Deciphering the preservative effects of protamine from Xinjiang Coregonus peled on grass carp (Ctenopharyngodon idellus) fillets during refrigerated storage: a perspective from the microbiome.

Protamine is a natural cationic peptide which has been utilized as a food preservative, since its antibacterial capability against a wide range of Gram-negative and -positive bacteria. Despite the antibacterial mechanism has been well uncovered, its role in complex food microbial communities is largely elusive. In the present study, grass carp (Ctenopharyngodon idellus) fillets were treated with protamine and a protamine-based compound preservative, and stored at 4 °C for 15 days.

Safety and Probiotics Evaluation of Bifidobacterial Genomes Isolated from Probiotic Products.

Bifidobacterium is a common bacterium colonizing human intestines which is frequently used to produce probiotic-related products. Since the rapid development of probiotic products field over recent years, improving probiotic-related testing methods, as well as conducting systematic safety evaluations is urgently needed. Advances in sequencing technology enable clinicians to access the complete genome of bacteria more effectively via whole genome sequencing, thereby providing a solution for the safety evaluation of probiotics.

Gene print-based cell subtypes annotation of human disease across heterogeneous datasets with gPRINT.

Identification of disease-specific cell subtypes (DSCSs) has profound implications for understanding disease mechanisms, preoperative diagnosis, and precision therapy. However, achieving unified annotation of DSCSs in heterogeneous single-cell datasets remains a challenge. In this study, we developed the gPRINT algorithm (generalized approach for cell subtype identification with single cell's voicePRINT).

Human Hair Follicle Mesenchymal Stem Cell-Derived Exosomes Attenuate UVB-Induced Photoaging via the miR-125b-5p/TGF-β1/Smad Axis.

Cutaneous photoaging, induced by chronic exposure to ultraviolet (UV) radiation, typically manifests as alterations in both the physical appearance and functional properties of the skin and may predispose individuals to cancer development. Recent studies have demonstrated the reparative potential of exosomes derived from mesenchymal stem cells in addressing skin damage, while specific reports highlight their efficacy in ameliorating skin photoaging. However, the precise role of exosomes derived from human hair follicle mesenchymal stem cells (HFMSC-Exos) in the context of cutaneous photoaging remains largely unexplored.

Spatial distribution of maternal factors in pig mature oocytes.

It is known that asymmetrical maternal transcripts play an important role in the cell fate of the early embryo, but few studies are available in mammal oocytes especially in pig. To investigate the spatial factors in pig oocytes, the oriented bisection was established for collecting karyoplasts (NSOs) and cytoplasts (SSOs) with more than 95% efficiency. Subsequently, RNA-Seq and LC-MS/MS analysis were performed on NSOs and SSOs.

Alterations of the bile microbiome is associated with progression-free survival in pancreatic ductal adenocarcinoma patients.

Background: Patients with pancreatic ductal adenocarcinoma (PDAC) display an altered oral, gastrointestinal, and intra-pancreatic microbiome compared to healthy individuals. However, knowledge regarding the bile microbiome and its potential impact on progression-free survival in PDACs remains limited.

Methods: Patients with PDAC (n = 45), including 20 matched pairs before and after surgery, and benign controls (n = 16) were included prospectively.

Vaginal microbial profile of cervical cancer patients receiving chemoradiotherapy: the potential involvement of Lactobacillus iners in recurrence.

The vaginal microbiome is an immune defense against reproductive diseases and can serve as an important biomarker for cervical cancer. However, the intrinsic relationship between the recurrence and the vaginal microbiome in patients with cervical cancer before and after concurrent chemoradiotherapy is poorly understood. Here, we analyzed 125 vaginal microbial profiles from a patient cohort of stage IB-IVB cervical cancer using 16S metagenomic sequencing and deciphered the microbial composition and functional characteristics of the recurrent and non-recurrent both before and after chemoradiotherapy.

Global biogeography of microbes driving ocean ecological status under climate change.

Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography.

Effects of different assembly strategies on gene annotation in activated sludge.

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture.

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g.

Phages in different habitats and their ability to carry antibiotic resistance genes.

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks.

Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats.

Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern.

Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.

The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats.

Gravity-driven and rotation-controlled microfluidic chip for point-of-care nucleic acid detection in the fully closed environment.

Point-of-care nucleic acid detection is essential for diagnosis and food safety, especially in resource-limited areas. This study reports a gravity-driven and rotation-controlled (GR) chip-coupled lateral flow-based assay (LFA) for point-of-care nucleic acid detection. The sample solution is added to the inlet of the GR chip and flows into the loop-medicated isothermal amplification (LAMP) chamber by the action of gravity.

Effects of dietary supplement with licorice and rutin mixture on production performance, egg quality, antioxidant capacity, and gut microbiota in quails (Turnix tanki).

This study was conducted to evaluate the effect of licorice and rutin on production performance, egg quality, and mucosa antioxidant levels in Chinese yellow quail. A total of 240 Chinese Yellow Quail (400-day-old) were randomly distributed into 5 groups: the Control group, fed with a basic diet; the LR1 group, fed with basal diet supplemented with 300 + 100 mg licorice and rutin mixture/kg diet; the LR2 group, fed with basal diet supplemented with 300 + 200 mg licorice and rutin mixture/kg diet; the LR3 group, fed with basal diet supplemented with 600 + 100 mg licorice and rutin mixture/kg diet and the LR4 group, fed with basal diet supplemented with 600 + 200 mg licorice and rutin mixture/kg diet. Compared with the control, supplementation with the licorice and rutin mixture improved the laying rate and eggshell thickness whereas decreased the feed conversion ratio of quails.

A global atlas of marine antibiotic resistance genes and their expression.

Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans.

Proteomics reveals the underlying mechanism by which the first uneven division affects embryonic development in pig.

One of the most typical abnormal cleavage patterns during early embryonic development is uneven division, but the first uneven division of pig zygote is common. Uneven division results in different daughter cell sizes and an uneven distribution of organelles such as lipid droplet, mitochondria, but the developmental capacity of daughter cells and proteomic changes of daughter cells are still unclear. Therefore, the developmental ability and proteomic quantification were investigated on blastomeres from even division (ED) or uneven division (UD) embryos at 2-cell stage in the present study.

Epigenetic Iinsights into the Senescence of Porcine Fetal Fibroblasts induced by Passaging.

Epigenetic status of fetal fibroblasts (FFs) is one of the crucial factors accounted for the success of somatic cell nuclear transfer and gene editing, which might inevitably be affected by passaging. But few systematic studies have been performed on the epigenetic status of passaged aging cells. Therefore, FFs from large white pig were passaged to the 5, 10, and 15 (F5, F10, and F15) passages in the present study to investigate the potential alteration of epigenetic status.

Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.

Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents.

Dietary cysteine drives body fat loss via FMRFamide signaling in Drosophila and mouse.

Obesity imposes a global health threat and calls for safe and effective therapeutic options. Here, we found that protein-rich diet significantly reduced body fat storage in fruit flies, which was largely attributed to dietary cysteine intake. Mechanistically, dietary cysteine increased the production of a neuropeptide FMRFamide (FMRFa).

Global distribution of marine microplastics and potential for biodegradation.

Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea.

Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.).

The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice.