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PubMed2026

Mechanistic insights into flavor deterioration in bitter sturgeon caviar: Evidence from lipidomics and metagenomics.

This study systematically compared the flavor and multi-omics differences between normal caviar and bitter caviar based on quantitative descriptive analysis (QDA), volatile compounds (VOCs) analysis, untargeted lipidomics, and metagenomics. The results showed that bitter caviar was characterized not only by increased bitterness, but also by decreased positive sensory attributes, including buttery, nutty, and marine fresh. VOCs analysis indicated that the volatile profile of bitter caviar was reorganized. Compounds such as 3-hydroxy-2-butanone, 1-octen-3-ol, and (E, Z)-2,6-nonadienal showed higher relative odor activity values (rOAVs); however, these changes did not improve its overall sensory experience. Untargeted lipidomics identified 492 differential lipids. These changes were mainly characterized by decreased PC and increased DG and LPC in bitter caviar. KEGG pathways analysis showed that these differential lipids were mainly associated with glycerophospholipid metabolism, choline metabolism in cancer, and retrograde endocannabinoid signaling. Metagenomic analysis showed that bacteria dominated the microbial community of caviar. Among them, Bacillus and Micromonospora showed relatively high abundance in the caviar microbiota. They were also closely associated with lipid metabolic changes involving PC, DG, and LPC, suggesting their potential as candidate targets for future microbiota-directed regulation of caviar quality. These findings provide new insights into the mechanisms underlying sensory deterioration and flavor formation in bitter caviar, and offer a theoretical basis for improving caviar quality in industrial production.

Animals↗
PubMed2026

Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios-a retrospective study from a single center.

BACKGROUND: Plasma cell-free DNA metagenomic next-generation sequencing (mNGS) is a non-invasive comprehensive method for the etiological diagnosis of various infectious diseases. However, research on the early diagnosis and real-world clinical impact of plasma mNGS in patients with suspected infection are still limited. MATERIALS AND METHODS: This study retrospectively included 140 patients with suspected infections who underwent early plasma mNGS and conventional culture testing. Referring to the clinical diagnosis of infectious diseases, the diagnostic performance of plasma mNGS and culture tests was compared, and the application scenarios and clinical effects of plasma mNGS were evaluated. RESULTS: The positive rate of plasma mNGS was significantly higher than that of culture methods (55.71% vs 25.10%, p&#x2009;<&#x2009;0.001) and blood cultures (55.71% vs 12.86%, p&#x2009;<&#x2009;0.001). Regarding clinical diagnosis, the sensitivity of plasma mNGS was significantly higher than that of culture (58.27% vs 37.80%, p&#x2009;=&#x2009;0.002). The combination of mNGS and culture achieved a higher detection sensitivity (69.29%), especially in patients with multi-site co-infections (73.68%) and blood infections (73.17%). Plasma mNGS demonstrated higher sensitivity in patients with procalcitonin (PCT) index > 5&#x2009;ng/ml or human neutrophil lipocalin (HNL) index > 200&#x2009;ng/ml. In terms of treatment, a total of 69 patients (54.33%) benefited from plasma mNGS. CONCLUSION: This study highlights the significant improvement in pathogen detection performance by combining conventional culture with plasma mNGS detection, especially in patients with multi-site co-infections and blood infections. Early use of plasma mNGS as an adjunct to culture can better guide clinicians to initiate appropriate anti-infective therapy.

Humans↗
PubMed2026

Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.

The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.

Fermentation↗
PubMed2026

Alternative genetic codes in bacteria and archaea identified with a fast k-mer-based algorithm.

The genetic code is conserved across all domains of life and is often described as universal. Nevertheless, many exceptions to the "universal" code have now been documented, most of these through manual or semiautomated inspection of highly conserved genes. Modern bioinformatics tools improved our ability to find alternative genetic codes but remain computationally expensive, preventing widespread use on thousands of new species identified by sequencing environmental samples. Here, I report a >100-fold accelerated method for inferring the genetic code directly from assembled genomes and apply it to thousands of previously uncharacterized assemblies from archaea and bacteria. I describe three candidate genetic code variations, one of which, an alternative genetic code used by a family of Asgard archaea, is a unique example of sense codon reassignments for this domain. Identifying genetic code variations is important for understanding evolution of the standard code and improving accuracy of protein databases and open reading frame identification.

Genetic Code↗
PubMed2026

Reference genome of the Californian trapdoor spider Aptostichus stephencolberti Bond 2008 (Araneae: Mygalomorphae: Euctenizidae).

