SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

Protection against experimental necrotizing enterocolitis by fecal filtrate transfer requires an active donor virome

Necrotizing enterocolitis (NEC) remains a frequent catastrophic disease in preterm infants, and fecal filtrate transfer (FFT) has emerged as a promising prophylactic therapy. This study explored the role of virome viability for the protective effect of FFT. Using ultraviolet (UV) irradiation, we established a viral inactivation protocol and administered FFT, UV-inactivated FFT (iFFT) or sterile saline orally to preterm piglets at risk for experimental NEC. The gut pathology and barrier properties were assessed, while the microbiome was explored by 16S rRNA amplicon and metavirome sequencing. Like in prior studies, FFT reduced NEC severity and intestinal inflammation, while these effects were absent in the iFFT group. Unexpectedly, piglets receiving FFT exhibited mild side effects in the form of early-onset diarrhea. The FFT also converged the gut colonization by increased viral heterogeneity and a reduced abundance of pathobionts like Clostridium perfringens and Escherichia. In contrast, the gut microbiome of iFFT recipients diverged from both FFT and the controls. These findings highlight the clear distinction between the ability of active and inactivate viromes to modulate gut microbiota and decrease pathology. The efficacy of FFT may be driven by active bacteriophages, and loss of virome activity could have consequences for the treatment efficacy.

Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring

Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied a new wide-spectrum cfRNA sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA and all mitochondrial RNA. The cfRNA compositions, size distributions and highly abundant cfRNA genes were analysed for each type of cfRNA. We depicted the cfRNA cell types of origin profiles of 66 generally healthy individuals and found that BMI showed a significant impact on the kidney-derived cfRNA proportion. Three individuals with some liver problems were identified because of relatively high levels of hepatocyte-specific cfRNA. The abundance levels of different genes and RNA types, including mRNA, miRNA and lncRNA, were significantly correlated with the liver function test results. The genes of individual cfRNA variances were enriched in pathways associated with common diseases such as liver diseases, virus infections, cancers and metabolic diseases. This study provided a profiling of cfRNA and displayed the potential of cfRNA as a biomarker in health monitoring.

Phylogenomic analyses revealed a new lineage of house mouse (Mus musculus) in Gyirong Basin of Xizang Autonomous Region, China

In the present study, we collected 20 individuals and 12 individuals of wild mice from the Gyirong Basin of Xizang Autonomous Region in China and Sudurpashchim in Nepal. Phylogeny and genetic structure inferred from different types of genomic markers suggest that these samples all belong to Mus musculus, among which individuals from Gyirong Basin represent a new genomic lineage (named as M. m. gyirongus), and samples from Sudurpashchim represent an intermediate population between the central population and M. m. castaneus. M. m. gyirongus, along with M. m. domesticus and M. m. musculus, differentiated from the central population compactly during ∼ 272,000-251,000 years ago in the interglacial period. Three lineages all experienced continuous population decline before ∼ 70,000 years ago. Then, they underwent population fluctuations at different periods that might have been impacted by climate changes, migration history, and human activities. Genes related to the structure and function of neural synapses, reproduction and development, regulation of cell cycle and carcinogenesis, and immune response have undergone positive selection in the genome of M. m. gyirongus. The discovery of M. m. gyirongus not only helps us to better understand the evolutionary history of M. musculus, but also provides new regional resources for breeding novel laboratory mouse strains.

De novo assembly and annotation of the pantranscriptome of Astyanax lacustris on the liver and pituitary-gonadal axis

Astyanax lacustris is a model of laboratory native fish species. Reproductive studies of this species have already been performed. Nevertheless, there is a relative shortcoming of gene sequence information available in public databases, which hinder their use in more comprehensive investigations that employ sensitivity molecular biology techniques to assess gene expression profile for biomarker identification. In this data article, we report the first de novo transcriptome assembly of A. lacustris testicles, ovaries and male / female pituitary gland improving gene sequence data available for this fish species and transcriptome of male liver. Illumina sequencing generated 808,023,356 raw reads, filtered in 752,739,866 high-quality reads. Initially, a de novo assembly was filtered to include protein coding elements only in each tissue sample, which were merged in a final pantranscriptome (PAN) containing 109,232 contigs. The PAN was functionally annotated against a custom Actinopterygii proteins dataset and EggNOG terms with the aid of EnTAP, retrieving homology queries for about 90 % of all transcripts. Therefore, in this study we provide a PAN and a custom blast tool that can help discovery genomic information on metabolism pathways and their related genes in A. lacustris, enabling future research and molecular studies using this fish species as a model.

In silico exploration of biosynthetic gene clusters in marine Streptomyces sp. and Nocardiopsis sp. from the western coast of India: Genome-based profiling using whole genome sequencing

Actinomycetes are known for their ability to produce bioactive compounds with significant potency of antibiotics and natural product synthesis. With the growing threat of antimicrobial resistance, effective treatment for many infections has become increasingly challenging. Our study aims to explore the secondary metabolites produced by Actinomycetes isolated from marine sponge samples collected from the west coast of India using in silico approaches. The pre-processed high-throughput Illumina sequencing reads from six Actinomycete genomes showed high quality. Initial BLAST analysis followed by phylogenetic analysis revealed that isolates A01 and A96 closely matched Nocardiopsis sp., while isolates A03, A45, A57, and A90 were closely related to Streptomyces sp. In silico biosynthetic gene clusters (BGC) prediction indicated that Streptomyces sp. A57 had the highest number of BGCs, with 28 clusters identified. All Streptomyces sp. (A03, A45, A57, and A90) were predicted to contain a high number of terpene gene clusters. Ectoine was commonly found in all genomes of Streptomyces sp. and Nocardiopsis sp. Most of the BGCs identified in Actinomycete genomes revealed less similarity to the known BGCs, indicating their potential for producing novel secondary metabolites. The study reveals the genomic potential of the Actinomycetes by providing new insights into the ecological roles and potential applications of marine Actinomycetes, highlighting their promise as candidates for the discovery of new pharmaceuticals. Future investigations could benefit from integrating functional genomics and metabolomics to gain deeper insights into the metabolic pathways governing the biosynthesis of these secondary metabolites.

Tracking Antimicrobial Resistant Organisms Timely: a workflow validation study for successive core-genome SNP-based nosocomial transmission analysis

Background and Objectives

Effective infection prevention and control (IPC) interventions in hospitals require timely information to determine the potential transmission of antimicrobial-resistant (AMR) organisms. We proposed and developed a successive core-genome SNP (cgSNP)-based phylogenetic analysis workflow, 'Tracking Antimicrobial Resistant Organisms Timely' (TAROT), using the Oxford Nanopore Technologies (ONT) sequencer for MRSA, and compared the results with those obtained using the Illumina sequencer.

Methods

We have developed a TAROT workflow for successive phylogenetic analysis using ONT data. We sequenced 34 MRSA strains isolated from Toho University Omori Medical Center using MinION (ONT) and MiSeq (Illumina). Each strain's ONT data were inputted into TAROT (TAROT-ONT), and successive cgSNP-based phylogenetic analyses were conducted. Illumina data were processed with a batched cgSNP-based phylogenetic analysis. Assembly-based analysis identified AMR genes, AMR mutations and virulence genes.

