This study provides a bootstrap readout framework for DNA data storage based on multiple-fold hidden references. We employ a multi-stage alignment and error correction strategy, transforming the de novo readout into a resequencing-like workflow. Correlation to the hidden watermark reference identifies low-error-rate reads, and bit-wise consensus generates soft-decision information, enabling fast data recovery. In the presence of indels, the read-by-read forward–backward algorithm corrects indel errors, and alignment to the regenerative reference fills in low-coverage regions, enabling reliable data recovery.

The integrated microbiome data analysis platform on Majorbio Cloud (https://cloud.majorbio.com/) encompasses 26 analytical workflows, with a core architecture of two modules: single-omics workflows and cross-omics integration and correlation workflows. The platform supports multi-scale microbiome research (strain to community levels) and cross-omics analyses spanning DNA, RNA, protein, and metabolite layers. The platform features four key functions: (1) Application guide, streamlines analytical workflows for user convenience; (2) Default analysis parameters and one-click analysis, enables one-step data processing; (3) One-click plot enhancement, optimizes figures to meet academic publication standards; (4) Plot patchwork feature, stores optimized images in my gallery, facilitates the creation of publication-ready image composites, supports composite downloads in PDF/PNG/SVG formats, and allows the preservation of patchwork templates for subsequent applications. By late 2025, the platform has facilitated over 5,050 scientific publications, accelerating microbiome research advances.

Traditional 16S rRNA gene and Internal Transcribed Spacer region amplicon sequencing provides only relative abundance, often leading to biased ecological interpretations. To overcome this limitation, we developed Accu16S/AccuITS, an absolute quantification method for bacterial and fungal amplicons based on synthetic internal spike-in DNA with known copy numbers. By adding internal standards prior to Polymerase Chain Reaction and sequencing, absolute microbial abundances can be calculated using standard curve regression. Accu16S/AccuITS exhibits sensitivity and consistency comparable to quantitative Polymerase Chain Reaction and is applicable to diverse sample types. A single sequencing run simultaneously yields relative abundance, total absolute abundance, and taxon-specific absolute abundance. Case studies across diverse ecosystems demonstrate that absolute quantification provides ecologically and functionally meaningful insights beyond those obtained from relative abundance analyses.

AT9(C/G), an oligopeptide derived from human defensin 5, enriches Bifidobacterium pseudolongum and increases lithocholic acid (LCA) levels in the intestine. Reduced levels of LCA link to increased severity of ionizing radiation-induced intestinal injury (IRIII) in both murine and clinical studies. Administration of LCA confers radioprotection across cells, mouse models, and human small intestinal organoids. Mechanistically, LCA activates Takeda G protein-coupled receptor 5 (TGR5) and leads to the upregulation of sterol regulatory element-binding protein 1 (SREBP1), which transcriptionally modulates stearoyl-CoA desaturase 1 (SCD1) to catalyze monounsaturated fatty acid production, thereby suppressing ferroptosis in irradiated cells. Leveraging the radioprotective properties of LCA, AT9(C/G) effectively mitigates IRIII.

Research on the mechanism of OPR restoring intestinal epithelial cell (IEC) structure and function in inflammatory bowel disease (IBD) treatment. (A) Schematic diagram of OPR structure and the rate of GP release under different conditions. (B) Schematic diagram of OPR targeting IBD colonic lesions through charge interaction. (C) After entering cells, OPR targets outer mitochondrial membrane (OMM) proteins and releases GP. The released GP restores MMP by inhibiting UCP2 protein, thereby restoring mitochondrial function. (D) ① ROS is activated during mitochondria damage through GSDME signal and promotes pyroptosis in IECs. ② Mitochondrial damage and release of mtDNA from IECs are sensed by macrophages, and activate the STING pathway. ③ Clostridium difficile disrupts the cytoskeletal network of IECs through the release of TcdB, which mediates the glycosylation of Rac1. ④ OPR targets (OMM) proteins to clear ROS while releasing UCP2 inhibitor (GP) to restore mitochondrial function and inhibit cytoplasmic acidification to resist the toxic effects of TcdB.

