, two Enterobacter kobei isolates harboured mobile colistin resistance genes, mcr-4.3 and mcr-9.1.

CONCLUSIONS

The presence and persistence of bacterial ColR-GN clones in the sink and shower drains of high-risk hospital units highlights the importance of monitoring such environments for antibiotic-resistant bacteria to identify reservoirs and prevent further spread.

Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica

Genomic data are lacking for most Antarctic marine invertebrates, predicating our ability to understand physiological adaptation and specific life-history traits, such as longevity. The environmental stress response of the Antarctic infaunal clam Laternula elliptica is much diminished in older adult animals compared with younger juvenile individuals. However, the mechanism underlying this reduced capacity is unknown. In this study, we describe and analyse the genome of L. elliptica and use it as a tool to understand transcriptomic responses to shell damage across different age cohorts. Gene expression data were combined with reduced representation enzymic methyl sequencing to identify if methylation was acting as an epigenetic mechanism driving age-dependent transcriptional profiles. Our transcriptomic results demonstrated a clear bipartite molecular response in L. elliptica, associated with a rapid growth phase in juveniles and a stabilization phase in reproductively mature adults. Genes active in the response to damage repair in juvenile animals are silent in adults but can be reactivated after several months following damage stimulus; however, these genes were not methylated. Hence, the trigger for this critical and imprinted change in physiological state is, as yet, unknown. While epigenetics is likely involved in this process, the mechanism is unlikely to be methylation.

The First Genome Assembly Of The Dogwhelk Nucella lapillus, a Bioindicator Species For The Marine Environment

The dogwhelk (Nucella lapillus) is a predatory marine gastropod widely distributed across temperate intertidal zones. Renowned for its ecological role in controlling prey populations, N. lapillus is also an important bioindicator species for marine pollution through imposex. The molecular genetic basis of imposex, characterised by the abnormal development of male sex organs in females and reductions in fertility and lifespan, however remains poorly understood due to the absence of a reference genome sequence. Here we provide the first genome assembly comprising 2.41 Gb of sequence, predicted to encode 47,238 proteins. This inaugural assembly lays the foundations for implementing genomic approaches to better quantify and characterise imposex, in addition to elucidating adaptations to life within changeable intertidal ecosystems. To counter challenges of DNA fragmentation and contamination often associated with the sequencing of marine organisms, we found that a hybrid approach that integrates complementary long-read data from PacBio HiFi and Oxford Nanopore Technology (ONT) platforms helped maximise the final assembly. This innovative combination may be a useful approach for similar marine species.

Spiral phyllotaxis predicts left-right asymmetric growth and style deflection in mirror-image flowers of Cyanella alba

Many animals and plants show left-right (LR) asymmetry. The LR asymmetry of mirror-image flowers has clear functional significance, with the reciprocal placement of male and female organs in left- versus right-handed flowers promoting cross-pollination. Here, we study how handedness of mirror-image flowers is determined and elaborated during development in the South African geophyte Cyanella alba. Inflorescences of C. alba produce flowers with a largely consistent handedness. However, this handedness has no simple genetic basis and individual plants can switch their predominant handedness between years. Rather, it is the direction of the phyllotactic spiral that predicts floral handedness. Style deflection is driven by increased cell expansion in the adaxial carpel facing the next oldest flower compared to the other adaxial carpel. The more expanding carpel shows transcriptional signatures of increased auxin signaling and auxin application can reverse the orientation of style deflection. We propose that a recently described inherent LR auxin asymmetry in the initiating organs of spiral phyllotaxis determines handedness in C. alba, creating a stable yet non-genetic floral polymorphism. This mechanism links chirality across different levels of plant development and exploits a developmental constraint in a core patterning process to produce morphological variation of ecological relevance.

Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts

Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions

Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE

Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.

The genomic characteristics of dominant Salmonella enterica serovars from retail pork in Sichuan province, China