Results

MinION generated an average sequence depth of 262× for the ST8 reference genome within 3 h. TAROT-ONT successively generated 11 phylogenetic trees for 14 ST8 strains, 7 trees for 10 ST1 strains and 2 trees for 5 ST5 strains. Highly suspected transmission pairs (pairwise cgSNP< 5) were detected in trees #6 through #11 for ST8, trees #3, #5 and #7 for ST1, and tree #2 for ST5. Differences in pairwise cgSNP value between TAROT-ONT and Illumina ranged from zero to two within pairs with fewer than 20 cgSNPs using Illumina. TAROT-ONT bioinformatic analysis for each strain required 5-42 min. The identification of AMR genes, mutations and virulence genes showed high concordance between ONT and Illumina.

Conclusions

TAROT-ONT can facilitate effective IPC intervention for MRSA nosocomial transmissions by providing timely feedback through successive phylogenetic analyses based on cgSNPs.

Evaluation of antibody variants using a ribosome display and Brevibacillus choshinensis secretion system

In antibody engineering, the development of rapid and efficient strategies for improving affinity is highly necessary. In this study, we aimed to establish a method to efficiently enrich and analyze high-affinity antibody variants by combining protein synthesis using recombinant elements (PURE) ribosome display with next-generation sequencing (NGS) and Brevibacillus choshinensis secretion system using the NZ-1 antibody, which targets the PA tag peptide (GVAMPGAEDDVV) as a model antibody. From the mutated scFab library designed based on the structure, we performed a single-round of PURE ribosome display selection and analyzed the data by NGS to obtain high-affinity scFab candidates with high enrichment factor and high read counts. Subsequently, the most promising candidate was produced as a Fab in the B. choshinensis secretion system, and the purified Fab had an affinity (KD = 1.6 × 10-9 M) similar to the wild type. Overall, this study highlights the potential of the integrated PURE ribosome display with NGS analysis and the B. choshinensis secretion system for the rapid identification and analysis of high-affinity antibody variants.

Whole genome sequencing data of greater burdock (Arctium lappa) naturalized in the United States of America

This dataset comprises whole genome sequencing burdock (Arctium lappa) naturalized in a residential yard in Rochester, New York, USA. Total DNA was extracted from a leaf sample and processed using the Illumina Nextera XT DNA library preparation kit. Sequencing on the NextSeq 2000 platform produced 127.4 GB of raw data, yielding 125.8 GB of high-quality reads after filtering, with an average genome coverage of 75x. The genome was assembled de novo into 792,817 contigs, achieving a total genome length of 1,075,454,921 base pairs with a GC content of 37.03 %. Scaffolding against a Chinese A. lappa reference genome improved genome completeness from 49.1 % to 94.93 %, successfully recovering the majority of protein-coding genes. Variant analysis identified approximately 20.8 million Single Nucleotide Polymorphisms (SNPs) and 1.3 million indels, including functionally significant mutations. The Internal Transcribed Spacer 2 (ITS2) ribosomal region was isolated and compared with global references, revealing significant genetic differentiation between the U.S.A and Chinese populations. This comprehensive genomic dataset has been deposited in publicly accessible repositories, including National Center for Biotechnology Information (NC and Zenodo. The sequencing of this sample provides a valuable resource for comparative genomics, population genetics, and investigations into bioactive compounds with antimicrobial properties, supporting agricultural and pharmaceutical applications. Direct access to the dataset is available at 10.5281/zenodo.14607136.

Alphanudiviral segments found in transcriptomes of the two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae)

Nudiviruses (family Nudiviridae) are a diverse group of enveloped, rod-shaped viruses with double-stranded DNA genomes that infect a wide range of insects and crustaceans. These viruses are of significance both as biological control agents in agriculture and as agents of disease in aquaculture and insect rearing. In this work, we found four segments of a novel and divergent nudivirus identified through RNA-seq data from the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae). The sequences of this virus were detected only in a subset of mite transcriptomes. The assembled segments covered a total of 100,780 bp, with 122 annotated ORFs, including all the 28 conserved nudiviral core genes. Phylogenetic analysis based on the predicted amino acid sequences of 17 selected nudiviral core genes placed the virus within the Alphanudivirus genus, in a clade containing nudiviruses identified from flea transcriptomes. This placement was confirmed by phylogenies of segment-specific concatenated core gene alignments. Indeed, the virus was designated as Tetranychus urticae alphanudivirus (TuNV). Transcriptional profiling revealed variable levels of transcriptional activity among genomic segments and viral genes. Arthropod gene homologs were found interspersed among nudiviral genes across all segments along with several unique genes. This genomic and phylogenetic characterization enhances our understanding of nudivirus diversity and evolution within arthropod hosts.

Comparative analysis of simple sequence repeats and synteny across ten Oryza species: Implications for stress response and genetic diversity

Rice is a pivotal food source for most of the global population, necessitating a strategic focus on maximizing its production under diverse conditions through various methods. As molecular markers, simple sequence repeats (SSRs) emerge as instrumental tools in product enhancement and molecular research. This study employs in silico methods to predict the presence of molecular markers across distinct genomic and genic regions within ten Oryza species. Subsequently, we conducted a comprehensive comparison and synteny analysis of common molecular markers shared among most species, particularly those implicated in stress responses, utilizing McscanX. Beyond identifying common SSRs across the ten species under investigation, we delved into the functional analysis of these markers, specifically pinpointing those associated with stress. Additionally, our investigation illustrated the uniform distribution of SSRs along chromosomes and created a physical map showcasing their prevalence. Notably, chromosomes 1, 2, and 3 exhibited a higher density of molecular markers compared to their counterparts. Furthermore, our study highlighted that Oryza glumipatula, Oryza brachyantha, Oryza meridionalis, and Oryza longistaminata species manifested more pronounced differences in SSR markers compared to other Oryza species. The implications of these findings extend to applications in genetic diversity assessment, genetic mapping, and molecular marker-assisted selection breeding, providing valuable insights for future research and development in the field.

Development and characterization of a saturated transposon mutant library of Salmonella enterica serovar Enteritidis LA5

We created and characterized a saturated Tn-seq mutant library in Salmonella enterica subsp. enterica ser. Enteritidis strain LA5. The set of essential genes after culture in rich medium was determined. This functional genomics tool will aid in identifying the roles of chromosomal and plasmid virulence determinants.

