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The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a region with diverse altitudes, ethnic groups, and unique environmental exposures. WCBC had enrolled 15,093 pregnant women across eight clinical centers in five provinces (Qinghai, Gansu, Guizhou, Chongqing, and Sichuan), spanning from the high-altitude Qinghai-Tibet Plateau to lowland regions. WCBC has collected over 220,000 medical records, 80,000 questionnaires, and 12 different types of biological samples, including peripheral blood, cord blood, dried blood spots, placenta, umbilical cord, decidua, saliva, feces, throat and nasal swabs, vaginal swabs, and breast milk. By integrating advanced multi-omics measurement, including genomics, proteomics, exosome profiling, metabolomics, spatial transcriptomics, single-cell RNA sequencing, culturome, metagenomics, and virosome analysis, WCBC provides a valuable platform to explore gene-environment interplay, early-life determinants of health, and long-term disease risks in diverse populations in Western China.

Incremental evidence on the effect of cold atmospheric plasma (CAP) in specifically killing transformed cells and advances in sequencing technologies at multiple omics have led to the demand of in-depth exploration on the mechanisms of action driving the potency of CAP against cancer cells at the molecular level. However, high-throughput data detailing the effect of CAP on cancer cells is lacking, let alone the corresponding database and analytical tool. Here, we sequenced the whole transcriptome, proteome, phosphorylome, acetylome, and lactylome of transformed cells in response to CAP using breast cancer cells as the disease model; and advanced our previously developed Hiplot platform by establishing a focus-driven tumor-specific module, namely CAP medicine in breast cancer (CAPmed-BC) (https://capbc.hiplot.com.cn). CAPmed-BC is the first multi-omics data resource in plasma medicine for analyzing the treatment response of breast cancer cells to CAP. It can analyze each type of omics data regarding differentially expressed biomarkers, expression landscape, gene ontology analysis, pathway interpretation, gene set enrichment analysis, and protein-protein interaction network. It can also interrogate the dynamic fluctuation, functional activity, and metabolic vulnerability of cancer cells in response to CAP by combinatorially analyzing omics at multiple carefully defined dimensions. We also built in a visualization module to support users for producing personalized graphs via adjusting parameters. We believe that CAPmed-BC will become a valuable resource for characterizing the outcome of CAP on breast cancers at the omics and molecular levels, and make considerable contributions to both plasma medicine and oncology.

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. Chickens, with their controlled rearing conditions and stable genotypes, provide a promising model for investigating microbiome transmission in birds. This study aims to determine whether host genotype-associated bacteria are vertically transmitted between generations, and how maternal nutritional intervention with soyasaponin modulates this microbial transfer, thereby shaping chick intestinal development and informing effective nutritional strategies. We established a microbial vertical transmission model across various anatomical sites in breeder hens, chicken embryos, and chicks. Avian gut microbiota and reproductive tract microbiota can both be found in chicks at various developmental stages. Supplementing breeder hen diets with soyasaponin interacts with vertically transmitted Bifidobacterium adolescentis to produce γ-aminobutyric acid. This compound modulates offspring intestinal development through distinct mechanisms in chick epithelial cells, including the inhibition of LC3 and caspase3-associated autophagy and apoptosis pathways, as well as the promotion of proliferation and differentiation pathways mediated by LGR5 and Olfm4. Our study highlights that avian gut and reproductive tract microbiota are transmitted to chicks through the cloaca, with the yolk sac also being instrumental in this vertical transfer. The incorporation of soyasaponin in avian diets affects microbial transfer, providing a theoretical basis for studying maternal effects in poultry and formulating corresponding dietary strategies.