We present a reference genome assembly for the trapdoor spider Aptostichus stephencolberti. This species, described in 2008, is endemic to the highly fragmented coastal dune habitats of Northern California from Monterey to the San Francisco Bay Area. Trapdoor spiders are ideal taxa for landscape scale genomic studies owing to their extreme site fidelity and limited dispersal capabilities; these same characteristics make them prone to extinction. Genomic studies of species like A. stephencolberti can reveal novel areas of endemism and high conservation value that may not be evident in species with wider ranges and greater dispersal capabilities. As part of the California Conservation Genomics Project, we constructed the A. stephencolberti reference genome from high quality long-read sequences, scaffolded with proximity ligation Omni-C data. The primary assembly comprises 551 scaffolds spanning 3.63 Gbp, a scaffold N50 of 62.2 Mbp and BUSCO completeness of 95.6%. We estimate 52 chromosomes yet find no (TTAGG)n telomer repeats. Expanding the telomeric repeat search finds an ancestral loss of the repeat from all spiders. Automated annotation using the NCBI refseq pipeline and RNAseq data from whole adults finds 14,067 genes with a BUSCO annotation completeness of 95.56%. Repeat annotation identified 77% of the genome to be interspersed repeats. This resource, the first for family Euctenizidae will facilitate future study and resulting conservation actions of A. stephencolberti and other Aptostichus sp. populations associated with the rapidly changing California coastal dune ecosystem.

Aptostichus stephencolberti↗
PubMed2026

Draft genome sequence of Enterococcus casseliflavus strain MBBL_MP4 isolated from healthy bovine milk.

We report the draft genome sequence of Enterococcus casseliflavus MBBL_MP4, recovered from healthy bovine milk. The 3.45-Mbp genome assembly comprises 27 contigs and indicates low pathogenic potential, with no acquired antimicrobial resistance or known virulence genes. This genome provides a valuable resource for the genomic characterization of bovine-associated E. casseliflavus.

Enterococcus casseliflavus↗
PubMed2026

A review into the recent advances in the world of amoebiasis.

PURPOSE OF REVIEW: Amoebiasis is a parasitic infection caused by Entamoeba histolytica , affecting 10% of the global population. It is a well recognized cause of morbidity and mortality in low-middle-income countries where it is endemic. However, with increased migration and global travel, amoebiasis is now more common in high-income countries, although diagnosis is often delayed or even missed due to lack of awareness of the latest epidemiology and optimal diagnostic testing. This review discusses the evolving prevalence, and the current international guidelines for the investigation and treatment of amoebiasis, focusing on recent advances. RECENT FINDINGS: The recent literature shows that the primary investigations for amoebiasis remain the same, though newer modalities such as artificial intelligence-powered microscopy and metagenomics have been developed recently, which aids the accuracy and speed of diagnosis. Treatment remains the same, though current research has found potential new drugs and drug targets which show promise. SUMMARY: This review reinforces the importance of early clinical suspicion, diagnosis and treatment for amoebiasis. What was once a disease only seen in endemic countries or travel-associated imported cases is now more common and must not be missed.

Humans↗
PubMed2026

Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.

Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV&#xa0;>&#xa0;1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.

Volatile Organic Compounds↗
PubMed2026

Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.

Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P&#xa0;=&#xa0;0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3&#xa0;&#xb0;C; +4.5&#xa0;&#xb0;C relative to CK_M), and its group-mean temperature remained &#x2265; 60&#xa0;&#xb0;C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.

Bacillus↗
PubMed2026

Transcriptomic responses of Porphyrophora sophorae larvae during licorice root colonization reveal coordinated remodeling of translation, mitochondrial energy metabolism and defense-related genes.

BACKGROUND: Porphyrophora sophorae is a subterranean piercing-sucking scale insect that damages licorice (Glycyrrhiza uralensis) roots, but the molecular responses associated with larval root colonization remain insufficiently defined. METHODS: We compared non-parasitic larvae (NP) and root-colonizing larvae (RC) using six RNA-seq libraries, de novo transcriptome assembly, DESeq2-based differential expression analysis, GO/KEGG enrichment, annotation-based candidate gene screening, and RT-qPCR validation of selected genes. RESULTS: Sequencing yielded 260.91 million clean reads, and de novo assembly produced 60,794 non-redundant transcripts. DESeq2 identified 703 FDR-significant DEGs, including 49 upregulated and 654 downregulated genes in RC larvae. Upregulated genes were mainly associated with translation- and ribosome-related processes, whereas downregulated genes were enriched in mitochondrial, oxidation-reduction, energy metabolism, and oxidative phosphorylation-related functions. Annotation-based screening identified 75 FDR-significant candidate genes associated with chemosensation, defense-related responses, and energy metabolism, with mitochondrial energy metabolism-related genes forming the largest module. RT-qPCR validation based on the raw Ct data showed concordant expression directions for ten selected transcript targets. CONCLUSIONS: Root colonization in P. sophorae larvae was associated with coordinated transcriptional remodeling involving selective activation of translation-related processes, adjustment of mitochondrial energy metabolism, and changes in defense-related gene expression. These results provide candidate molecular targets for future functional studies of host contact, feeding establishment, and physiological adjustment in this subterranean scale insect.

Animals↗
PubMed2026

Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.

In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.

Multiomics↗
PubMed2026

Desert-derived Ensifer sp. SA403 enhances potato salt tolerance by reshaping rhizosphere microbiome functions and host responses.