Development and application of sex-specific indel markers for Hippophae salicifolia based on third-generation sequencing

Hippophae salicifolia, a dioecious shrub endemic to the Himalayan region, holds substantial ecological and economic value. The lack of pre-flowering morphological traits for sex identification has long impeded efficient germplasm management and breeding efforts. In this study, we utilized third-generation sequencing technology to conduct whole-genome comparative analysis of known-sex individuals, identifying insertion/deletion loci significantly associated with sex. Based on these loci, we designed a specific primer pair, Hsa09. PCR amplification results demonstrated 100% accuracy in sex differentiation, with female individuals showing a single band and male individuals exhibiting a double-band pattern. Cross-species validation revealed limited applicability of Hsa09 in closely related Hippophae species, suggesting notable divergence in sex determination mechanisms within the genus. This study establishes the first molecular tool for early sex identification in H. salicifolia, overcoming the dependence on reproductive organ development in traditional methods. It provides essential technical support for understanding the evolutionary pathways of sex chromosomes and advancing sex-regulated breeding strategies within the Hippophae genus.

An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples

DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.

Metatranscriptomic analysis of colonic mucosal samples exploring the functional role of active microbial consortia in complicated diverticulitis

In this study, we investigated complicated diverticulitis, an inflammatory condition associated with abscesses, fistulas, intestinal obstructions, perforations, and primarily affects adults over the age of 60. Although the exact etiology remains unclear, the gut microbiome has been suggested as a contributing factor. Previous studies have used 16S rRNA gene analysis from patient fecal samples, which is limited to identifying the bacterial communities present. Herein, we employed shotgun metatranscriptomics on 40 patient-matched samples of diseased and adjacent normal colonic mucosal tissues from 20 patients with complicated diverticulitis to gain a more comprehensive understanding of active microbial taxa and gene expression patterns that may be involved in this disease state. Our findings revealed distinct beta diversity and a conglomerate of pathogenic microbiota in the diseased tissues, including Staphylococcus cohnii, Corynebacterium jeikeium, Kineococcus, Talaromyces rugulosus, Campylobacteraceae, and Ottowia, among others. The adjacent normal tissues were a stark contrast, harboring anti-inflammatory taxa such as Streptococcus salivarius and housekeeping genes and pathways such as the ABC-2 type transport system ATP-binding protein. These results align with previous amplicon sequencing studies and provide novel functional insights that may be crucial for understanding the etiology of complicated diverticulitis.IMPORTANCEComplicated diverticulitis is a virulent condition with no clear cause other than the association with colonic diverticulosis. We assessed the microbial gene expression in complicated diverticulitis patients using colonic tissue samples, revealing microbes in the diseased tissue known to exacerbate the diverticular condition and to live in extreme places, and microbes in patients' normal tissue known to maintain normal bodily functions. This functional information is therefore important for understanding what microbial taxa are present and what they are doing. It is possible clinicians could someday harness this information to more effectively treat complicated diverticulitis symptoms. For example, clinicians may suggest dietary changes and prescribe probiotics to increase beneficial bacteria. Clinicians may also prescribe targeted antibiotics or consider the emerging treatment option of fecal transplants in complicated diverticulitis patients. While not curing complicated diverticulitis, each potential treatment option mentioned addresses balancing out dysbiosis of the gut microbiome, therefore alleviating associated symptoms.

Meiosis-associated expression patterns during starvation-induced cell fusion in the protist Fisculla terrestris

BACKGROUND

Unicellular eukaryotes were widely considered to r eproduce without sex. However, recent findings suggest that meiosis, and by extension (sometimes cryptic) sexual reproduction, might be present in almost all eukaryotic lineages.

RESULTS

Here, we investigate the transcriptomic response underlying starvation-induced fusion in the Rhizaria protist Fisculla terrestris. Investigations of differentially expressed genes (DEGs) with a particular focus on the expression of meiosis-associated genes suggest that some form of meiosis and recombination might occur in these Rhizaria.

CONCLUSIONS

We showed that starvation triggered changes in gene expression of meiosis-associated genes in F. terrestris. However, if these processes are coupled with sexual reproduction remains to be investigated.

Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis

PREMISE

Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.

METHODS

We determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.

RESULTS

Our results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.

CONCLUSIONS

The study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.

Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs

Understanding how hybrids integrate lineage-specific regulatory variants at the haplotype level is crucial for elucidating the genetic basis of heterosis in livestock. In this study, we established three crossbred pig families derived from distant genetic lineages and systematically identified variants from different lineages, including single nucleotide polymorphisms (SNPs) and structural variations (SVs). At the phase level, we quantitatively analyzed gene expression, four histone modifications (H3K4me3, H3K27ac, H3K4me1, and H3K27me3), and the binding strength of transcription factor (CTCF) in backfat (BF) and longissimus dorsi (LD) muscle. By colocalization analysis of phased genetic variants with phased gene expression levels and with phased epigenetic modifications, we identified 18,670 expression quantitative trait loci (eQTL) (FDR < 0.05) and 8,652 epigenetic modification quantitative trait loci (epiQTL) (FDR < 0.05). The integration of eQTL and epiQTL allowed us to explore the potential regulatory mechanisms by which lineage-specific genetic variants simultaneously influence gene expression and epigenetic modifications. For example, we identified a Large White lineage-specific duplication (DUP) encompassing the KIT gene that was significantly associated with its promoter activity (FDR = 7.83 × 10-4) and expression levels (FDR = 9.03 × 10-4). Additionally, we found that a Duroc lineage-specific SNP located upstream of AMIGO2 was significantly associated with a Duroc-specific H3K27ac peak (FDR = 0.035) and also showed a significant association with AMIGO2 expression levels (FDR = 5.12 × 10-4). These findings underscore the importance of phased regulatory variants in shaping lineage-specific transcriptional programs and highlight how the haplotype-resolved integration of eQTL and epigenetic signals can reveal the mechanistic underpinnings of hybrid regulatory architecture. Our results offer insights for molecular marker development in precision pig breeding.

Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.)

Elsholtzia splendens, a perennial herb native to East Asia, is valued for its ornamental and medicinal uses, particularly in treating inflammatory and febrile conditions. Recent studies have highlighted its antibacterial, anti-inflammatory, antidepressant, antithrombotic, and lipid-lowering properties of its compounds. Additionally, E. splendens shows potential for phytoremediation owing to its ability to hyperaccumulate copper (Cu), lead (Pb), zinc (Zn), and cadmium (Cd). However, its role in remediation conflicts with its medicinal use because of the risk of heavy metal accumulation. Genome sequencing will be key to boosting beneficial compound production and reducing heavy metal risks. In this study, we generated a high-resolution, haplotype-resolved, chromosome-scale genome sequence of E. splendens using PacBio Revio long-read, Illumina short-read, and Hi-C sequencing technologies. The haplotype genome assemblies, spanned 275.4 and 265.0 Mbp with a scaffold N50 of 33.9 and 33.8 Mbp for haplotype 1 and 2, respectively. This assembly provides valuable insights into medicinal compound biosynthesis and supports genetic conservation efforts, facilitating future genetic and biotechnological applications of E. splendens for medicinal and ecological uses.

