On April 25, we interpreted 15 articles, focusing on: gut-liver axis, macrophages, colorectal cancer models, intestinal bacteria metabolism, post-COVID sequelae, bioinformatics tools, metagenomics, probiotics, traditional Chinese medicine, Xingsai Biologics, Shanghai Medicine, Huadong Medicine, Palisade, Strand Life Sciences.
The daily newspaper was published by R. AI-assisted creation generation, manual review and proofreading.
Nature：肠菌诱导一类肝门静脉免疫细胞，抑制肝脏炎症
Nature——[64.8]
(1) This study found that there is a class of macrophages in the periportal region (PV) of the liver, which can inhibit hyperinflammation of the liver driven by commensal bacteria, and the failure of this self-limiting system can exacerbate liver inflammatory diseases; In vivo imaging showed that the inflammatory response in the PV region was inhibited, and single-cell transcriptomics revealed that a subset of immunosuppressive macrophages (MP2) was enriched in this region, which was highly expressed by the anti-inflammatory cytokine IL-10 and the scavenger receptor Marco (which sequesters pro-inflammatory pathogen-associated molecular patterns and damage-associated molecular patterns) ;(3) The induction of MP2 is dependent on the intestinal flora, especially Odoribacteraceae, which induces MP2 by producing the bile acid metabolite isoallo-LCA;(4) In mice, intestinal barrier leakage leads to inflammation in the PV region, which is exacerbated by Marco deficiency and promotes chronic liver inflammatory diseases such as colitis-associated primary sclerosing cholangitis (PSC) and nonalcoholic steatohepatitis (NASH) ;(5) In patients with PSC and NASH, the number of MP2 decreases.
【Original Information】
Periportal macrophages protect against commensal-driven liver inflammation
2024-04-24 , doi: 10.1038/s41586-024-07372-6
Nature: Using a new "mini colon" to study colorectal cancer in depth
Nature——[64.8]
(1) In this study, an ex vivo mini-colon model was developed that can be used to study the tumorigenesis of colorectal cancer (CRC) and its environmental determinants, bridging the gap between existing in vitro and in vivo models, (2) a mini-colon model with physiological structures such as crypts and intestinal lumen was constructed through scaffold-guided organoid tissue engineering techniques, and (3) the system can be passed by drugs+Blue light irradiation controls the activation of oncogenes at the spatiotemporal level, thereby reproducing the process of CRC tumorigenesis in vitro and enabling real-time tracking of induced tumors at single-cell resolution for weeks without breaking the culture;(4) These induced minicolons exhibit rich intra- and intertumoral diversity and reproduce key pathophysiological features of CRC in vivo;(5) By fine-tuning cellular intrinsic and non-intrinsic parameters, minicolons can be used to identify carcinogenic determinants (such as bacterial metabolites and dietary components) and for drug research.
【Original Information】
Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo
2024-04-24 , doi: 10.1038/s41586-024-07330-2
Guo Chunjun's team Cell sub-journal: analysis of the effect of intestinal bacteria amino acid metabolism on host nutritional balance and physiology
Cell Host and Microbe——[30.3]
(1) The team of Chunjun Guo from Weill Cornell Medical School of Cornell University in the United States revealed how intestinal microbes affect the nutritional balance and physiological function of the host by metabolizing amino acids;(2) developed a high-throughput in vitro live bacteria detection method based on metabolomics, and identified the intestinal microbes that can efficiently use amino acids by screening 104 kinds of intestinal commensal bacteria;(3) identified multiple genes responsible for amino acid metabolism in different phylogenic gut microbes through genetic manipulation;(4) By transplanting wild-type strains and strains lacking homologous mutants of a single amino acid metabolism gene into germ-free mice, it was found that these gut microbial genes affect the host by regulating amino acid availability in the gut and blood;(5) branched-chain amino acid and tryptophan metabolism genes in gut microbes indirectly affect the glucose homeostasis of the host through peripheral serotonin;(6) this study provides new insights into how the metabolic activities encoded by microorganisms affect host nutrient balance, and provides a research avenue for improving human health.
