A novel extracellular mannan from Bacillus velezensis ameliorates metabolic-associated fatty liver disease by modulating gut microbiota in mice model.

Metabolic associated fatty liver disease (MAFLD) is a globally recognized chronic metabolic disorder characterized by lipid metabolism abnormalities. Accumulating evidence indicates that exopolysaccharides (EPS) could modulate the gut microbiota structure and function to prevent and treat MAFLD. Herein, a novel EPS designated BVP1 was isolated from Bacillus velezensis CGMCC 24752.

Soyasaponin and vertical microbial transmission: Maternal effect on the intestinal development and health of early chicks.

Multiple factors, including genetics, nutrition, and health, influence the vertical transmission of microbiota from mothers to their offspring. Recent studies have shown that avian microbiota can be passed to the next generation via the eggshell and egg albumen. However, it remains unclear whether these microbial communities are regulated by nutrition and how they are associated with the host genotype.

Genomic landscape and immunological profile of glioblastoma in East Asian patients.

Glioblastoma multiforme (GBM) shows profound inter- and intratumoral heterogeneity, but differences across ancestries remain understudied. We assemble the largest cohort of GBMs from East Asian patients (EAS-GBM) and perform genomic and transcriptomic analyses. Transcriptomic clustering reveals distinct EAS-GBM molecular subtypes-proliferative (PL), neurosynaptic (NS), metabolic (MB), and immunomodulatory (IM)-based on activated biological pathways.

Overall assessment of antimicrobial peptides in broiler chickens: A meta-analysis.

Antimicrobial peptides (AMPs) are considered promising alternatives to traditional antibiotics for promoting growth and reducing disease incidence in livestock. However, the effects of AMP additives on broiler chickens remain uncertain. Here, we performed a meta-analysis of 43 studies published from January 2000 to January 2024 to evaluate the effects of AMPs on growth performance, intestinal morphology, and immune organ development in broiler chickens.

Emerging epidemic of the predominant clusters of FC428-like Neisseria gonorrhoeae in Guangdong, China.

Objectives: This study aimed to investigate the molecular characteristics of predominant epidemic clusters of FC428-like N. gonorrhoeae in Guangdong, China in 2022.

Methods: Minimum inhibitory concentrations (MICs) were determined for N.

Effects of a new compound probiotic on growth performance, antioxidant capacity, intestinal health, gut microbiota and metabolites of broilers.

Compound probiotics have gained increasing recognition as feed additives for improving feed conversion ratio and intestinal health of broilers. Two Lactobacillus strains (Ligilactobacillus salivarius CML391 and Limosilactobacillus reuteri CML393) and two Bacillus strains (Bacillus velezensis CML396 and Bacillus paralicheniformis CML399) were isolated from broiler intestines and combined to form a new compound probiotic (referred to as "CML compound probiotic"). The effects of CML compound probiotic on broiler growth performance, antioxidant capacity, intestinal health, cecal microbiota, and microbial-derived metabolites were assessed in this study.

Accurate Transcription Factor Activity Inference to Decipher Cell Identity from Single-Cell Transcriptomic Data with MetaTF.

Cellular heterogeneity within cancer tissues determines cancer progression and treatment response. Single-cell RNA sequencing (scRNA-seq) has provided a powerful approach for investigating the cellular heterogeneity of both cancer cells and stroma cells in the tumor microenvironment. However, the common practice to characterize cell identity based on the similarity of their gene expression profiles may not really indicate distinct cellular populations with unique roles.

A global atlas and drivers of antimicrobial resistance in Salmonella during 1900-2023.

Although previous studies using phenotypic or/and genomic approaches monitoring have revealed the spatiotemporal distribution of antimicrobial resistance (AMR) in Salmonella in local areas, their geographical patterns and driving factors remain largely unknown at a global scale. Here, we performed an analysis of publicly available data of 208,233 Salmonella genomes in 148 countries/regions between 1900 and 2023 and explored driving indicators of AMR. Overall, we found that the geographic distribution of AMR varied depending on the location, source, and serovar.

Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.

Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota.

Deep learning-driven survival prediction in pan-cancer studies by integrating multimodal histology-genomic data.

Accurate cancer prognosis is essential for personalized clinical management, guiding treatment strategies and predicting patient survival. Conventional methods, which depend on the subjective evaluation of histopathological features, exhibit significant inter-observer variability and limited predictive power. To overcome these limitations, we developed cross-attention transformer-based multimodal fusion network (CATfusion), a deep learning framework that integrates multimodal histology-genomic data for comprehensive cancer survival prediction.