Nanopore RNA direct sequencing identifies that m6A modification is essential for sorbitol-controlled resistance to Alternaria alternata in apple

Sorbitol, a main photosynthate and transport carbohydrate in all tree fruit species in Rosaceae, acts as a signal controlling resistance against Alternaria (A.) alternata in apple by altering the expression of the MdNLR16 resistance gene via the MdWRKY79 transcription factor. However, it is not known if N6-methyladenosine (m6A) methylation of the mRNAs of these genes participates in the process. Here, we found that decreased sorbitol synthesis in apple leaves leads to a transcriptome-wide reduction in the m6A modification, with fewer transcripts containing two or more methylation sites. We identified two methyltransferases, MdVIR1 and MdVIR2, that respond to sorbitol and A. alternata inoculation and positively control resistance to A. alternata. MdVIR1 and MdVIR2 act on MdWRKY79 and MdNLR16 mRNAs, and the resulting m6A modification stabilizes their mRNAs and improves translation efficiency. These data identify that m6A modification through MdVIR1 and MdVIR2 methyltransferases is essential for sorbitol-controlled resistance to A. alternata.

Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis

BACKGROUND

Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor protein bound to an adapter sequence, which is added either using ligation-based methods (ligation sequencing kit), or transposase-based methods (rapid sequencing kit). However, these methods have enzymatic steps that may be susceptible to motif bias, including the underrepresentation of adenine-thymine (AT) sequences due to ligation and biases from transposases. This study aimed to compare the recognition motif and relative interaction frequencies of these library preparation methods and assess their effects on relative sequencing coverage, microbiome, and methylation profiles. The impacts of DNA extraction kits and basecalling models on microbiome analysis were also investigated.

RESULTS

By using sequencing data generated by the ligation and rapid library kits, we identified the recognition motif (5'-TATGA-3') consistent with MuA transposase in the rapid kit and low frequencies of AT in the sequence terminus of the ligation kit. The rapid kit showed reduced yield in regions with 40-70% guanine-cytosine (GC) contents, while the ligation kit showed relatively even coverage distribution in areas with various GC contents. Due to longer reads, ligation kits showed increased taxonomic classification efficiency compared to the rapid protocols. Rumen microbial profile at different taxonomic levels and mock community profile showed significant variation due to the library preparation method used. The ligation kit outperformed the rapid kit in subsequent bacterial DNA methylation statistics, although there were no significant differences.

CONCLUSIONS

Our findings indicated that careful and consistent library preparation method selection is essential for quantitative methods such as bovine-related microbiome analysis due to the systematic bias induced by the enzymatic reactions in Oxford Nanopore library preparation.

Phylogenetic Analysis of the Family Lepidostomatidae (Trichoptera: Integripalpia) Using Whole Mitochondrial Genomes

Lepidostomatidae is a relatively large family of the infraorder Plenitentoria (Integripalpia), comprising four fossil genera and seven extant genera. Lepidostomatid adults exhibit pronounced sexual dimorphism and have thus been referred to as the 'cabinet of curiosities' within Trichoptera. However, only five annotated mitogenomes of Lepidostoma have been recorded in the GeneBank database, and some of these mitogenomes are incomplete. To better understand the structure of mitogenome and phylogenetic relationships of Lepidostomatidae, we present mitogenomes of 13 Lepidostoma species and one Paraphlegopteryx species for the first time. We combined these new mitogenomes with previously published data for a comparative analysis. The results showed that the structure of mitogenome was relatively conserved, the nucleotide composition was significantly AT biased, and the control region showed the highest A + T content. Evolutionary rate analysis showed that all protein-coding genes underwent purification selection. The phylogenetic relationships supported the monophyly of Lepidostomatidae and restored the taxonomic positions of the two subfamilies. Meanwhile, two monophyletic branches (Lepidostoma ferox branch and Lepidostoma hirtum branch) within the genus Lepidostoma were also strongly supported. These findings significantly advance our understanding of the mitogenome and phylogeny of Lepidostomatidae.

Genetic Isolation among Four Lineages of Silene nutans

Speciation is the process leading to the emergence of new species. While being usually progressive, it can sometimes be fast with rapid emergence of reproductive barriers leading to high level of reproductive isolation. Some reproductive barriers might leave signatures in the genome, through elevated level of genetic differentiation at specific loci. Similar signatures might also be the results of linked selection acting in low recombination regions. Nottingham catchfly (Silene nutans) is a Caryophyllaceae species composed of four genetically differentiated lineages for which strong and asymmetric levels of reproductive isolation have been identified. Using population transcriptomic data from several individuals of the four lineages, we inferred the best evo-demographic scenario leading to the current reproductive isolation of these four lineages. We also tested whether loci exhibiting high level of genetic differentiation represented barrier loci or were located in low recombination regions, evolving under strong influence of linked selection. Overall, the four lineages of S. nutans have diverged in strict isolation, likely during the different glacial period, through migration in distinct glacial refugia. Speciation between these four lineages appeared to be particularly fast, likely due to fast evolving plastid genome accelerating plastid-nuclear co-evolution and the probability of plastid-nuclear incompatibilities in inter-lineage hybrids.

Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption

The major spliceosome contains five small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) essential for splicing. Variants in RNU4-2, encoding U4, cause a neurodevelopmental disorder called ReNU syndrome. We investigated de novo variants in 50 snRNA-encoding genes in a French cohort of 23,649 individuals with rare disorders and gathered additional cases through international collaborations. Altogether, we identified 145 previously unreported probands with (likely) pathogenic variants in RNU4-2 and 21 individuals with de novo and/or recurrent variants in RNU5B-1 and RNU5A-1, encoding U5. Pathogenic variants typically arose de novo on the maternal allele and cluster in regions critical for splicing. RNU4-2 variants mainly localize to two structures, the stem III and T-loop/quasi-pseudoknot, which position the U6 ACAGAGA box for 5' splice site recognition and associate with different phenotypic severity. RNU4-2 variants result in specific defects in alternative 5' splice site usage and methylation patterns (episignatures) that correlate with variant location and clinical severity. This study establishes RNU5B-1 as a neurodevelopmental disorder gene, suggests RNU5A-1 as a strong candidate and highlights the role of de novo variants in snRNAs.

The RNA Chaperone Hfq and Small Non-Coding RNAs Modulate the Biofilm Formation of the Fish Pathogen Yersinia ruckeri

The fish pathogen Yersinia ruckeri forms biofilms on abiotic surfaces, contributing to recurrent infections in aquaculture. Increasing evidence suggests that the RNA chaperone Hfq and small non-coding RNAs (sRNAs) are key regulators of bacterial biofilm formation. However, the regulatory mechanisms mediated by these factors remain largely unexplored in Y. ruckeri. In this study, we investigated the roles of Hfq and the Hfq-dependent sRNAs RprA, ArcZ, and RybB in the biofilm formation of Y. ruckeri. We first characterized the sRNAome of biofilm-forming cells, identifying the conserved RprA, ArcZ, and RybB, among the upregulated sRNAs. We then evaluated motility, biofilm formation, and architecture in strains lacking either hfq (Δhfq) or these sRNAs (ΔsRNA). Our results reveal that both Δhfq and ΔsRNA strains exhibit significant alterations in biofilm and motility phenotypes, including changes in bacterial morphology and extracellular matrix. Furthermore, expression analyses indicate that these sRNAs modulate the transcription of key regulatory factors, flagellar and phosphodiesterase genes, ultimately influencing intracellular cyclic di-GMP levels, a key second messenger in biofilm formation. Together, our findings demonstrate that Hfq and its associated sRNAs play critical regulatory roles in Y. ruckeri biofilm formation by controlling the expression of genes involved in motility, bacterial envelope proteins, and c-di-GMP metabolism.

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing

Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE

Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

The gut microbiome and metabolome in children with a first febrile urinary tract infection: a pilot study

BACKGROUND

Urinary tract infection (UTI) is a common bacterial infection in the pediatric population. Febrile urinary tract infection (fUTI) can lead to severe complications such as urosepsis as well as kidney scarring, chronic kidney disease, and systemic hypertension. Recent research supports the hypothesis that dysbiosis of the microbiome may play a role in the pathogenesis and development of fUTI in infants. Our main aim was to compare the shift in gut microbiota composition between children with the first fUTI and controls.

METHODS

We conducted an observational study with 17 children with the first fUTI compared to 18 healthy controls. We performed analysis of the gastrointestinal microbiome and measurements of metabolites in stool and urine.

RESULTS

In the gut microbiome, we found significant differences with lower α-diversity the Shannon index) and significantly lower relative abundance of probiogenic bacteria (short-chain fatty acids (SCFA)) in children with the first episode of fUTI before the start of antibiotic therapy. Furthermore, our findings confirm that the length of breastfeeding has significant influence on gut microbiota composition, reducing pathogenic bacteria and enhancing beneficial taxa. Shannon diversity, duration of breastfeeding, and specific taxa, particularly Faecalibacterium and Escherichia, emerged as strong predictors linked to the development of fUTI.

CONCLUSIONS

This study demonstrates that gut microbiome changes are associated with the onset of fUTI in children. Machine learning models identified Shannon index, specific bacterial taxa, and breastfeeding as strong predictors of fUTI. The study highlighted the potential role of the gut microbiome in preventing fUTI.

Metagenomic biodiversity assessment within an offshore wind farm

Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.

Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library

BACKGROUND

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these sequences remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) in a phylogenetic context. We sequenced and assembled de novo the genome of Actinostella flosculifera and analyzed a total of 38 nuclear genomes to create the first ActiniariaREP library (Actiniaria-REPlib). We compared Actiniaria-REPlib with Repbase and RepeatModeler2 libraries, and used dnaPipeTE to annotate REPs from genomic short-read datasets of 36 species for divergence landscapes.

RESULTS

Our study assembled and annotated the mitochondrial genomes, including 27 newly assembled ones. We re-annotated ~92% of the unknown sequences from the initial nuclear genome library, finding that 6.4-30.6% were DNA transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, and 1.2-7% unclassifiable sequences. Actiniaria-REPlib recovered 9.4x more REP sequences from actiniarian genomes than Dfam and 10.4x more than Repbase. It yielded 79,903 annotated TE consensus sequences (74,643 known, 5,260 unknown), compared to Dfam with 7,697 (3,742 known, 3,944 unknown) and Repbae (763 known).

CONCLUSIONS

Our study significantly enhances the characterization of sea anemone repetitive DNA, assembling mitochondrial genomes, re-annotating nuclear sequences, and identifying diverse repeat elements. Actiniaria-REPlib vastly outperforms existing databases, recovering significantly more REP sequences and providing a comprehensive resource for future genomic and evolutionary studies in Actiniaria.

Molecular characterization and phylogenetic analyses of the mitogenome of Wan-Xi white goose, a native goose breed in China

BACKGROUND

The Wan-Xi white goose (WXG), an indigenous Chinese waterfowl (Anserini: Anserinae), is crucial for goose germplasm conservation. This study aimed to sequence and analyze the complete mitochondrial DNA (mtDNA) of WXG using the BGISEQ-500 platform. The mtDNA's structure and function were investigated to gain insights into its genetic diversity and population structure.

RESULTS

The mtDNA was found to be 16,743 bp long and comprised 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes, a complement of 13 protein-coding genes (PCGs), as well as a single noncoding control region known as the D-loop. Notably, all tRNA genes, except for trnS1-tRNA which lacked the dihydrouridine stem, were predicted to adopt the typical cloverleaf structure. Given the genetic variability across the mtDNA of Anser spp. and the intergenic gaps identified by codon analysis, the codon usage patterns were comprehensively examined via comparative analysis of the mtDNAs of WXG and 24 other Anser spp. The relative synonymous codon usage (RSCU) values of the 13 mitochondrial PCGs of WXG were consistent with those of the mitochondrial PCGs of the 24 other Anser spp. Analysis of the neutrality (GC3-GC12), the effective number of codons (ENCs)-GC3, and parity rule 2-bias plots further revealed that natural selection emerged as the primary factor influencing codon bias in Anser sp. High nucleotide diversity (Pi > 0.02) was observed in several regions, including the D-loop, ATP6, 12S rRNA, ND1, 16S rRNA_ND1, COX2, and ND5. Furthermore, the results of nonsynonymous (Ka)/synonymous (Ks) analysis of the 13 mitochondrial PCGs of the 25 species under Anser revealed that the genes were subject to strong purifying selection. The findings of phylogenetic analysis further revealed that WXG and 10 other members of Anser cygnoides clustered into a single branch to form a monophyletic group.

CONCLUSION

This research provides valuable insights into the mtDNA of WXG, highlighting its genetic diversity and population structure. The identified mutation hotspots and purifying selection on mitochondrial PCGs suggest potential areas for future research on Anser cygnoides. The findings contribute to our understanding of this rare species and its conservation efforts.

Multiplex polymerase chain reaction (PCR) with Nanopore sequencing for sequence-based detection of four tilapia pathogens

Background

Tilapia aquaculture faces significant threats posed by four prominent pathogens: tilapia lake virus (TiLV), infectious spleen and kidney necrosis virus (ISKNV), Francisella orientalis, and Streptococcus agalactiae. Currently, employed molecular diagnostic methods for these pathogens rely on multiple singleplex polymerase chain reactions (PCR), which are time-consuming and expensive.

Methods

In this study, we present an approach utilizing a multiplex PCR (mPCR) assay, coupled with rapid Nanopore sequencing, enabling the one-tube simultaneous detection and one-reaction Nanopore sequencing-based validation of four pathogens.

Results

Our one-tube multiplex assay exhibits a detection limit of 1,000 copies per reaction for TiLV, ISKNV, and S. agalactiae, while for F. orientalis, the detection limit is 10,000 copies per reaction. This sensitivity is sufficient for diagnosing infections and co-infections in clinical samples from sick fish, enabling rapid confirmation of the presence of pathogens. Integrating multiplex PCR and Nanopore sequencing provides an alternative approach platform for fast and precise diagnostics of major tilapia pathogens in clinically sick animals, adding to the available toolbox for disease diagnostics.