DMC/CUR antagonize viral hijacking of host nucleic acid resources and finely regulate the induction and effector phases of the type I interferon (IFN-I) pathway through the CRYAB-RBM26 axis. This molecular axis serves as a key downstream regulator for DMC/CUR activation of the IFN-I pathway.

In this study, we develop a flexible Ccc-Chip (protein microarray + bioorthogonal click chemistry) for high-throughput screening of natural covalent active molecules from medicinal plant extracts, identifying flavokawain C from Piper methysticum Forst as a novel covalent mIDH1 inhibitor.

Climate adaptation genomics of cattle. We comparatively analyzed genomic data from 85 Old World cattle breeds/populations of Eurasia and Africa to identify genetic factors associated with climate factors. Environmental genome-wide association studies revealed 3165 single-nucleotide polymorphisms (SNPs) with strong correlations between climate factors and allele frequencies. We also identified loci that were significantly associated with temperature factors in the regulatory regions, such as promoter regions, of genes (ANKRD11, RPL13, CDK10, and VPS9D1) under strong selection pressure on Bos taurus autosome 18, which might regulate the expression of these genes. These significantly associated SNPs could be used as potential resources for marker-assisted breeding programs aimed at climate resilience and sustainable cattle production under changing environmental conditions.

Massive burn injuries (MBIs) are associated with high mortality and disability rates, primarily due to microbial-driven sepsis from extensive skin barrier loss and subsequent scar formation. This makes MBI a compelling model for studying multi-system microbial dysbiosis following skin barrier destruction. We launched the Burn & Trauma Injury Organisms and Microbiome Ecology (BIOME) project, planning to enroll at least 150 MBI patients from 50 hospitals across 28 provinces, autonomous regions, and municipalities in China. The cohort includes skin swabs, intestinal and oral samples, and longitudinal clinical data collected from within 72 h post-injury through 1 year of follow-up. This multicenter, prospective, longitudinal cohort will establish a comprehensive clinical microbiota resource for patients with MBI. By integrating multi-system microbiome profiling with clinical outcomes, the BIOME project aims to elucidate the translational role of microbiota reconstruction as a potential target for diagnosis, prognosis, and therapeutic intervention in severe burn care.

This study is the first to elucidate mechanisms of high-altitude adaptation from the perspective of the rumen ecosystem by using indigenous yaks and Holstein cows that have lived at high altitude since birth as comparative models. Through a systematic comparison of their rumen ecology using multi-omics approaches—including rumen metagenomics, metatranscriptomics, and single-nucleus transcriptomics—we identified distinct adaptive strategies employed by the two species under extreme plateau environments. Specifically, the rumen microbiota of yaks was enriched in central carbon metabolism pathways, whereas the microbiota of Holstein cows was enriched in pathways related to the degradation of specific complex carbohydrates. Concurrently, yak rumen epithelial cells exhibited increased expression of genes associated with ketone body metabolism, along with higher pathway activity scores for ketone body biosynthesis and fatty acid beta-oxidation. Moreover, we introduced rumen fluid transplantation from yaks for the first time and observed that, under the conditions of this study, yak microbiota transplantation increased milk yield in Holstein cows. After transplantation, the carbon metabolism of the rumen microbiota gradually declined, further confirming the key role of the rumen microbiota in regulating host energy supply in the context of yak high-altitude adaptation. Overall, this study deciphers the mechanisms by which gastrointestinal microbiota contributes to high-altitude adaptation in ruminants and provides a new perspective for addressing challenges related to adaptation to high-altitude environments.

Evidence for liver metabolism of gut-derived microbial compounds into beneficial secondary metabolites has been lacking. Here, we demonstrate that Cetobacterium somerae (C. somerae), enriched by mannose supplementation under high-fat diet conditions, convert arginine into putrescine. The liver subsequently converts this microbial-derived putrescine to spermidine, which functions as an effector molecule to reduce hepatic lipid accumulation. These findings uncover a novel host-microbiota collaborative mechanism in which the arginine-putrescine-spermidine metabolic pathway is completed through inter-kingdom cooperation to ameliorate hepatic steatosis.

