Search Results (40)

Background: Fish skin mucus contains proteins involved in diverse biological pathways, representing a valuable non-invasive diagnostic of fish health. Methods: Skin mucus from three male and three female barramundi was analysed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) following protein extraction and S-Trap digestion. Results and Discussion: A total of 1801 protein groups were matched to the L. calcarifer reference proteome and functionally annotated using Gene Ontology (GO) terms via UniProt ID mapping, with representation across Biological Process, Cellular Component, and Molecular Function categories. Functional classification using eggNOG-mapper further associated leading protein group sequences with Clusters of Orthologous Groups (COGs) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. GO-based screening prioritised 352 putatively immune-relevant protein groups and 24 protein groups associated with sex- and reproduction-related processes, highlighting the functional complexity of the skin mucus proteome. Comparative analysis revealed sex-associated patterns in protein group detection and relative abundance, with differential abundance analysis identifying 244 protein groups exhibiting statistically significant differences between male and female samples. Conclusions: This study provides the first comprehensive discovery-based characterisation of the barramundi skin mucus proteome and establishes a baseline reference dataset for this aquaculture-relevant species. The findings support the utility of skin mucus proteomics for exploring immune and sex-associated molecular patterns and provide a baseline dataset for future validation studies investigating non-invasive health and reproductive monitoring. Full article

Vagococcus species have been isolated from diverse environments, including aquatic, terrestrial, food-associated, and clinical sources; however, plant- and flower-associated representatives remain poorly characterized at the genomic level. In this study, we report the complete genomic sequence and analysis of Vagococcus sp. JNUCC 83, isolated from flowers of Camellia japonica collected on Jeju Island, Republic of Korea. The genome comprises a single circular chromosome of 2,472,896 bp with a GC content of 33.5 mol% and was assembled at high depth (555.43×), resulting in a high-quality complete genome. Genome-based phylogenomic analysis using the Type (Strain) Genome Server (TYGS) showed that strain JNUCC 83 forms a distinct lineage within the genus Vagococcus. Digital DNA–DNA hybridization (dDDH) values were far below the 70% species threshold, and 16S rRNA gene-based phylogeny consistently supported its independent placement, suggesting that JNUCC 83 represents a previously undescribed genomic species. Functional annotation based on EggNOG/COG analysis indicated the enrichment of genes involved in core metabolism and genome maintenance, while antiSMASH analysis identified a terpene-precursor-type biosynthetic locus encoding a polyprenyl synthase. Overall, this study expands the genomic understanding of flower-associated Vagococcus lineages and provides a foundation for future investigations into their ecological roles and potential applications as plant-derived microbial resources. Full article

The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus. Full article

Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation. Full article

Several strains of Bifidobacterium animalis subsp. lactis are blockbusters of commercial dietary supplement cocktails, widely recognized for their probiotic properties and found in various ecological niches. The present study aimed to perform an in-depth comparative genomic analysis on 71 B. animalis subsp. lactis strains isolated from diverse sources, including human and animal feces, breast milk, fermented foods, and commercial dietary supplements, to better elucidate the strain level diversity and biotechnological potential of this species. The average genome size was found to be 1.93 ± 0.05 Mb, with a GC content of 60.45% ± 0.2, an average of 1562 ± 41.3 coding sequences (CDS), and 53.4 ± 1.6 tRNA genes. A comparative genomic analysis revealed significant genetic diversity among the strains, with a core genome analysis showing that 34.7% of the total genes were conserved, while the pan-genome remained open, indicating ongoing gene acquisition. Functional annotation through EggNOG-Mapper and CAZYme clustering highlighted diverse metabolic capabilities, particularly in carbohydrate metabolism. Nearly all (70 of 71) Bifidobacterium animalis subsp. lactis strains were found to harbor CRISPR-Cas adaptive immune systems (predominantly of the Type I-E subtype), underscoring the ubiquity of this phage defense mechanism in the species. A comparative analysis of spacer sequences revealed distinct strain-specific CRISPR profiles, with certain strains sharing identical spacers that correlate with common phylogenetic clades or similar isolation sources—an indication of exposure to the same phage populations and shared selective pressures. These findings highlight a dynamic co-evolution between B. lactis and its bacteriophages across diverse ecological niches and point to the potential of leveraging its native CRISPR-Cas systems for future biotechnological applications. Our findings enhance our understanding of the genetic and functional diversity of B. animalis subsp. lactis, providing valuable insights for its use in probiotics and functional foods. Full article

Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat’s microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat’s unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods. Full article