Trends and characteristics of multidrug-resistant MRSA in Norway 2008-2020

Infections caused by multidrug-resistant (MDR) bacteria are recognized as a critical One Health concern which poses a significant threat to public health, leading to increased morbidity and mortality across both high- and low-income countries. In this study, we investigated the epidemiology and molecular mechanisms of multidrug-resistant methicillin-resistant Staphylococcus aureus (MDR-MRSA) strains identified in Norway from 2008 to 2020, in order to gain a better understanding of the evolution and dissemination of multidrug resistance in S. aureus. A total of 452 MDR-MRSA strains isolated from 429 individuals were analyzed from a dataset of 23,412 MRSA strains. Methods included epidemiological characterization, antimicrobial susceptibility testing (AST), and genetic analysis of a selection of strains using nanopore sequencing to identify antimicrobial resistance (AMR) genes and mutations, as well as their location on plasmids, SCCmec and other mobile genetic elements (MGEs). The study revealed an overall increasing trend in MDR-MRSA strains, with healthcare-associated strains being more prevalent among MDR-MRSA compared to the overall MRSA population. Significant heterogeneity in spa-types and clonal complexes exhibiting multidrug resistance was observed, with high resistance rates against multiple antibiotic groups, particularly erythromycin, ciprofloxacin/norfloxacin, tetracycline, gentamicin, and clindamycin in addition to cefoxitin. The predominant MDR-MRSA clones included t1476/CC8, t127/CC1, t189/CC188, and t030, t037/CC239. Among these, MRSA t1476/CC8 showed an upward trend toward the conclusion of the study period, indicating the emergence of a MDR-MRSA clone. A broad range of AMR genes and mutations were detected, linked to a wide variety of MGEs, highlighting the complex mechanisms of resistance development and dissemination within the MRSA population. This study highlights the rising challenge posed by MDR-MRSA strains, and reveals the multifactorial nature of AMR in S. aureus, thus emphasizing the importance of continued surveillance, antibiotic stewardship and infection control measures, as well as global cooperation, in order to combat the spread of these multidrug-resistant pathogens.

Complete genome sequence of Desulfovibrio sp. GTC20076 isolated from a clinical specimen in Japan

Desulfovibrio is a genus of sulfate-reducing, anaerobic bacteria ubiquitously present in the environment. Herein, we report the complete genome sequence of an isolate of a new Desulfovibrio species obtained from a human clinical specimen in Japan. The genome comprised a circular chromosome with a length of 3,213,183 bp.

Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen

The rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for nonmodel organisms. However, these methods often require exceptionally fresh material containing unfragmented high-molecular-weight nucleic acids. Researchers who preserve field-collected specimens in ethanol at ambient temperatures, prior to transferring them to long-term frozen archives, face challenges in applying advanced genomic approaches due to DNA and RNA fragmentation under suboptimal preservation conditions. To explore the potential of such preserved specimens as sources of reference genomes, we utilized Nanopore MinION technology to generate genomic data from a frozen archived specimen of the endemic alpine ground beetle Carabus (Platycarabus) depressus. Using a rapid in-house protocol for high-molecular-weight DNA extraction, followed by sequencing on a single flow cell, we produced 8.75 million raw reads with an N50 of 2.8 kb. The resulting assembly achieved remarkable completeness, recovering up to 98% of Benchmarking Universal Single-Copy Orthologs genes, despite a moderate N50 of 945 kb. This genome is only the second available for the taxonomically diverse genus Carabus, demonstrating the feasibility of using short-to-long-read sequencing on frozen archived specimens commonly housed in natural history collections. These findings open new avenues for advancing nonmodel organism genomics and its downstream applications.

Genetic Variation and Gene Expression of the Antimicrobial Peptide Macins in Asian Buffalo Leech (Hirudinaria manillensis)

With the growing severity of antibiotic resistance, antimicrobial peptides demonstrate significant potential for medical applications. Here, we performed genome and transcriptome sequencing of 30 Asian buffalo leech (Hirudinaria manillensis) individuals and integrated data from three other leech species (Whitmania pigra, Hirudo nipponia, and Hirudo medicinalis) to investigate genetic variation and gene expression of H. manillensis macins. Three macins (Hman1, Hman2, and Hman3), along with their encoding genes (Hman1, Hman2, and Hman3), were identified in H. manillensis. Hman1 exhibited the highest similarity (63.5 ± 12.0%) to macins from other leeches, followed by Hman2 (57.8 ± 7.4%) and Hman3 (30.0 ± 3.5%). Both amino acid and codon sequences of Hman1 were conserved within the species, whereas Hman2 and Hman3 exhibited markedly higher variability. All Hman1 sequences were translatable, while four Hman2 and 28 Hman3 sequences had degenerated into pseudogenes. Transcripts per million (TPM) values for Hman1, Hman2, and Hman3 were 2196.63, 242.35, and 1.22, respectively. Total macin expression in H. manillensis was less than 1/20 of that in W. pigra. Based on sequence variation and expression patterns, we propose that Hman1 retains functionality while Hman2 and Hman3 have lost or are losing their antibacterial functions.

A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome

The hourglass dolphin (Lagenorhynchus cruciger) is a small cetacean species of the Southern Ocean, with significance to iwi Māori (Māori tribes) of Aotearoa New Zealand as taonga (treasured/valued). Due to the remoteness and difficulty of surveying Antarctic waters, it remains one of the least-studied dolphin species. A recent stranding of an hourglass dolphin represented a rare opportunity to generate a genome assembly as a resource for future study into the conservation and evolutionary biology of this species. In this study, we present a high-quality genome assembly of an hourglass dolphin individual using a single sequencing platform, Oxford Nanopore Technologies, coupled with computationally efficient assembly methods. Our assembly strategy yielded a genome of high contiguity (N50 of 8.07 Mbp) and quality (98.3% BUSCO completeness). Compared to other Delphinoidea reference genomes, this assembly has fewer missing BUSCOs than any except Orcinus orca, more single-copy complete BUSCOs than any except Phocoena sinus, and 20% fewer duplicated BUSCOs than the average Delphinoidea reference genome. This suggests that it is one of the most complete and accurate marine mammal genomes to date. This study showcases the feasibility of a cost-effective mammalian genome assembly method, allowing for genomic data generation outside the traditional confines of academia and/or resource-rich genome assembly hubs, and facilitating the ability to uphold Indigenous data sovereignty. In the future, the genome assembly presented here will allow valuable insights into the past population size changes, adaptation, vulnerability to future climate change of the hourglass dolphin and related species.

Evolution of far-red light photoacclimation in cyanobacteria

Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.

Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment

Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.

