Microbiome最新文献

Background: Long-term abuse of methamphetamine (MA) is strongly associated with severe lung injury. Microbiome metabolites are one way to understand the interactions between microbes and disease. Although gut microbes and their metabolites play a crucial role in the gut-lung axis, the microbial mechanism by which MA induces lung injury is unclear. The purpose of this work was to identify the omics characteristic factor associated with MA abuse and explore its immune regulatory mechanism by 16 s rDNA sequencing, LC-MS/MS non-targeted metabolomics analysis, hemodynamics, flow cytometry, and some methods of cellular and molecular biology and morphology.

Results: Based on the joint analysis of the gut microbiome and metabolomics, it was found that MA abuse disrupted the structure of the gut microbiome and drove the reprogramming of metabolites, leading to a reduction in Lactobacillus rhamnosus and its metabolite L-kynurenine (L-KYN). Activated Lactobacillus increased L-KYN level in MA-administrated mice. L-KYN, as a product of Lactobacillus, is a key omics signature factor for MA abuse, which has been further confirmed in vivo. L-KYN induced Treg cells differentiated from CD4⁺ T cells and reshaped the immune microenvironment. L-KYN induced the secretion of IL-10 by Treg cells, mediated the communication between Treg cells and alveolar epithelial cells (AEC) through IL-10, and alleviated MA-induced lung inflammation and alveolar barrier damage through the IL-10/JAK1/STAT3 pathway.

Conclusions: From the perspective of intestinal microbiome-metabolite-immune network regulation, the omics characteristic factor L-KYN reshaped the immune microenvironment and alleviated methamphetamine-induced chronic lung injury through the gut-lung axis, providing a new theoretical and experimental basis for the prevention and treatment of MA-induced chronic lung injury. Video Abstract.

Background: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.

Results: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.

Conclusions: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.

Background: Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.

Results: Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.

Conclusions: By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx . Video Abstract.

Background: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean.

Results: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses.

Conclusions: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.

Background: Microbiome data, like other high-throughput data, suffer from technical heterogeneity stemming from differential experimental designs and processing. In addition to measured artifacts such as batch effects, there is heterogeneity due to unknown or unmeasured factors, which lead to spurious conclusions if unaccounted for. With the advent of large-scale multi-center microbiome studies and the increasing availability of public datasets, this issue becomes more pronounced. Current approaches for addressing unmeasured heterogeneity in high-throughput data were developed for microarray and/or RNA sequencing data. They cannot accommodate the unique characteristics of microbiome data such as sparsity and over-dispersion.

Results: Here, we introduce quantile thresholding (QuanT), a novel non-parametric approach for identifying unmeasured heterogeneity tailored to microbiome data. QuanT applies quantile regression across multiple quantile levels to threshold the microbiome abundance data and uncovers latent heterogeneity using thresholded binary residual matrices. We validated QuanT using both synthetic and real microbiome datasets, demonstrating its superiority in capturing and mitigating heterogeneity and improving the accuracy of downstream analyses, such as prediction analysis, differential abundance tests, and community-level diversity evaluations.

Conclusions: We present QuanT, a novel tool for comprehensive identification of unmeasured heterogeneity in microbiome data. QuanT's distinct non-parametric method markedly enhances downstream analyses, serving as a valuable tool for data integration and comprehensive analysis in microbiome research. Video Abstract.

Background: Prepartum obesity predisposes dairy cows to a higher risk of postpartum metabolic disorder. Volatile fatty acids (VFA) produced through ruminal microbial fermentation of feed substrates serve as a key form of energy for dairy cows. However, the precise mechanisms through which the rumen microbiota promote adipocyte lipid accumulation in obese dairy cows remain to be elucidated. Thus, the aim of this study was to investigate the mechanisms by which rumen microbiota regulates prepartum obesity in dairy cows.

