Exploring the Prebiotic Potential of Fermented Astragalus Polysaccharides on Gut Microbiota Regulation In Vitro.

Astragalus polysaccharides (APS) are known for their prebiotic properties, and fermentation by probiotics is a promising strategy to enhance the prebiotic activity of polysaccharides. In this study, Lactobacillus rhamnosus was used to ferment APS, and response surface methodology was applied to optimize the fermentation parameters. The optimal conditions were determined as follows: 10.

MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality.

The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow.

A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau.

The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated.

Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model.

Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability.

Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.

Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns.

Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine.

Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM.

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis.

Background: Infectious diseases have caused huge economic loss and food security issues in fish aquaculture. Current management and breeding strategies heavily rely on the knowledge of regulative mechanisms underlying disease resistance. Though the intestinal microbial community was linked with disease infection, there is little knowledge about the roles of intestinal microbes in fish disease resistance.

Limosilactobacillus fermentum-fermented ginseng improved antibiotic-induced diarrhoea and the gut microbiota profiles of rats.

Aims: This study investigated the efficacy of Limosilactobacillus fermentum-fermented ginseng for improving colitis and the gut microbiota profiles in rats and explored the benefits of the L. fermentum fermentation process to ginseng.

Methods And Results: Ginseng polysaccharide and ginsenoside from fermented ginseng were analysed by UV and HPLC.

TCM-Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis.

DNA-based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM.

-fermented ameliorate diabetic nephropathy in mice by modulating the gut microbiota.

The occurrence and development of diabetic nephropathy (DN) are closely related to gut microbiota. is a medicinal and edible fungus. is a therapeutic material for unifying Chinese Qi.

Microbial Dark Matter: from Discovery to Applications.

With the rapid increase of the microbiome samples and sequencing data, more and more knowledge about microbial communities has been gained. However, there is still much more to learn about microbial communities, including billions of novel species and genes, as well as countless spatiotemporal dynamic patterns within the microbial communities, which together form the microbial dark matter. In this work, we summarized the dark matter in microbiome research and reviewed current data mining methods, especially artificial intelligence (AI) methods, for different types of knowledge discovery from microbial dark matter.

Microbiome Resilience and Health Implications for People in Half-Year Travel.

Travel entail change in geography and diet, both of which are known as determinant factors in shaping the human gut microbiome. Additionally, altered gut microbiome modulates immunity, bringing about health implications in humans. To explore the effects of the mid-term travel on the gut microbiome, we generated 16S rRNA gene and metagenomic sequencing data from longitudinal samples collected over six months.

How much metagenome data is needed for protein structure prediction: The advantages of targeted approach from the ecological and evolutionary perspectives.

It has been proven that three-dimensional protein structures could be modeled by supplementing homologous sequences with metagenome sequences. Even though a large volume of metagenome data is utilized for such purposes, a significant proportion of proteins remain unsolved. In this review, we focus on identifying ecological and evolutionary patterns in metagenome data, decoding the complicated relationships of these patterns with protein structures, and investigating how these patterns can be effectively used to improve protein structure prediction.

Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome.

Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists.

The ncRNA-Mediated Overexpression of Ferroptosis-Related Gene EMC2 Correlates With Poor Prognosis and Tumor Immune Infiltration in Breast Cancer.

Ferroptosis is an iron-dependent programmed cell death process. Although ferroptosis inducers hold promising potential in the treatment of breast cancer, the specific role and mechanism of the ferroptosis-related gene in breast cancer have not been entirely determined. The potential roles of in different tumors were explored based on The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Gene Expression Profiling Interactive Analysis 2 (GEPIA2), Tumor Immune Estimation Resource (TIMER), Shiny Methylation Analysis Resource Tool (SMART), starBase, and cBioPortal for cancer genomics (cBioPortal) datasets.

Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome.

Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites.

Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.

Information derived from metagenome sequences through deep-learning techniques has significantly improved the accuracy of template free protein structure modeling. However, most of the deep learning-based modeling studies are based on blind sequence database searches and suffer from low efficiency in computational resource utilization and model construction, especially when the sequence library becomes prohibitively large. We proposed a MetaSource model built on 4.