Identification of essential genes by transposon insertion sequencing and genome-scale metabolic model construction in Streptococcus suis

Bacterial essential genes are indispensable for the survival of bacteria and therefore are attractive targets for novel anti-microbial drugs. Identifying essential genes provides a roadmap for developing novel antibiotics and anti-microbial therapies. In this study, combining high-throughput transposon sequencing (Tn-seq) and genome-scale metabolic model (GEM) construction, essential genes of Streptococcus suis, an important emerging zoonotic bacterial pathogen, were analyzed. A highly efficient transposon (Tn) mutagenesis system was developed in S. suis. This system facilitated the construction of a high-density library containing over 160,000 Tn mutants. By sequencing the library and data analysis, more than 21,000 insertion sites and 150 essential genes for growth in the rich medium were identified. Subsequently, a GEM of S. suis SC19 strain was constructed, and 165 essential genes were predicted via flux balance analysis (FBA). A total of 244 essential genes were obtained by combining the results of Tn-seq, and FBA performed. Gene identity analysis revealed 101 essential genes as potential anti-bacterial drug targets. Among them, apart from many known antibiotic targets, some interesting essential genes were also identified, including those involved in capsule biosynthesis, aminoacyl-tRNA biosynthesis, lipid biosynthesis, cell division, and cell signaling. This work identified essential genes of S. suis at the whole-genome level, providing a reference for the mining of novel anti-microbial drug targets.

IMPORTANCE

Anti-microbial resistance (AMR) presents an escalating challenge, making anti-microbial drug development an urgent need. Bacterial essential genes represent promising targets for anti-microbial drugs. However, conventional approaches to identifying bacterial essential genes are time and labor intensive. Techniques such as Tn-seq and GEM construction offer a high-throughput approach for this identification. Streptococcus suis is an emerging zoonotic bacterial pathogen, posing a big threat to public health as well as the pig industry, and the levels of AMR are increasing. Our study has successfully identified essential genes in S. suis, providing crucial insights for the discovery of new anti-microbial drug targets.

A megatransposon drives the adaptation of Thermoanaerobacter kivui to carbon monoxide

Acetogens are promising industrial biocatalysts for upgrading syngas, a gas mixture containing CO, H2 and CO2 into fuels and chemicals. However, CO severely inhibits growth of many acetogens, often requiring extensive adaptation to enable efficient CO conversion (carboxydotrophy). Here, we adapt the thermophilic acetogen Thermoanaerobacter kivui to use CO as sole carbon and energy source. Isolate CO-1 exhibits rapid growth on CO and syngas (co-utilizing CO, H2 and CO2) in batch and continuous cultures (µmax ~ 0.25 h-1). The carboxydotrophic phenotype is attributed to the mobilization of a CO-dependent megatransposon originating from the locus responsible for autotrophy in T. kivui. Transcriptomics reveal the crucial role the redox balance plays during carboxydotrophic growth. These insights are exploited to rationally engineer T. kivui to grow on CO. Collectively, our work elucidates a primary mechanism responsible for the acquisition of carboxydotrophy in acetogens and showcases how transposons can orchestrate evolution.

DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions

Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional TE costs become miniscule. How, then, do TEs and host suppression invoke further addition of massive DNA amounts? We analyze TE proliferation histories, deletion rates, and community diversities in six salamander genomes (21.3 - 49.9 Gb), alongside gonadal expression of TEs and suppression pathways. We show that TE activity is higher in testes than ovaries, attributable to lower KRAB-ZFP suppression. Unexpectedly, genome size and expansion are uncorrelated with TE deletion rate, proliferation history, expression, and host suppression. Also, TE community diversity increases with genome size, contrasting theoretical predictions. We infer that TE-host antagonism in gigantic genomes produces stochastic TE accumulation, reflecting noisy intermolecular interactions in huge genomes and cells.

Evolution of Wolbachia male-killing mechanism within a host species

Male-killing bacterial symbionts, prevalent in arthropods, skew population sex ratios by selectively killing male progeny, profoundly impacting ecology and the evolution of their hosts. Male killing is a convergently evolved trait, with microbes evolving diverse male-killing mechanisms across host species with widely divergent sex determination pathways. A common evolutionary response to male-killing presence is the spread of suppressor mutations that restore male survival. In this study, we demonstrate the evolution of a novel male-killing mechanism that is insensitive to an existing male-killing suppressor. Hypolimnas bolina butterflies from Yogyakarta, Indonesia, showed extreme female-biased population sex ratio associated with high prevalence of a male-killing Wolbachia. This strain, wBol1Y, shared a very recent common ancestor with the previously characterized "suppressed" male-killing strain in the species, wBol1, but it retained its male-killing ability in the presence of the male-killing suppressor. The genome of wBol1Y differed from the suppressed wBol1 in carrying an additional prophage that included strong candidate genes for male killing. In vitro and in vivo data demonstrated that wBol1Y feminized splicing and expression of lepidopteran sex determination pathway genes and that the gene Hb-oscar-present on wBol1Y's unique prophage insert-was sufficient to disrupt the male sex determination pathway. Our study demonstrates that the diversity of male-killing mechanisms is a product both of interaction with varying insect sex determination systems and the evolution of male killing within a host species. Our data indicate that the male killer and host may be involved in escalating arms races, where spreading male-killing suppression drives the evolution of additional systems that reestablish male killing by the symbiont.

De novo assembly and annotation of the Empoasca fabae mitochondrial genome

This study presents the assembly and annotation of the full-length mitochondrial genome for the leafhopper species Empoasca fabae Harris, 1841. The mitogenome was obtained from a contig-level assembly with the identified mitochondrial genome being 14,873 bp in length. The base composition was A (38.8%), T (39.1%), C (11.7%), and G (10.4%). The mitogenome comprised 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and showed a unique, non-AT-rich D-loop region. Phylogenetic analysis confirmed the placement of E. fabae within the subfamily Typhlocybinae, clustering with other species in the Empoasca genus.

Validation of a modified rapid test to detect the cefazolin inoculum effect in methicillin-susceptible Staphylococcus aureus from bloodstream infections in hospitals from North and Latin America

BACKGROUND

The cefazolin inoculum effect (CzIE), defined here as a cefazolin MIC at high inoculum (107 colony-forming units/mL)  ≥16 mg/L in MSSA, has been associated with less favourable clinical outcomes. However, detection of this phenotype is challenging in the clinical microbiology laboratory. We previously described modification of a rapid nitrocefin test using ampicillin disks rather than ampicillin powder for induction of the Staphylococcus aureus β-lactamase (BlaZ).

OBJECTIVE

Evaluate the performance of the modified rapid nitrocefin test in a blinded fashion using MSSA isolates recovered from patients with bacteraemia.

METHODS

We evaluated 200 MSSA isolates recovered from Latin American (LA) and North American (NA) hospitals (67 and 133 from NA and LA, respectively). The CzIE was determined using the modified rapid nitrocefin test with ampicillin disks and compared with MIC determination at high inoculum (gold standard). All isolates were subjected to whole-genome sequencing on an Illumina Hi-Seq platform. Performance metrics were calculated for the complete dataset and according to specific BlaZ types.

RESULTS

The prevalence of the CzIE was 53% (105/200). Compared with the gold standard, the modified nitrocefin rapid test had a sensitivity of 96% and a specificity of 91.6%, with an overall accuracy of 94%. There were no false-positive results among blaZ-negative MSSA strains.