Soil salinization increasingly threatens global food security, and potato (Solanum tuberosum L.), a moderately salt-sensitive crop, is particularly vulnerable to saline soils. Plant growth-promoting rhizobacteria (PGPR) offer a promising strategy to improve crop performance, yet how PGPR interact with native microorganisms to enhance potato salt tolerance remains poorly understood. In this study, we identified a desert-derived PGPR strain, Ensifer sp. SA403, which substantially enhanced potato performance under high salinity across sterile, non-sterile and field conditions. Physiologically, inoculation with SA403 reduced shoot Na&#x207a; accumulation and increased the K&#x207a;/Na&#x207a; ratio; notably, these effects were markedly stronger in non-sterile substrates than under sterile conditions, indicating that SA403-mediated ion homeostasis relies on cooperation with the resident microbiota rather than on the strain acting alone. Metagenomic profiling indicated that SA403 strain reshaped rhizosphere communities, significantly enriching beneficial taxa such as Priestia and Bradyrhizobium, and upregulated functional pathways involved in glutathione and sulfur metabolism. Furthermore, host transcriptomic analyses showed that SA403 modulated plant responses to salt stress, with differentially expressed genes enriched in jasmonic acid signaling, ethanolamine metabolism and amino-acid biosynthesis pathways. Field trials on saline soils confirmed that SA403 significantly increased seedling emergence and tuber weight. Together, our results demonstrate that SA403 functions as a biological mediator that optimizes rhizosphere microecology and coordinates ion balance and host signaling to enhance potato salt tolerance. These findings support the potential of SA403 as a robust PGPR-based tool for sustainable potato production on saline soils.

Rhizosphere↗
PubMed2026

Comparison of paralog identification methods and their impact on species tree topologies in target capture phylogenomics within the Sindora clade (Detarioideae: Leguminosae).

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

Phylogeny↗
PubMed2026

Transcriptomic insights into temperature regulation of proliferation and differentiation in skeletal muscle cells of Nibea albiflora.

Myogenesis involves sequential stages of muscle satellite cell activation, myoblast proliferation, differentiation, and fusion into multinucleated myotubes. Teleost muscle exhibits indeterminate growth and is highly sensitive to environmental temperature, yet the underlying mechanisms by which temperature regulate proliferation and differentiation remain poorly understood. In this study, we established a primary skeletal muscle cell culture from the yellow drum (Nibea albiflora), an economically important marine fish, and integrated morphological observations with comparative transcriptomics analysis to characterize cellular and molecular responses at 28&#xa0;&#xb0;C and 20&#xa0;&#xb0;C during both proliferation and differentiation stages. Phenotypic analysis revealed that 28&#xa0;&#xb0;C significantly enhanced both myoblast proliferation and myogenic differentiation ability compared with 20&#xa0;&#xb0;C. Transcriptomic profiling revealed that at 28&#xa0;&#xb0;C, differentiation upregulated extracellular matrix(ECM) organization, calcium signaling, and sarcomere assembly, while proliferation enhanced focal adhesion, growth factor signaling, and lipid metabolism. At 20&#xa0;&#xb0;C, differentiation was characterized by glutathione metabolism, and ferroptosis, while proliferation involved cytokine-cytokine receptor interaction and negative regulation of signal transduction. Core myogenic regulatory factors (MRFs), particularly myogenin, were strongly upregulated at 28&#xa0;&#xb0;C during the differentiation stage, serving as an internal control. Based on these findings, we propose a testable model that elevated temperature coordinates Ca2+-dependent MRF activation with ECM-integrin signaling to drive sarcomere assembly and muscle growth. Key differentially expressed genes (DEGs) regulating myogenesis in N. albiflora were also identified. This study provides a mechanistic framework for temperature adaptation in teleost skeletal muscle and identifies candidate genes for functional validation and marker-assisted selection, as well as a rationale for temperature management strategies to improve aquaculture yield of N. albiflora.

Animals↗
PubMed2026

Distinct functions of mammalian RAD51 paralogs in genome maintenance.

RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) are evolutionarily conserved essential proteins for cell survival and genome maintenance. RAD51 paralogs were originally identified to play a role in homologous recombination-mediated repair of DNA double-strand breaks (DSBs). However, investigations over the last decade have uncovered new roles of RAD51 paralogs beyond DSB repair in replication stress responses, including replication fork progression, fork stability, and its restart. Recent structural studies have not only uncovered the molecular architecture of previously known RAD51 paralog complexes but also identified novel paralog complex assemblies, providing mechanistic insights into their various genome-maintenance functions. Additionally, a role for RAD51 paralogs in resolving R-loops has been identified, and studies with cancer-associated variants suggest that RAD51 paralogs are potential determinants of cancer susceptibility and therapeutic responses. In the present review, we highlight the recently deciphered structures and novel functions of RAD51 paralog complexes and discuss the clinical and therapeutic implications.

Rad51 Recombinase↗