【Original Information】
Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology
2024-04-23 , doi: 10.1016/j.chom.2024.04.004
Huang Xiujuan's team Cell sub-journal: The association between intestinal microbiota and different post-COVID sequelae
Cell Host and Microbe——[30.3]
(1) Huang Xiujuan of the University of Chinese Hong Kong published a study to explore the association between the gut microbiome and various phenotypic manifestations of PACS by characterizing the intestinal bacteria of patients with post-COVID-19 acute syndrome (PACS); (2) The heterogeneity of gut microbiota and PACS was closely related, and three types of gut microbiota associated with different phenotypic manifestations of PACS were identified;(3) A multi-label machine learning model based on microbiome was constructed, which could accurately predict the specific symptoms of PACS patients with an accuracy of 89% , with a sensitivity of 86% and a specificity of 82% for future symptoms ;(4) This study shows that the gut microbiome is associated with the phenotypic manifestations of PACS, which has potential clinical application value and can be used for the prediction and diagnosis of PACS.
【Original Information】
The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome
2024-04-23 , doi: 10.1016/j.chom.2024.04.005
Nature: New metagenomic tools improve read annotation accuracy and sensitivity
Nature Communications——[16.6]
(1) the development of a new metagenomic analysis tool, RAT, to improve the annotation accuracy and sensitivity of metagenomic reads by integrating robust classification signals from metagenomic assembly genomes (MAGs) and contigs; (2) RAT can annotate a large number of metagenomic reads in highly diverse groundwater samples, enabling the identification of new taxa at a high taxonomic level;(3) The RAT has demonstrated greater precision and sensitivity in reconstructing taxonomic information than other advanced tools;(4) The integrated analysis of the RAT, which provides an accurate and comprehensive view of the microbiome from metagenomic sequencing data, is now GTDB annotated and available on GitHub.
【Original Information】
Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes
2024-04-20 , doi: 10.1038/s41467-024-47155-1
Benchmark virus identification tools with metagenomic data across biomes
Genome Biology——[12.3]
(1) independent benchmarking of actual metagenomic data provides objective guidance for the selection of virus identification tools and parameter tuning;(2) performance comparison of nine advanced virus identification tools in thirteen modes on eight viral and microbial datasets for three different biomes;(3) PPR-Meta performs best at distinguishing between viral and microbial sequences, followed by DeepVirFinder, VirSorter2, and VIBRANT;(4) All tools except Sourmash were able to identify unique virus sequences, and the performance of the tools was improved by adjusting the parameter thresholds;(5) The results of this study suggest that adjusting the parameter thresholds before use is an effective strategy to improve the performance of virus identification tools.
【Original Information】
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
2024-04-15 , doi: 10.1186/s13059-024-03236-4
Evaluate and improve bacterial recognition in long-read metagenomic assembly
Genome Biology——[12.3]
(1) k-mer and 16S RNA-based methods were proposed to assess and improve the integrity of bacterial content in metagenomic assembly; (2) abundant species were often unable to assemble even with PacBio high-fidelity reading technology, as high strain diversity could lead to fragmented contigs; (3) a novel reference-free sequence-free algorithm was developed to recover rich metagenomic assembly genomes (MAGs) by identifying circular assembly subgraphs;(4) Combined with the dimensionality-reduction-based non-reference genome boxing heuristic, it is possible to salvage many of the abundant species that would be lost using existing methods and to rival state-of-the-art assembly box methods in terms of the total number of near-intact genome bindings.
【Original Information】
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies
2024-04-11 , doi: 10.1186/s13059-024-03234-6
Fang Zhencheng + Zhou Hongwei et al.: MetaProbiotics, a new tool for mining probiotics from metagenomic binning data
Briefings in Bioinformatics——[9.5]
(1) Zhencheng Fang and Hongwei Zhou from Zhujiang Hospital, Southern Medical University, developed a metaProbiotics tool that uses a word vector language model to characterize DNA sequences, and uses a random forest algorithm to quickly identify bins derived from probiotics from metagenomic data, and demonstrates superior performance in the simulated benchmark dataset; MetaProbiotics was able to better identify bins with probiotic properties when testing using the gut metagenomes of individuals who received probiotic interventions, including a plasmid-like bins that showed synergistic probiotic functions with the intervention strains;(3) Gene function analysis showed that the probiotic bins identified by metaProbiotics had multiple probiotic mechanisms, and the bai operon was a potential key marker for some of the beneficial Rumen coccidae family;(4) (5) Large-scale probiotic analysis using metaProbiotics has shown that the functional integrity of probiotic communities is more critical in maintaining gut homeostasis than merely increasing the abundance of specific genes, and that blind addition of probiotics may not promote health due to the heterogeneous effects of different gene modules on the same probiotic on various diseases.