Foodborne Salmonella is the main cause of salmonellosis in China. Porcine animals are a reservoir for this bacterium consequently posing a threat to food safety and public health. In this study, 157 out of 240 pork samples (65.42 %) were identified as Salmonella-positive. From these, after isolation and deduplication, 376 Salmonella isolates were collected. Twenty four serovars were identified based on WGS, among which S. London/ST155 (24.47 %), S. Rissen/ST469 (23.40 %), S. Derby/ST40 (13.56 %), and S. 4,[5],12:i:- (monophasic S. Typhimurium)/ST34 (13.30 %) were dominant. In all, 69.68 % (262/376) of these isolates expressed multidrug resistance (MDR, defined as resistance to compounds in three or more antimicrobial classes) phenotypes with S. London (54.35 %, 50/92) accounting for the highest proportion of these. Notably, the resistance to front-line critically important antimicrobial agents (CIA), including cephalosporins, ciprofloxacin, and azithromycin was 0.80 %. Based on in silico analysis, antimicrobial resistant-encoding genes (ARG) identified in the MDR isolates included aac(3)-IId, aac(6')-Iaa, blaTEM-1B, mph(A), qnrB6, aac(6')-Ib-cr, sul1, sul2, and tet(A), which expressed resistance to aminoglycosides, β-lactams, macrolides, quinolones, sulfonamides, and tetracyclines. Furthermore, diverse biocide and heavy metal resistance-encoding genes were distributed across different serovars with triC encoding triclosan resistance being identified exclusively in S. London. Moreover, monophasic S. 4,[5],12:i:- carried the greatest number of virulence factors and heavy metal resistance genes among the dominant serovars. This study extended our understanding of the genomic epidemiology and multidrug resistance of Salmonella derived from pork and highlighted the potential risk to human health, posed by commonly encountered serovars.

Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation

Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.

Geometric deep learning framework for de novo genome assembly

The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing complex graph tangles, leading to fragmented assemblies. Here, we introduce GNNome, a framework for path identification based on geometric deep learning that enables training models on assembly graphs without relying on existing assembly strategies. By leveraging only the symmetries inherent to the problem, GNNome reconstructs assemblies from PacBio HiFi reads with contiguity and quality comparable to those of the state-of-the-art tools across several species. With every new genome assembled telomere-to-telomere, the amount of reliable training data at our disposal increases. Combining the straightforward generation of abundant simulated data for diverse genomic structures with the AI approach makes the proposed framework a plausible cornerstone for future work on reconstructing complex genomes with different degrees of ploidy and aneuploidy. To facilitate such developments, we make the framework and the best-performing model publicly available, provided as a tool that can directly be used to assemble new haploid genomes.

A Hitchhiker's Guide to long-read genomic analysis

Over the past decade, long-read sequencing has evolved into a pivotal technology for uncovering the hidden and complex regions of the genome. Significant cost efficiency, scalability, and accuracy advancements have driven this evolution. Concurrently, novel analytical methods have emerged to harness the full potential of long reads. These advancements have enabled milestones such as the first fully completed human genome, enhanced identification and understanding of complex genomic variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from initial data processing to variant calling and annotation, focusing on how these methods improve our ability to interpret a wide array of genomic variants. Additionally, we discuss the current challenges, limitations, and future directions in the field, offering a detailed examination of the state-of-the-art bioinformatics methods for long-read sequencing.

Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres

The human fungal pathogen Candida albicans poses a significant burden on global health, causing high rates of mortality and antifungal drug resistance. C. albicans is a heterozygous diploid organism that reproduces asexually. Structural variants (SVs) are an important source of genomic rearrangement, particularly in species that lack sexual recombination. To comprehensively investigate SVs across clinical isolates of C. albicans, we conducted long-read sequencing and genome-wide SV analysis in three distantly related clinical isolates. Our work includes a new, comprehensive analysis of transposable element (TE) composition, location, and diversity. SVs and TEs are frequently close to coding sequences and many SVs are heterozygous, suggesting that SVs might impact gene and allele-specific expression. Most SVs are uniquely present in only one clinical isolate, indicating that SVs represent a significant source of intraspecies genetic variation. We identify multiple, distinct SVs at the centromeres of Chromosome 4 and Chromosome 5, including inversions and transposon polymorphisms. These two chromosomes are often aneuploid in drug-resistant clinical isolates and can form isochromosome structures with breakpoints near the centromere. Further screening of 100 clinical isolates confirms the widespread presence of centromeric SVs in C. albicans, often appearing in a heterozygous state, indicating that SVs are contributing to centromere evolution in C. albicans Together, these findings highlight that SVs and TEs are common across diverse clinical isolates of C. albicans and that the centromeres of this organism are important sites of genome rearrangement.

Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)

Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.

The complete and circular genome of nitrogen-fixing Mesorhizobium sp. AaZ17, isolated from the root nodule of Astragalus armatus growing in a lead- and zinc-abandoned mine in Morocco

In this study, we sequenced the genome of Mesorhizobium sp. strain AaZ16, a nitrogen-fixing rhizobial species isolated from the root nodules of Astragalus armatus growing wild in a lead- and zinc-rich mine tailings in the High Atlas, Morocco. This study reveals the genomic characteristics of the root microsymbiont.

Genome sequence of Lacticaseibacillus paracasei ORD 0998 (CECT 30660), a probiotic bacterium for women's health

Lacticaseibacillus paracasei is commonly isolated from dairy products and the microbiome of the human reproductive and gastrointestinal tract. We report the genome assembly of Lacticaseibacillus paracasei ORD 0998 (CECT 30660) with two contigs, having a size of 3,150,431 bp and a GC content of 46.33%.