Phage-mediated horizontal transfer of virulence genes can enhance the transmission and pathogenicity of Salmonella enterica (S. enterica), a process potentially regulated by its regulatory mechanisms. In this study, we explored the global dynamics of phage-mediated horizontal transfer in S. enterica and investigated the role of its regulatory mechanisms in transduction. A total of 5178 viral sequences encoding 12 S. enterica virulence genes were retrieved from the Integrated Microbial Genomes and Virome (IMG/VR) database, alongside 466,136 S. enterica genomes from EnteroBase. Virulence genes, including iacP (acyl carrier protein), mgtB (P-type Mg²⁺ transporter), misL (autotransporter porin), and fliC (flagellar filament protein), were widely distributed in phages and S. enterica across North America, Europe, and Asia. Phylogenetic analysis revealed close genetic affinity between phage- and bacterial-encoded virulence genes, suggesting shared ancestry and historical horizontal gene transfer events. The global regulator carbon storage regulator A (csrA) was highly conserved and ubiquitous in S. enterica. Overexpression of csrA inhibited prophage cyclization and release by upregulating the prophage cI repressor during horizontal gene transfer. Overall, these findings enhance our understanding of phage-mediated horizontal transfer of virulence genes, explore new areas of bacterial regulators that inhibit gene exchange and evolution by affecting phage life cycles, and offer a novel approach to controlling the transmission of phage-mediated S. enterica virulence genes.

The involvement of gut microbiota in calcific aortic valve disease (CAVD) pathogenesis remains underexplored. Here, we provide evidence for a strong association between the gut microbiota and CAVD development. ApoE^−/− mice were stratified into easy- and difficult- to calcify groups using neural network and cluster analyses, and subsequent faecal transplantation and dirty cage sharing experiments demonstrated that the microbiota from difficult-to-calcify mice significantly ameliorated CAVD. 16S rRNA sequencing revealed that reduced abundance of Faecalibacterium prausnitzii (F. prausnitzii) was significantly associated with increased calcification severity. Association analysis identified F. prausnitzii-derived butyric acid as a key anti-calcific metabolite. These findings were validated in a clinical cohort (25 CAVD patients vs. 25 controls), where serum butyric acid levels inversely correlated with disease severity. Functional experiments showed that butyric acid effectively hindered osteogenic differentiation in human aortic valve interstitial cells (hVICs) and attenuated CAVD progression in mice. Isotope labeling and ¹³C flux analyses confirmed that butyric acid produced in the intestine can reach heart tissue, where it reshapes glycolysis by specifically modifying GAPDH. Mechanistically, butyric acid-induced butyrylation (Kbu) at lysine 263 of GAPDH competitively inhibited lactylation (Kla) at the same site, thereby counteracting glycolysis-driven calcification. These findings uncover a novel mechanism through which F. prausnitzii and its metabolite butyric acid contribute to the preservation of valve function in CAVD, highlighting the gut microbiota-metabolite-glycolysis axis as a promising therapeutic target.

Microbiome and resistome transmission from mother to child, as well as from animal to environment, has been widely discussed in recent years. Dairy cows mainly provide milk and meat. However, in the dairy production system, the characteristics and transmission trends of resistome assembly and the microbiome in the gastrointestinal tract (GIT) remain unclear. In this study, we sequenced the GIT (rumen fluid and feces) microbiome of dairy cow populations from two provinces in China (136 cows and 36 calves), determined the characteristics of their resistome profiles and the distribution of antibiotics resistance genes (ARGs) across bacteria and further tracked the temporal dynamics of the resistome in offspring during early life using multi-omics technologies (16S ribosomal RNA [rRNA] sequencing, metagenome, and metatranscriptome). We characterized the GIT resistome in cows, distinguished by gut sites and regions. The abundance of ARGs in calves peaked within the first 3 days after birth, with Enterobacteriaceae as the dominant microbial host. As calves aged, resistome composition stabilized, and overall ARG abundance gradually decreased. Both diet and age influenced carbohydrate-active enzymes and ARG profiles. Resistance profiles in ecological niches (meconium, colostrum, soil, and wastewater) were unique, resembling maternal sources. Mobile genetic elements (MGEs), mainly found in soil and wastewater, played an important role in mediating these interactions. Multidrug resistance consistently emerged as the most significant form of resistance at the both the metagenome and metatranscriptome levels. Several antibiotic classes showed higher proportions at the RNA level than at the DNA level, indicating that even low-abundance gene groups can have a considerable influence through high expression. This study broadens our understanding of ARG dissemination in livestock production systems, providing a foundation for developing future preventive and control strategies.