【Original Information】
metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model
2024-03-14 , Yogurt: 10.1093/Bib/BBAE085
Northern TCM: A database of the interaction between microbiota and TCM – MicrobeTCM
Pharmacological Research——[9.3]
(1) Hua Qian and Chen Jianxin of Beijing University of Chinese Medicine and their team published research to develop a comprehensive TCM microbiome database, MicrobeTCM, which aims to accelerate TCM research and address the connection between traditional medicine and microecosystems;(2) Identify literature through standardized search strategies to achieve a repeatable process, and identify 419 experimental articles from PubMed and six authoritative databases, achieving high-quality data integration and reducing the uncertainty of natural language extraction;(3) Using drug similarity, Target entity similarity and known drug-target entity associations enable prediction of the effect of new TCM or acupuncture point prescriptions;(4) Overall, MicrobeTCM includes 171 diseases, 725 microorganisms, 1,468 herbal formulas, 1,032 herbs, 15,780 chemical components, 35 acupuncture point formulas, and 77 acupuncture points. (5) MicrobeTCM provides a comprehensive microecological database for TCM research, which is expected to promote the research and application of TCM and microecosystem.
【Original Information】
MicrobeTCM: a comprehensive platform for the interactions of microbiota and traditional Chinese medicine
2024-01-23 , doi: 10.1016/j.phrs.2024.107080
Luqi Huang/Yongxin Liu/Tongtong Chen: EVenn, the most complete visualization of Wayne Diagram and Set Diagram Tool, User Manual
iMeta——[0]
(1) Huang Luqi and Chen Tong of the China Academy of Chinese Medical Sciences and Liu Yongxin and their team from the Shenzhen Institute of Genomics, Chinese Academy of Agricultural Sciences, published an article outlining the various applications of EVenn;(2) Comprehensive Wayne Functions: EVenn provides a unified platform that includes a variety of Wayne graph tools, from interactive graphs to network diagrams, to meet the complex needs of multi-omics data analysis such as metabolomics, genomics, transcriptomics, and proteomics;(3) Efficient Data Exploration: EVenn's data centers support standardized data formats, simplifying the process of uploading and analyzing data. (4) User-friendly interface: EVenn has an easy-to-use interface that simplifies the generation process of various Venn diagrams, Euler diagrams, and UpSet diagrams. EVenn is a useful tool for researchers to interpret multi-omics data.
【Original Information】
Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams
2024-04-11 , doi: 10.1002/imt2.184
Biotech company Star Biotech announced the completion of its strategic financing
(1) Recently, Xingsai Biopharma announced the completion of strategic financing and introduced Moutai Science and Technology Innovation (Beijing) Investment Fund Partnership (Limited Partnership) (hereinafter referred to as "Moutai Fund") as a strategic investor;(2) This round of financing will deepen the industrial cooperation of Xingsai Biotech in the field of liquor brewing, accelerate the application of its "Raman group" technology and series products in the industrial end, and promote the development of single-cell Raman analysis-sorting-sequencing-culture solutions; (3) Xingsai Biopharma focuses on the field of single-cell analysis and sorting, aiming to promote the development of "Raman group" The technology probes the "heterogeneity" of cellular metabolic functions and provides a "panoramic" perspective of single-cell precision correlation for single-cell multiomics research;(4) Previously, Kweichow Moutai Co., Ltd. has participated in the 2022 National Key R&D Program "Basic Scientific Research Conditions and Major Scientific Instruments and Equipment R&D" project hosted by Xingsai Biotech to jointly promote the application of single-cell Raman technology in the solid-state fermentation process.
【Original Information】
Xingsai Biotech completed strategic financing, led by Moutai Fund
2024-04-23 , Star Race Biotech
The clinical trial application of Shanghai Pharmaceutical Xinyi WST03 live bacteria was accepted
(1) Recently, the clinical trial application of WST03 live bacteria drug developed by Shanghai Pharmaceutical Xinyi Pharmaceutical Co., Ltd. was accepted by the State Food and Drug Administration;(2) WST03 is a live vaginal microecological drug in the form of a capsule preparation, which is intended to be used for the treatment of bacterial vaginosis (BV);(3) Preclinical studies have shown that WST03 can effectively treat BV and prevent its recurrence, and Shanghai Pharmaceutical Xinyi has complete intellectual property rights for the drug;(4) At present, there is no microecological live bacteria drug with the same strain composition on the market in the world.