CONCLUSIONS

The modified nitrocefin rapid test exhibited a robust performance to detect the CzIE in isolates from the Americas. This methodology is inexpensive and can be implemented in clinical microbiology laboratories around the world, including those with limited resources.

HDAC4 Inhibits NMDA Receptor-mediated Stimulation of Neurogranin Expression

The coordination of neuronal wiring and activity within the central nervous system (CNS) is crucial for cognitive function, particularly in the context of aging and neurological disorders. Neurogranin (Ng), an abundant forebrain protein, modulates calmodulin (CaM) activity and deeply influences synaptic plasticity and neuronal processing. This study investigates the regulatory mechanisms of Ng expression, a critical but underexplored area for combating cognitive impairment. Utilizing both in vitro and in vivo hippocampal models, we show that Ng expression arises during late developmental stages, coinciding with the processes of synaptic maturation and neuronal circuit consolidation. We observed that Ng expression increases in neuronal networks with heightened synaptic activity and identified GluN2B-containing N-methyl-D-aspartate (NMDA) receptors as key drivers of this expression. Additionally, we discovered that nuclear-localized HDAC4 inhibits Ng expression, establishing a regulatory axis that is counteracted by NMDA receptor stimulation. Analysis of the Ng gene promoter activity revealed regulatory elements between the - 2.4 and - 0.85 Kbp region, including a binding site for RE1-Silencing Transcription factor (REST), which may mediate HDAC4's repressive effect on Ng expression. Further analysis of the promoter sequence revealed conserved binding sites for the myocyte enhancer factor-2 (MEF2) transcription factor, a target of HDAC4-mediated transcription regulation. Our findings elucidate the interplay between synaptic activity, NMDAR function, and transcriptional regulation in controlling Ng expression, offering insights into synaptic plasticity mechanisms and potential therapeutic strategies to prevent cognitive dysfunction.

mKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data

The advanced single-microbe RNA sequencing (smRNA-seq) technique addresses the pressing need to understand the complexity and diversity of microbial communities, as well as the distinct microbial states defined by different gene expression profiles. Current analyses of smRNA-seq data heavily rely on the integrity of reference genomes within the queried microbiota. However, establishing a comprehensive collection of microbial reference genomes or gene sets remains a significant challenge for most real-world microbial ecosystems. Here, we developed an unbiased embedding algorithm utilizing K-mer signatures, named mKmer, which bypasses gene or genome alignment to enable species identification for individual microbes and downstream functional enrichment analysis. By substituting gene features in the canonical cell-by-gene matrix with highly conserved K-mers, we demonstrate that mKmer outperforms gene-based methods in clustering and motif inference tasks using benchmark datasets from crop soil and human gut microbiomes. Our method provides a reference genome-free analytical framework for advancing smRNA-seq studies.

Patterns of Gene Family Evolution and Selection Across Daphnia

Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species of Daphnia, a group of freshwater microcrustaceans that are insightful model systems for evolutionary genetics' research. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers across Daphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species-specific manner. Additionally, while we show general trends toward positive selection within some expanding gene families, many genes are not under selection, highlighting the complexity of diversification and evolution within Daphnia. Our research enhances the understanding of individual gene family evolution within Daphnia and provides a case study of ecologically relevant genes prone to change.

Temporal and regional X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing

Random X-chromosome inactivation is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long noncoding RNA Xist, occurs in the early embryo and is stably maintained throughout life, although inactivation is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on developing mouse PGCs, we provide a detailed map of X-linked gene reactivation. Despite the absence of Xist expression, PGCs still harbor a fully silent X chromosome at embryonic day 9.5 (E9.5). Subsequently, X-linked genes undergo gradual and distinct regional reactivation. At E12.5, a substantial part of the inactive X chromosome resists reactivation, retaining an epigenetic memory of its silencing. Our findings define the orchestration of reactivation of the inactive X chromosome, a key event in female PGC reprogramming with direct implications for reproduction.

An expanded metabolic pathway for androgen production by commensal bacteria

Commensal bacteria have been implicated in the modulation of steroid hormones, including circulating androgen levels in the host. However, the microbial genetic pathways involved in androgen production have not been fully characterized. Here we identify a microbial gene encoding an enzyme that catalyses the conversion of androstenedione to epitestosterone in the gut microbiome member Clostridium scindens and named this gene desF. We demonstrate that epitestosterone impacts androgen receptor-dependent prostate cancer cell proliferation in vitro. We also demonstrate that stool desF levels are elevated in patients with prostate cancer who are unresponsive to abiraterone/prednisone therapy. Bacterial isolates from urine or prostatectomy tissue produced androgens, and 17β-hydroxysteroid dehydrogenase activity encoded by the desG gene was detected in strains of the urinary tract bacterium Propionimicrobium lymphophilum. Furthermore, we demonstrate that urinary androgen-producing bacterial strains can promote prostate cancer cell growth through metabolism of cortisol and prednisone. Abiraterone, which targets host desmolase (CYP17A1), a rate-limiting enzyme in adrenal steroidogenesis, does not inhibit bacterial desmolase (DesAB), whereas the conversion of prednisone to androgens by DesAB, DesF and DesG drives androgen-receptor-dependent prostate cancer cell line proliferation in vitro. Our results are a significant advance in steroid microbiology and highlight a potentially important role for gut and urinary tract bacteria in host endocrine function and drug metabolism.

Genetic effect of the Ph1 locus on transcriptome atlas of anther development-related genes, meiotic chromosome behavior and agronomic traits in bread wheat

Proper spatiotemporal expression of meiosis-related genes (MRGs) and other male-microsporogenesis/microgametogenesis-related genes (MMRGs) is crucial for normal anther development, yet their expression patterns remain largely unknown in wheat. The Ph1 locus in wheat is known to contain the Ph1 gene that plays a dual role in promoting pairing between homologous chromosomes but repressing pairing between homoeologous chromosomes, but its genetic function is still unclear. Here, we investigated these issues by conducting a comprehensive transcriptome analysis during wheat anther development in Chinese Spring (CS) and its ph1b deletion mutant under greenhouse and field conditions. Our results revealed that MRGs and MMRGs are predominantly expressed during pre-meiosis stages, with MMRGs also being highly expressed in meiotic-II. Gene co-expression analysis showed that C2H2 and B3 transcriptional factors (TFs) are associated with MRGs, and MYB regulators interacted mainly with MMRGs during microgametogenesis. Deletion of genes within the Ph1 locus failed to induce compensatory transcriptional activation of their homoeologous counterparts, while genes outside the Ph1 locus showed environmental-specific responses, especially during meiotic-II and mature pollen stages. Notably, early disjunction of bivalent chromosomes is a primary factor leading to defective meiocytes during metaphase I. Furthermore, the ph1b deletion mutant exhibited a substantially delayed heading date, potentially contributing to environment-stable and environment-specific alterations in fertility and grain-related traits. Our study highlights the significant impact of the Ph1 locus on the transcriptome during anther development, and a previously unheeded effect on meiotic chromosome pairing and agronomic traits, suggesting potential for genetic manipulations within the Ph1 locus for wheat improvement.

Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation

Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.