Reliable and Interpretable Mortality Prediction With Strong Foresight in COVID-19 Patients: An International Study From China and Germany.

Cohort-independent robust mortality prediction model in patients with COVID-19 infection is not yet established. To build up a reliable, interpretable mortality prediction model with strong foresight, we have performed an international, bi-institutional study from China (Wuhan cohort, collected from January to March) and Germany (Würzburg cohort, collected from March to September). A Random Forest-based machine learning approach was applied to 1,352 patients from the Wuhan cohort, generating a mortality prediction model based on their clinical features.

Monascus ruber fermented Panax ginseng ameliorates lipid metabolism disorders and modulate gut microbiota in rats fed a high-fat diet.

Ethnopharmacological Relevance: Ginseng (Panax ginseng Meyer) is rich in a variety of biologically active ingredients, which shows good effect in the treatment of metabolic diseases. Monascus has lipid-lowering activity and one of its metabolites, lovastatin, is widely used in clinical practice.

Aim Of The Study: The main purpose of this study was to clarify the effects of fermented Panax ginseng by Monascus ruber (PM) on lipid metabolism and gut microbiota in rats fed a high-fat diet.

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.

Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.

Stratification of athletes' gut microbiota: the multifaceted hubs associated with dietary factors, physical characteristics and performance.

Gut microbial communities of athletes differ from that of sedentary persons in both diversity and the presence of certain taxa. However, it is unclear to what degree elite athletes and non-elite athletes harbor different gut microbial community patterns and if we can effectively monitor the potential of athletes based on microbiota. A team of professional female rowing athletes in China was recruited and 306 fecal samples were collected from 19 individuals, which were separated into three cohorts: adult elite athlete's (AE), youth elite athlete's (YE), and youth non-elite athlete's (YN).

Effects of fermented ginseng on the gut microbiota and immunity of rats with antibiotic-associated diarrhea.

Ethnopharmacological Relevance: Ginseng (Panax ginseng Meyer) is a well-known herb in traditional Chinese medicine and has been used to treat many diseases for thousands of years. Recent studies have shown that ginseng is a promising agent for improving the gut microbiota and treating ulcerative colitis. Fermentation is a common process in traditional Chinese medicine making that can be used to enhance efficacy and reduce toxicity.

Paecilomyces cicadae-fermented Radix astragali activates podocyte autophagy by attenuating PI3K/AKT/mTOR pathways to protect against diabetic nephropathy in mice.

Radix astragali, a medicinal material for tonifying Chinese Qi, has widely been used for the treatment of Kidney disease in China and East Asia, especially in reducing the apoptosis of glomerular podocytes. Paecilomyces Cicadidae is a medicinal and edible fungus. In recent years, the application of traditional Chinese medicine (TCM) in solid-state fermentation of edible and medicinal fungi has become a hot issue.

Multiscale study on the enhancing effect and mechanism of borneolum on transdermal permeation of drugs with different log P values and molecular sizes.

D-borneolum is commonly used as a permeation enhancer in Traditional Chinese Medicine (TCM) formulas for transdermal application. Additionally, two other sources of borneolums were recorded in the 2015 edition of the Chinese Pharmacopoeia (ChP), including L-borneolum and borneolum syntheticum. To guide the selection and application of borneolum, the safety and enhancing effect of three sources of borneolums were investigated on transdermal permeation of compounds with different octanol-water partition coefficient (log P) values and molecular weights (MWs).

Analysis of chemical constituents and six compounds in Qu-feng-sheng-shi Granules via HPLC-ESI-Q/TOF-MS and HPLC-UV technique.

Qu-feng-sheng-shi Granules (QFSSG), a common prescription for the treatment of chronic inflammation and allergic rhinitis, is widely used in the clinic as a traditional Chinese medicine. Chemical analysis and quality control studies of this formulation are relatively limited compared with pharmacological studies. In this study, a high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (HPLC-ESI-Q/TOF-MS ) was used to identify the components in this prescription.