Acute chemoradiotherapy-induced intestinal injury (ACRIII) is a common and debilitating complication in patients with colorectal cancer, significantly impairing both quality of life and treatment outcomes. This study aimed to investigate the role of the gut microbiome in mitigating ACRIII. Through bioinformatics analysis of clinical fecal samples and fecal microbiota transplantation (FMT) experiments in mice, we identified a strong association between a high abundance of Lactobacillus species and the absence of ACRIII. From the fecal samples of rectal cancer patients who achieved complete remission without experiencing ACRIII during chemoradiotherapy, 10 novel Lactobacillus strains were isolated and characterized. Among these, Lacticaseibacillus rhamnosus DY801 exhibited a robust capacity to synthesize methionine through metB. This microbial methionine production modulated methionine metabolism in host gut lymphoid tissue inducer (Lti) cells, without diminishing the therapeutic efficacy of chemoradiotherapy. Supplementation with methionine increased intracellular levels of S-adenosylmethionine and enhanced histone H3 lysine 4 trimethylation (H3K4me3) in Lti cells. These epigenetic modifications led to the suppression of pro-inflammatory cytokines interleukin-17A (IL-17A) and interleukin-22 (IL-22), ultimately reducing ACRIII severity. Our findings suggest that specific Lactobacillus strains derived from patients with exceptional treatment responses may offer a novel therapeutic avenue for preventing or alleviating ACRIII. This microbiome-based approach holds significant potential for improving patient outcomes and enhancing the tolerability of chemoradiotherapy in colorectal cancer.

The gut microbiota is a highly dynamic and complex ecosystem. However, the processes by which its members respond to dietary fibers remain incompletely understood. Here, we performed daily sampling over a 14-day observational period under the habitual diet, followed by a 14-day dietary fiber intervention in overweight participants with and without type 2 diabetes mellitus. By combining daily sampling, guild-level approach, and time-series analysis, we revealed diverse temporal response patterns among various microbiota members that are often missed by conventional sampling. These patterns were closely linked to their genetic capacities for carbohydrate utilization and transport. Moreover, time-delayed analysis of longitudinal multi-omics data identified specific metabolites that potentially mediate the beneficial effects of gut microbiota on host metabolism. Overall, our findings demonstrate the necessity of high-frequency sampling for capturing dynamic microbial responses and offer reliable targets for mechanistic investigations.

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

Wang, Ling, Yi-Xuan Tu, Lu Chen, Ke-Chun Yu, Hong-Kai Wang, Shu-Qiao Yang, Yuan Zhang, et al. 2024. “Black Rice Diet Alleviates Colorectal Cancer Development Through Modulating Tryptophan Metabolism and Activating AHR Pathway.” iMeta 3(1): e165. https://doi.org/10.1002/imt2.165

In Wang et al. [1], the content of C3G in Table S1 of Supporting Information should be corrected; the content of C3G (accounted for 6.59 μg/mg) should be 0.659 μg/mg.

The correct table should be as follows:

We apologize for this error.

REFERENCE

1. Wang, Ling, Yi-Xuan Tu, Lu Chen, Ke-Chun Yu, Hong-Kai Wang, Shu-Qiao Yang, Yuan Zhang, et al. 2024. “Black Rice Diet Alleviates Colorectal Cancer Development Through Modulating Tryptophan Metabolism and Activating AHR Pathway.” iMeta 3, e165. https://doi.org/10.1002/imt2.165