Soda lakes are extreme saline–alkaline environments that harbor metabolically versatile microbial communities with significant biotechnological potential. This study employed shotgun metagenomics (NovaSeq PE150) to investigate the functional diversity and metabolic potential of microbial communities in Ethiopia’s Chitu and Shala Lakes. An analysis of gene content revealed 554,609 and 525,097 unique genes in Chitu and Shala, respectively, in addition to a substantial fraction (1,253,334 genes) shared between the two, underscoring significant functional overlap. Taxonomic analysis revealed a diverse phylogenetic composition, with bacteria (89% in Chitu Lake, 92% in Shala Lake) and archaea (4% in Chitu Lake, 0.8% in Shala Lake) as the dominant domains, alongside eukaryotes and viruses. Predominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were prominent among archaea. Key genera identified in both lakes were Nitriliruptor, Halomonas, Wenzhouxiangella, Thioalkalivibrio, Aliidiomarina, Aquisalimonas, and Alkalicoccus. Functional annotation using the KEGG, eggNOG, and CAZy databases revealed that the identified unigenes were associated with various functions. Notably, genes related to amino acid, carbohydrate, and energy metabolism (KEGG levels 1–2) were predominant, indicating that conserved core metabolic functions are essential for microbial survival in extreme conditions. Higher-level pathways included quorum sensing, two-component signal transduction, and ABC transporters (KEGG level 3), facilitating environmental adaptation, stress response, and nutrient acquisition. The eggNOG annotation revealed that 13% of identified genes remain uncharacterized, representing a vast untapped reservoir of novel enzymes and biochemical pathways with potential applications in biofuels, bioremediation, and synthetic biology. This study identified 375 unique metabolic pathways, including those involved in pyruvate metabolism, xenobiotic degradation, lipid metabolism, and oxidative stress resistance, underscoring the microbial communities’ ability to thrive under fluctuating salinity and alkalinity. The presence of carbohydrate-active enzymes (CAZymes), such as glycoside hydrolases, polysaccharide lyases, and oxidoreductases, highlights their role in biomass degradation and carbon cycling. Enzymes such as alkaline proteases (Apr), lipases (Lip), and cellulases further support the lakes’ potential as sources of extremophilic biocatalysts. These findings position soda lakes as reservoirs of microbial innovation for extremophile biotechnology. Future research on unannotated genes and enzyme optimization promises sustainable solutions in bioenergy, agriculture, and environmental management. Full article

Arabica coffee, one of the most valuable crop commodities, harbors diverse microbial communities with unique genetic and functional traits that influence bean safety and final coffee quality. In Ecuador, coffee production faces challenges due to the spread of pathogenic organisms across cultivars, leading to reduced yields and compromised quality. This study employed a shotgun metagenomic approach to characterize the indigenous microbial diversity present in the cell biomass of fermented coffee cherries from three Coffea arabica varieties: Typica (Group A), Yellow Caturra (Group B), and Red Caturra (Group C), originating from the Intag Valley in northern Ecuador, at two ripe stages: green (immature fruits) and ripe (red/yellow mature fruits). Gene prediction and functional annotation were performed using multiple databases, including EggNOG, COG, KEGG, CAZy, CARD, and BacMet, to explore the potential impact of microbial communities on bean quality and safety. Metagenomic sequencing generated over 416 million high-quality reads, averaging 66 million clean reads per sample and yielding a total of 47 Gbps of data. Analysis revealed distinct differences in species abundance based on the coffee variety and ripening stage. A total of 799,658 protein-coding sequences (CDSs) were predicted, of which 205,937 genes were annotated with EggNOG, 181,723 with COG, 155,220 with KEGG, and 10,473 with CAZy. Additionally, 432 antibiotic resistance genes (ARGs) were identified using CARD, and 8974 biocide and metal resistance genes (BMRGs) were annotated with BacMet. Immature cherries exhibited enriched pathways associated with resistance to antibiotics such as fluoroquinolones, penams, rifamycin, macrolides, carbapenems, and cephalosporins. The abundance of these pathways varied with the ripening stage and variety. Furthermore, green cherries showed a significant increase in BMRGs associated with resistance to substances including hydrochloric acid, copper, nickel, hydrogen peroxide, arsenic, and zinc. Among mature cherries, Typica and Red Caturra shared similar profiles, while Yellow Caturra displayed a divergent microbial and functional profile. These study findings emphasize the interplay between microbial diversity, ripening stages, and coffee varieties, providing a foundation for innovative approaches to enhance coffee quality through microbiome management. Full article