Integrated genetic analysis and single cell-RNA sequencing for brain image-derived phenotypes and Parkinson's disease.

Background: Previous studies have reported Parkinson's disease (PD) patients usually have changes in brain image-derived phenotypes (IDPs). However, the role of genetic factors in their association and biological mechanism remains unclear. We aimed to unveil genetic and biological links between brain IDPs and PD.

The multi-kingdom microbiome catalog of the chicken gastrointestinal tract.

Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries.

Biological Data Resources and Machine Learning Frameworks for Hematology Research.

Hematology research has greatly benefited from the integration of diverse biological data resources and advanced machine learning (ML) frameworks. This integration has not only deepened our understanding of blood diseases such as leukemia and lymphoma, but also enhanced diagnostic accuracy and personalized treatment strategies. By applying ML algorithms to analyze large-scale biological data, researchers can more effectively identify disease patterns, predict treatment responses, and provide new perspectives for the diagnosis and treatment of hematologic disorders.

Regional antimicrobial resistance gene flow among the One Health sectors in China.

Background: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

Results: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples.

Anaerostipes caccae CML199 enhances bone development and counteracts aging-induced bone loss through the butyrate-driven gut-bone axis: the chicken model.

Background: The gut microbiota is a key regulator of bone metabolism. Investigating the relationship between the gut microbiota and bone remodeling has revealed new avenues for the treatment of bone-related disorders. Despite significant progress in understanding gut microbiota-bone interactions in mammals, research on avian species remains limited.

The effect of Lonicerae flos and Rhizoma curcumae longae extract on the intestinal development and function of broilers.

This study was conducted to explore effects of Lonicerae flos and Rhomoma curcumae longae extracts (LR) on intestinal function of broilers. Three hundred broiler chickens were randomly assigned to the following 5 groups. The control group were fed the basal diet; the antibiotic group were fed the basal diet supplemented with spectinomycin hydrochloride (50 million units/ton) + lincomycin hydrochloride (25 g/ton); the LRH, LRM and LRL groups were fed the basal diet supplemented with a high dose (750 g/ton of feed), normal dose (500 g/ton of feed), or low dose (250 g/ton of feed) of LR, respectively.

Bispecific antibodies targeting two glycoproteins on SFTSV exhibit synergistic neutralization and protection in a mouse model.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with a high fatality rate of up to 30% caused by SFTS virus (SFTSV). However, no specific vaccine or antiviral therapy has been approved for clinical use. To develop an effective treatment, we isolated a panel of human monoclonal antibodies (mAbs).

A New Strain CML532 Improves Chicken Growth Performance and Reduces Intestinal Colonization.

has gained increasing recognition as a probiotic for improving animal growth performance and gut health. We identified six strains from sixty isolates that were isolated from the cecal samples of fifteen different chicken breeds. We characterized the probiotic properties of these six strains.

RIscoper 2.0: A deep learning tool to extract RNA biomedical relation sentences from literature.

RNA plays an extensive role in a multi-dimensional regulatory system, and its biomedical relationships are scattered across numerous biological studies. However, text mining works dedicated to the extraction of RNA biomedical relations remain limited. In this study, we established a comprehensive and reliable corpus of RNA biomedical relations, recruiting over 30,000 sentences manually curated from more than 15,000 biomedical literature.

Dynamic pathological analysis reveals a protective role against skin fibrosis for TREM2-dependent macrophages.

Systemic sclerosis (SSc) is a chronic and incurable autoimmune disease with high mortality rates, and skin fibrosis is one of distinguishing hallmarks in the pathogenesis. However, macrophage heterogeneity regulating skin fibrosis remain largely unknown. We established mouse disease model and performed single-cell RNA-sequencing (scRNA-seq) to resolve the dynamic and heterogenous characteristics of macrophages in skin fibrosis, and the role of TREM2-dependent macrophages in the pathological process was investigated using knockout mice and intraperitoneal transferring TREM2 macrophages combining with functional assays.

Enzymatically prepared neoagarooligosaccharides improve gut health and function through promoting the production of spermidine by Faecalibacterium in chickens.

Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated.

Integrated multi-omics reveals the roles of cecal microbiota and its derived bacterial consortium in promoting chicken growth.

The improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis.

Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid.

Accumulated evidence supports the beneficial role of inulin in alleviating metabolic dysfunction-associated fatty liver disease (MAFLD) by modulating gut microbiota. However, the underlying mechanisms are not fully understood. Here we used high-fat diet (HFD)-induced laying hen model of MAFLD to investigate the effect of inulin on ameliorating MAFLD and found that the inulin-enriched Megamonas genus was inversely correlated with hepatic steatosis-related parameters.