The pervasiveness of microplastic pollution poses a growing health risk, yet its long-term metabolic consequences remain poorly defined. Here, we exposed mice to polyethylene terephthalate nanoparticle (NP) and combined histopathology, biochemistry, metabolomics, and metagenomics to resolve their interactions. NP ingestion induced a severe systemic phenotype characterized by weight loss, organ atrophy, dyslipidemia, and gut barrier collapse. Mechanistically, NPs disrupted bile acid (BA) homeostasis by hyperactivating hepatic synthesis pathways while suppressing microbial 7α-dehydroxylation. This accumulation of cytotoxic BAs drove hepatic lipogenesis and aggravated mucosal inflammation. Crucially, metagenomics uncovered significant gut microbiota dysbiosis, where the enrichment of bile salt hydrolase-encoding taxa and depletion of 7α-dehydroxylating clades reinforced this BA imbalance. Furthermore, the microbiota exhibited functional deterioration, shifting toward glycan degradation with a concurrent loss of antibiotic resistance genes, signaling reduced ecological resilience. These findings identify BA dysregulation and specific microbiota functional losses as primary drivers of NP-induced systemic metabolic collapse.

Cancer-associated fibroblasts (CAFs) construct a protective stromal barrier that promotes tumor growth and resistance to therapy. To dismantle this, we developed CAT-BLAST, an engineered bacterial platform designed to potently eliminate these cells. We engineered a safe, high-expression E. coli chassis, arming it with a FAP-specific synthetic adhesin for precise CAF targeting and the ability to secrete the ClyA cytotoxin to induce apoptosis in both CAFs and adjacent tumor cells. This platform demonstrated robust, FAP-specific targeting across diverse human tumor xenograft models and achieved significant tumor suppression in both murine colorectal cancer and melanoma.

The figure shows side-by-side quality comparison of the data before and after preprocessing using fastp 1.0. As can be seen from this figure, the data quality has been significantly improved after fastp processing. The Q20 ratio and Q30 ratio increased, and the GC base ratio returned to balance.

EasyMetagenome is a user-friendly shotgun metagenomics pipeline designed for comprehensive microbiome analysis, supporting quality control, host removal, read-based, assembly-based, binning, genome and pan-genome analysis. It offers customizable settings, data visualizations, and parameter explanations. The pipeline is freely available at https://github.com/YongxinLiu/EasyMetagenome.

The concept of “gut–X axis”: the intestine and intestinal microbiota are proven to be able to modulate the pathophysiologic progressions of the extraintestinal organs' diseases. The bioactive chemicals and/or intestinal immune cells can translocate into the circulatory system and other organs and influence the immune reactions, metabolic status, cells physiology, and so forth of extraintestinal organs, finally regulating these organs' homeostasis. Meanwhile, other organs may reversely impact the intestine, namely such regulatory axis is bidirectional.

Fastp is a widely adopted tool for FASTQ data preprocessing and quality control. It is ultrafast and versatile and can perform adapter removal, global or quality trimming, read filtering, unique molecular identifier processing, base correction, and many other actions within a single pass of data scanning. Fastp has been reconstructed and upgraded with some new features. Compared to fastp 0.20.0, the new fastp 0.23.2 is even 80% faster.

Representative visualization results of ImageGP. ImageGP supports 16 types of images and four types of online analysis with up to 26 parameters for customization. ImageGP also contains specialized plots like volcano plot, functional enrichment plot for most omics-data analysis, and other 4 specialized functions for microbiome analysis. Since 2017, ImageGP has been running for nearly 5 years and serving 336,951 visits from all over the world. Together, ImageGP (http://www.ehbio.com/ImageGP/) is an effective and efficient tool for experimental researchers to comprehensively visualize and interpret data generated from wet-lab and dry-lab.

The ggtree object is designed to store phylogenetic tree and associated data, and the object itself is a graphic object that can be rendered as an image file. This work will increase the reproducibility and reusability of phylogenetic data, as well as facilitate integrative and comparative studies.

A new release of PhyloSuite, capable of conducting tree-based analyses. Detailed guidelines for each step of phylogenetic and tree-based analyses, following the “What? Why? and How?” structure. This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.