Current sperm sexing methods are costly and largely restricted to cattle, while immunological techniques targeting sex-specific membrane proteins may offer more economical alternatives. To advance these methods, understanding the proteomic differences between the cell membranes of X- and Y-chromosome-bearing spermatozoa is essential. This study aimed to characterize the cell surface proteome of bovine sperm and identify potential targets for sperm sexing through LC-MS/MS analysis. Cell surface protein lysates were extracted from unsexed, X-sperm (BX), and Y-sperm (BY) samples via biotinylation. Promising targets were identified through functional annotation (UniProt, eggNOG-mapper v.2.1.7) and topology prediction (DeepTMHMM v.1.0.13). Additionally, statistical overrepresentation (PANTHER 18.0) and orthology analyses were performed. Excluding contaminants, 130 proteins were detected, of which 64 proteins were detected in the BX samples and not in the BY samples. Of these, five transmembrane proteins stood out as potential X-sperm targets (ADAM2, ATP11C, DG1, MCT1, and PMCA4). They were identified as potential cell surface targets, based on GO terms and topology predictions, detected in at least two replicates of the BX samples, and shown to share orthology with other livestock species. These findings enhance our understanding of bovine sperm proteomics; however, further validation is required to confirm the utility of these five proteins in sperm sexing technologies. Full article

The Loess Plateau, with a fragile ecological environment, is one of the most serious water- and soil-eroded regions in the world, which has been improved by large-scale projects involving returning farmland to forest and grassland. This work is mainly aimed at exploring a more reasonable and efficient ecological forest restoration mode and revealing synergistic restoration mechanisms. This study sampled typical Loess Plateau areas and designed the restoration modes for pure forests of Armeniaca sibirica L. (AR), Amygdalus davidiana (Carrière) de Vos ex Henry. (AM), Medicago sativa L. (MS), and mixed forests of apricot–peach–alfalfa (AR&AM&MS), using abandoned land (AL) as a control treatment. The effects of these modes on the physical and chemical properties and enzyme activities of various soils were investigated in detail. Moreover, the soil microbial diversity and community structure, functional gene diversity, and differences in the restoration modes were deeply analyzed by meta-genomic sequencing technology, and the inherent driving correlation and mechanisms among these indicators were discussed. The results showed that the soil water content and porosity of the AR, AM, and AR&AM&MS treatments increased significantly, while the bulk density decreased significantly, compared with AL. Moreover, the total carbon, total nitrogen, nitrate nitrogen, total phosphorus, available phosphorus, total potassium, and available potassium contents of the AR&AM&MS restoration mode increased significantly. Compared to CK, there was no significant change in the catalase content of pure forest and mixed forest; however, the contents of urease, phosphatase, sucrase, B-glycanase, and N-acetylglucosaminidase in the restoration mode of the mixed forest all increased significantly. The species diversity index of the restoration modes is similar, and the dominant bacteria in soil microorganisms include Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. The mixed forest restoration mode had the highest microbial abundance. The functional gene diversity of the different restoration modes was also similar, including kegg genes, eggNOG genes, and carbohydrate enzymes. The functional genes of the mixed forest restoration mode were the most abundant, and their restoration mechanism was related to the coupling effect of soil–forest grass. After evaluation, the restoration mode of mixed forest was superior to that of pure forest or pure grass. This is attributed to the fact that the mode can improve soil structure, retain soil moisture, enhance soil enzyme activity, optimize soil microbial community structure, and improve microbial diversity and functional gene activity. This provides key data for the restoration of fragile ecological areas, and the promotion of sustainable management of forests and grass in hilly areas of the Loess Plateau. Full article

Euspira gilva, a member of the family Naticidae, is predominantly found in intertidal soft mud, sandy soil, and sandy seabeds along the coast of China, where it is valued for its nutritional richness and significant economic value. This study presents a comprehensive transcriptome sequencing and analysis of E. gilva specimens from the Lianyungang area, yielding 3385 high-quality isoform sequences and 3310 non-redundant transcripts. Annotation against various databases, including NR, Swiss-Prot, KEGG, KOG, eggNOG, GO, and Pfam, successfully annotated a significant number of transcripts. A total of 7929 simple sequence repeat (SSR) loci were identified, with single nucleotide repeats predominating at 85.0%. Predictive analysis of coding DNA sequences (CDS) resulted in 1340 BLAST comparisons, while ESTScan predicted 840. Further, 530 long non-coding RNAs (lncRNAs) were identified through the application of the CPC2, CNCI, Pfam, and PLEK algorithms. The highest overall sequence similarity in the NR database was observed with Pomacea canaliculata, a freshwater species, but with a similarity of only 36.6%, indicating a unique genetic makeup of E. gilva. The KEGG database annotation revealed a predominance of signal transduction pathways, particularly the PI3K-Akt signaling pathway, with 29 non-redundant transcripts encoding key genes such as IGH (immunoglobulin heavy chain), PCK (phosphoenolpyruvate carboxykinase), COL2A (collagen, type II, alpha), ITGB1 (integrin beta 1), and GNG7 (guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7). These genes play crucial roles in cellular processes, including cell growth, transcription, translation, proliferation, movement, and glycogen metabolism. The findings of this research elucidate the full-length transcriptome profile of E. gilva, thereby establishing a foundational dataset and providing valuable insights for the species’ aquaculture, health management, conservation efforts, and future molecular biological investigations. Full article