Complete genome sequence of three methicillin-resistant Staphylococcus aureus ST630 strains isolated from cattle in Algeria

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) is an emerging clone causing infections in humans. We report the complete genomes of three MRSA ST630 from cattle. The 2.8 Mbp genomes contained several antimicrobial resistance and virulence genes and were related to those of previously detected human-associated MRSA ST630.

Aspergillus terreus sectorization: a morphological phenomenon shedding light on amphotericin B resistance mechanism

Prolonged cultivation of certain filamentous fungi, including Aspergillus terreus, on drug-free medium leads to degeneration and morphological heterogeneity, marked by the emergence of fluffy mycelium-type sectors. This phenomenon may indicate alterations in antifungal susceptibility profiles (particularly to amphotericin B (AmB) in A. terreus), as well as reductions or losses in conidiation, sexuality, secondary metabolite production, and/or virulence. In the present study, various characteristics of an AmB-resistant wild-type (WT) strain and its AmB-susceptible sectorized derivative (ATSec) were characterized. Compared to WT, ATSec exhibited increased susceptibility to AmB, reduced sporulation, and comparable sterol contents and virulence in Galleria mellonella. To elucidate the genes involved in AmB resistance, gene expression levels were compared between WT and ATSec with and without AmB treatment. The expression of P-type ATPase-related genes, which are implicated in membrane composition changes and consequently in AmB resistance, was significantly higher in the WT strain compared to ATSec. Moreover, the up-regulation of genes involved in the biosynthesis of polyketides-a diverse group of secondary metabolites-was higher in WT compared to ATSec, with a significant number of these genes also carrying at least one mutation. The findings of this study indicate that P-type ATPases may significantly be involved in AmB susceptibility and resistance observed in ATSec and WT strains. Additionally, mutations in polyketide synthase genes in ATSec may contribute to the phenotypic alterations associated with the sectorized phenotype.

IMPORTANCE

Prolonged cultivation of certain filamentous fungi, including Aspergillus terreus, on drug-free medium leads to degeneration and morphological heterogeneity, marked by the emergence of fluffy mycelium-type sectors. This phenomenon may indicate alterations in antifungal susceptibility profiles (particularly to amphotericin B (AmB) in A. terreus), as well as reductions or losses in conidiation, sexuality, secondary metabolite production, and/or virulence. In the present study, various characteristics of an AmB-resistant wild-type strain (WT) and its AmB-susceptible sectorized derivative (ATSec) were characterized. Compared to WT, ATSec exhibited increased susceptibility to AmB, reduced sporulation, and comparable sterol contents and virulence in Galleria mellonella. To elucidate the genes involved in AmB resistance, gene expression levels were compared between WT and ATSec with and without AmB treatment. The expression of P-type ATPase-related genes, which are implicated in membrane composition changes and consequently in AmB resistance, was significantly higher in the WT strain compared to ATSec. Moreover, the up-regulation of genes involved in the biosynthesis of polyketides - a diverse group of secondary metabolites - was higher in WT compared to ATSec, with a significant number of these genes also carrying at least one mutation. The findings of this study indicate that P-type ATPases may significantly be involved in AmB susceptibility and resistance observed in ATSec and WT strains. Additionally, mutations in polyketide synthase genes in ATSec may contribute to the phenotypic alterations associated with the sectorized phenotype.

Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant

Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.

De novo genome assemblies of the dwarf honey bee subgenus Micrapis : Apis andreniformis and Apis florea

The Micrapis subgenus, which includes the black dwarf honey bee ( Apis andreniformis ) and the red dwarf honey bee ( Apis florea ), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies (ONT) long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb ( A. andreniformis ) and 4.3 Mb ( A. florea ), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,232 genes for A. andreniformis and 12,597 genes for A. florea , with >97% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, offering new insights into the genetic basis of dwarf honey bee adaptations.

Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks

Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.