Results: Plasma glucose, insulin, triglyceride, and free fatty acids were greater in obese dairy cows. In the adipose tissue, the triglyceride content and expression of genes involved in lipid synthesis were higher in obese dairy cows. In the liver, the expression of genes involved in gluconeogenesis and lipid synthesis was higher in obese dairy cows. The ruminal total VFA, acetate, and propionate were higher in obese dairy cows compared to normal cows. The 16S rRNA gene analysis revealed that rumen bacteria, including Tidjanibacter inops_A, Rikenella massiliensis, Papillibacter cinnamivorans, and Parabacteroides merdae, were enriched in the rumen of obese dairy cows. Enrichment of these bacteria promoted carbohydrate degradation and VFA production. The metabolome analysis showed that obese dairy cows had elevated citric acid level in the rumen, which was positively associated with body condition score, body weight, adipocyte diameter, ruminal VFA concentration, and the abundance of VFA-producing bacteria.

Conclusions: Our results suggest that rumen bacterial flora in prepartum obese dairy cows supply more VFA to the host, which may induce lipid deposition in adipocytes. Video Abstract.

Background: Tricholoma matsutake (TM), a prized wild mushroom in Eurasia, hosts distinct microbiomes in its mycorrhizal zone (shiro), with some microbes known to benefit TM. However, no study has systematically compared shiro-inhabiting microbiomes across multiple studies from either taxonomic or functional perspectives.

Results: We first compiled bacterial and fungal amplicon sequences from public and newly generated datasets, then applied phylogenetic tree-based clustering to integrate technically heterogeneous sequences. This enabled the identification of core microbial phylotypes conserved in shiro from geographically diverse regions. We also revealed niche-specific phylotypes within the shiro, distinguishing those associated with soil, TM-colonized root, and fruitbody, thereby demonstrating clear niche differentiation. Functional predictions and experimental validation highlighted key roles of the microbes in degradation of aromatic compounds, utilization of plant-derived compounds, and fruitbody development.

Conclusions: Our cross-study integration of shiro microbial sequences identified core and niche-specific phylotypes with distinct ecological roles. This study lays a foundation for advancing ecological research and cultivation strategies for TM.

Background: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.

Results: We found that in situ methane (CH₄) and nitrous oxide (N₂O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N₂O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH₄ and N₂O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.

Conclusions: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.

Background: Although endophytic microorganisms play a critical role in plant growth and stress resilience, the genetic basis underlying host selection of beneficial microbiota-particularly within the xylem-remains poorly understood. Cucumber (Cucumis sativus), as a crop model with a well-developed system for studying vascular biology, offers a valuable system to investigate the host genetic determinants of xylem microbiome assembly.

Results: By conducting population-level microbiome profiling across 109 cucumber accessions, we identified a conserved xylem microbiota dominated by Proteobacteria. Within this community, 20 core amplicon sequence variants (ASVs) were consistently present in xylem sap. Genome-wide association mapping identified a host genetic locus, CsXPR1, which encodes a tetratricopeptide repeat protein that regulates the abundance of the dominant xylem-colonized Pseudomonas ASV_4. Colonization patterns of ASV_4 varied across host genotypes and were correlated with CsXPR1 expression levels, suggesting a precision genetic regulation of bacterial entry into vascular tissues. Pseudomonas fulva strain 220, with 97% 16S rRNA gene identity with ASV_4, could colonize in cucumber xylem by inoculation of either roots or leaves. Genome analysis and plate assays revealed the biosynthesis of indole-3-acetic acid (IAA), solubilization of phosphate, and a range of plant beneficial traits in strain 220. Inoculation with strain 220 significantly enhanced growth in cucumber, but only in CsXPR1 haplotype that exhibited high gene expression and higher recruitment capacity of the strain. These benefits included notable increases in plant height (38%), stem diameter (36%), leaf area (61%), fresh and dry weight (51% and 85%, respectively), and a 4.57-fold increase in 4-methyleneglutamine content within the xylem sap.

Conclusion: Our findings reveal a complete "gene-to-function" pathway where the host gene CsXPR1 mediates a genotype-dependent growth promotion. It achieves this by regulating the xylem colonization of a beneficial bacterium, Pseudomonas fulva, which in turn enhances plant growth by enriching the xylem sap with the key metabolite 4-methyleneglutamine. Video Abstract.

Background: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

Results: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

Conclusions: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.