Objective: We took advantage of a single-center cross-sectional study to investigate the effect of different drugs on intestinal microbiota and function in Crohn’s disease. Methods: We studied the difference in fecal microbiota of Crohn’s disease patients treated with mesalazine, azathioprine, and infliximab, as well as untreated patients, by metagenome and screened for differential microbiota. Further, we investigated functional differences in intestinal microbiota among the four groups. Results: Through metagenomic sequencing, we found that there was no difference between the four groups in ACE and Chao1 indices, but IFX and mesalazine improved species diversity and homogeneity compared to the untreated group, as evidenced by statistically significant differences in the Shannon index, Simpson index, and pielou_evenness. In addition, beta diversity suggested a difference between groups, but the difference was not significant. Non-parametric tests revealed differences between the four groups at the phylum level, class level, and genus level. Further analysis by LEfSe analysis revealed that the level of short-chain fatty acid-producing microbiota was increased in the treated groups, while there was no difference between the treated groups when compared to each other. Finally, the KEGG database and EggNOG database revealed that there were functional differences in intestinal microbiota among the four groups, including microbial metabolism pathway, cysteine and methionine metabolism pathway, cytoskeleton, etc. Conclusions: Mesalazine, azathioprine, and infliximab can all affect the intestinal microbiota and function in patients with Crohn’s disease, and the drugs may alleviate intestinal inflammation in patients with Crohn’s disease by modulating the intestinal microbiota. Full article

Penaeus monodon is one of the world’s most important aquaculture species, with its host-associated microbial community playing a crucial role in its growth, metabolism, immune response, and adaptation. In our study, we utilized Illumina high-throughput sequencing to investigate the composition, structure, and function of the intestinal microbial communities of P. monodon from two different regions in Guangdong. Our results identified 176 phyla across both populations, with Proteobacteria and Firmicutes being predominant. Furthermore, we identified 3095 genera, with Photobacterium, Vibrio, and Aliiroseovarius being the most dominant. Functional gene analysis based on KEGG data indicated that the carbohydrate metabolism and amino acid metabolism were significant at the secondary metabolic pathway level. The eggNOG functional annotation revealed that the genes involved in replication, recombination, and repair are of paramount importance. The CAZy annotation results indicated that Glycoside Hydrolases (GH) have the highest abundance. The Pfam annotation analysis showed that the two most prevalent domains are P-loop NTPase and NADP Rossmann. Our investigation provides a reference for species-level and functional-level analyses of the intestinal microbiota of P. monodon, contributing valuable insights into its microbial ecology. Full article

Vairimorpha (Nosema) ceranae is a single-cellular fungus that obligately infects the midgut epithelial cells of adult honeybees, causing bee microsporidiosis and jeopardizing bee health and production. This work aims to construct the full-length transcriptome of V. ceranae and conduct a relevant investigation using PacBio single-molecule real-time (SMRT) sequencing technology. Following PacBio SMRT sequencing, 41,950 circular consensus (CCS) were generated, and 25,068 full-length non-chimeric (FLNC) reads were then detected. After polishing, 4387 high-quality, full-length transcripts were gained. There are 778, 2083, 1202, 1559, 1457, 1232, 1702, and 3896 full-length transcripts that could be annotated to COG, GO, KEGG, KOG, Pfam, Swiss-Prot, eggNOG, and Nr databases, respectively. Additionally, 11 alternative splicing (AS) events occurred in 6 genes were identified, including 1 alternative 5′ splice-site and 10 intron retention. The structures of 225 annotated genes in the V. ceranae reference genome were optimized, of which 29 genes were extended at both 5′ UTR and 3′ UTR, while 90 and 106 genes were, respectively, extended at the 5′ UTR as well as 3′ UTR. Furthermore, a total of 29 high-confidence lncRNAs were obtained, including 12 sense-lncRNAs, 10 lincRNAs, and 7 antisense-lncRNAs. Taken together, the high-quality, full-length transcriptome of V. ceranae was constructed and annotated, the structures of annotated genes in the V. ceranae reference genome were improved, and abundant new genes, transcripts, and lncRNAs were discovered. Findings from this current work offer a valuable resource and a crucial foundation for molecular and omics research on V. ceranae. Full article

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3–0.8 µm in diameter and 1.5–2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with “Fibrivirga algicola JA-25” (99.2%) and Fibrella forsythia HMF5405^T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO₂ fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture. Full article