Metabolic Segregation and Functional Gene Clusters in Anaerobic Digestion Consortia

A combined enrichment experiment and genome-centric meta-omics analysis demonstrated that metabolic specificity, rather than flexibility, governs the anaerobic digestion (AD) ecosystem. This study provides new insights into interspecies electron transfer in the AD process, highlighting a segregation in the metabolism of H2 and formate. Our findings show that H2 acts as the primary electron sink for recycling redox cofactors, including NAD+ and oxidised ferredoxin (Fdox), during primary fermentation, while formate is the dominant electron carrier in secondary fermentation, especially under conditions with elevated H2 concentrations. Importantly, no evidence of biochemical interconversion between H2 and formate was identified in the primary fermenting bacteria or in syntrophs enriched in this study. This segregation of H2 and formate metabolism likely benefits the anaerobic oxidation of butyrate and propionate with a higher tolerance to H2 accumulation. Moreover, this study highlights the functional partitioning among microbial populations in key AD niches: primary fermentation, secondary fermentation (syntrophic acetogenesis), hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Genome-centric analysis of the AD microbiome identified several key functional gene clusters, which could enhance genome-centric genotype-phenotype correlations, particularly for strict anaerobes that are difficult to isolate and characterise in pure culture.

Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization

A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.

Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health

Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.

High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei

Talaromyces marneffei is a dimorphic fungus that transitions from a filamentous form at 25 °C to a pathogenic yeast form at 37 °C, demonstrating pathogenicity mostly in immunocompromised individuals, such as those with human immunodeficiency virus/AIDS. Though it is one of the most severe infectious fungi in Southeast Asia, the lack of comprehensive genomic analysis has hindered advancement in strain differentiation, diagnosis and treatment. In this study, we assembled a high-quality genome of T. marneffei ATCC 18224, resulting in a 28.9 Mb genome distributed across 11 contigs, using third-generation Oxford Nanopore Technologies sequencing reads. Notably, we identified a strain-specific 740-kb segmental duplication in strain ATCC 18224, potentially mediated by inserting a Ty1/Copia long terminal repeat (LTR) retrotransposon. This segmental duplication includes various functional genes, with 75 differentially expressed during its dimorphic transition. Comparative genomic analysis revealed large-scale rearrangements in strains PM1 and 11CN-20-091, which were inconsistent with the phylogenomic trees of six T. marneffei strains and required further investigation. Additionally, we observed substantial genetic structural variations in LTR retrotransposons, particularly within the Ty1/Copia family, including two significant recent expansions in strain ATCC 18224. In summary, the identification and characterization of these extensive genomic structural variations in T. marneffei contribute to a deep understanding of its genetic diversity and will facilitate improvements in genotyping, classification and genomic surveillance.

Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment

There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.

Deep culturing the fecal microbiota of healthy laying hens

BACKGROUND

The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS

In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS

Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.

Biodegradation of isoprene by soil Actinomycetota from coffee-tea integrated plantations in a tropical evergreen forest

Isoprene, a biogenic volatile compound emitted largely by plants, can form greenhouse gases when it reacts with atmospheric radicals. A significant amount of isoprene is absorbed into soil and can be degraded by soil microorganisms, but our understanding of the microbial biodegradation of isoprene in tropical ecosystems remains limited. This study investigated isoprene degradation by soil microbes indigenous to a tropical evergreen forest, focusing on those associated with coffee and tea plants grown as integrated crops and their genome characteristics in relation to their biodegradation capabilities. Following a 96-hour incubation with 7.2 × 10⁵ parts per billion by volume (ppbv) of isoprene, soil samples exhibited degradation levels ranging from 11.95 % to 36.54 %. From these soils, bacterial isolates belonging to the genera Rhodococcus and Gordonia (Actinomycetota) were recovered. These isolates demonstrated high isoprene biodegradation activity (50.3 %-69.1 % over seven days) and carried the isoA gene associated with isoprene metabolism. According to genome analysis, the organization of genes in the iso cluster was homologous, and the encoded amino acid sequences were highly similar to those of previously known isoprene-degrading members of the same genera. These findings emphasized the contribution of these widespread isoprene-degrading bacterial genera in the biodegradation of isoprene and the role of their isoprene monooxygenases in modulating atmospheric isoprene flux.

A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector

Long-read sequencing technologies yield extended DNA sequences capable of spanning intricate, repetitive genome regions, thereby facilitating the generation of more precise and comprehensive genome assemblies. However, assembly errors are inevitable owing to inherent genomic complexity and limitations of sequencing technology and assembly algorithms, making assembly evaluation crucial. The genome assembly evaluation tool Inspector presents several advantages over existing long-read de novo assembly evaluation tools, including (1) both reference-free and reference-guided assembly evaluation; (2) the ability to detect both small- and large-scale structural errors; (3) the option of assembly error correction, which can improve the quality value of the original assembly; and (4) the ability to perform haplotype-resolved assembly evaluation. Inspector can provide not only basic contig and alignment statistics, but also the precise locations and types of the different structural errors. These advantages provide a robust framework for long-read assembly evaluation. In this Protocol, we showcase four procedures to demonstrate the different applications of Inspector for long-read assembly evaluation. Inspector software and additional guides can be found at https://github.com/ChongLab/Inspector_protocol .