【Original Information】
Shanghai Pharmaceutical's clinical trial application for WST03 preparation was accepted
2024-04-23 , Shanghai Pharmaceutical
Shanghai Children's Hospital signed a contract with Shanghai Pharmaceutical Xinyi to establish the Children's Microecological Medicine Research Center
(1) On April 22, Shanghai Children's Hospital and Shanghai Pharmaceutical Xinyi signed a cooperation agreement to jointly establish the Children's Microecological Medicine Research Center;(2) The research center aims to promote the scientific research and innovation of pediatric microecological medicine, especially in the field of pediatric intestinal bacteria transplantation;(3) The two parties will integrate resources, expand the children's strain bank, and promote the clinical application and efficacy research of pediatric intestinal bacteria transplantation;(4) In addition, the construction of platforms such as the Microecological Innovative Drug Transformation Center will promote the clinical transformation of scientific research results and strengthen the in-depth cooperation between the two sides.
【Original Information】
Shanghai Children's Hospital signed a contract with Shanghai Pharmaceutical Xinyi to establish the Children's Microecological Medicine Research Center
2024-04-23 , Shanghai Pharmaceutical
The Phase 1 clinical trial of Huadong Medicine's HDM1005 injection was approved by the FDA
(1) On April 22, Huadong Pharmaceutical announced that its subsidiary, Hangzhou Zhongmei Huadong Pharmaceutical, had obtained FDA approval for its HDM1005 injection and would conduct phase 1 clinical trials;(2) HDM1005 injection is a new class of chemical drugs, and Huadong Medicine has global intellectual property rights for weight management in adults who are overweight or obese;(3) HDM1005 can promote insulin release, suppress appetite, improve glucose tolerance, and exert significant hypoglycemic and weight-loss effects by activating GLP-1 receptors and GIP receptors;(4) HDM1005 clinical trial in China has been approved by the NMPA in March 2024 for the indications of type 2 diabetes mellitus and weight management.
【Original Information】
Announcement of Huadong Pharmaceutical Co., Ltd. on the Wholly-owned Subsidiary Obtaining the Notice of New Drug Clinical Trial Approval from the U.S. FDA
2024-04-22 , Huadong Medicine
Palisade与Strand Life Sciences合作开发UC精准疗法
(1) On April 23, Palisade Bio announced a strategic partnership with Strand Life Sciences to jointly develop precision therapies for ulcerative colitis (UC), (2) in the future, Palisade Bio will be able to use advanced bioinformatics tools provided by Strand Life Sciences to study UC pathogenesis and predict patient drug responses, and (3) Palisade Bio has conducted more than 10 UC clinical studies with transcriptomics and clinical outcome data from 1,600 UC patient samples;(4) Strand Life Sciences is a multi-omics research and diagnostics company dedicated to the development of biomarkers based on omics discovery as disease diagnostic and therapeutic targets.
【Original Information】
Palisade Bio Enters into Strategic Collaboration with Strand Life Sciences to Advance Precision Medicine Approach
2024-04-23 , Palisade Bio
感谢本期日报的审核者：mildbreeze，圆圈儿，九卿臣，刘永鑫-农科院-宏基因组，Alex Zhang，Richard，lxx
Click here to read the daily reports for the past 10 days:
0424 | Health Hub: Multi-article focuses on how the gut affects whole-body health
0423 | Today's Cell: Jiang Changtao/Qiao Jie/Pang Yanli/Zheng Minghua/Jia Yanxing, etc. have made a major breakthrough in bile acids
0422 | Expert voices: Two articles in Cell focus on microbiota and cancer treatment
0421 | Food as Medicine: 10 articles focusing on dietary interventions in disease
0420 | Science Debunked: The Bacterial Phage-Germ "Arms Race" in the Gut
0419 | Cheng Gong/Zhu Yibin/Wang Jinglin et al. Science breakthrough: clever use of symbiotic bacteria to block the transmission of mosquito-borne viruses
0418 | Focus on special populations: maternal and infant intestinal flora and health
0417 | High-score Nature sub-journal: Bringing together the power of global players to help intestinal microbiome research
0416 | Multi-article focus: To protect the gut, no one can do without immune cells and microflora
0415 | Cell Blockbuster Review: Systematic Analysis of Cancer Complexity, the Role of Microbiota Should Not Be Underestimated