An Asia-enriched survey of 239 respondents found that reported implementation of spatial biology and three-dimensional pathology varied across self-rated experience groups. Respondents identified cost, analytical complexity, limited standardization, and insufficient interdisciplinary expertise as barriers, highlighting the needs for practical workflows and computational support.

Multi-omics approaches have revealed a cross-species functional emergence phenomenon leading to emergent suppression of Fusarium wilt. We show that a three‑species consortium exhibits emergent suppression of Fusarium oxysporum f. sp. lycopersici (Fol) that is absent in single or pairwise cultures. This antifungal activity arises from coordinated activation of two phylogenetically distinct vitamin K2 biosynthesis pathways—the Men pathway (primarily Bacillus) and the Mqn pathway (Paenibacillus)—whose complementary actions enhance K2 production and directly inhibit the pathogen. A structural analogue, vitamin K3, recapitulates this effect, offering translational potential. Our findings establish that emergent microbiome functions depend on interaction‑triggered latent metabolic activation, not constitutive exchange or additive effects.

Using 26,339 model-eligible Traditional Chinese Medicine (TCM) formula records, we trained an autoencoder following TCM's compression–expansion logic to learn the TCM embedding space (TCM-ES), quantifying symptom-pattern–formula mappings. TCM-ES aligns with conventional TCM principles not used in training. Biomedical entities were mapped post hoc into the fixed space, supporting formula prediction, retrospective clinical analyses, and exploratory therapeutic prioritization.

This study reveals that plant-derived natural products confer protection against carbapenem-resistant Klebsiella pneumoniae (CRKP) infection via remodeling the gut microbiota, with Lactobacillus identified as the core beneficial genus. Mechanistically, Lactobacillus murinus (L. murinus)-derived mim-miR-21a-5p carried by membrane vesicles (MVs) targets PDCD4. This interaction further activates the Nrf2/SOD2 signaling axis, promotes M2 macrophage polarization, and ultimately suppresses CRKP infection.

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.