mSystems最新文献

Whole-genome sequencing has boosted our ability to explore microbial diversity by enabling the recovery of metagenome-assembled genomes (MAGs) directly from environmental DNA. As a result, the vast availability of sequencing data has prompted the development of numerous bioinformatics pipelines for MAG reconstruction, along with challenges to identify the most suitable pipeline to perform the analysis according to the user needs. This report briefly discusses the computational requirements of these pipelines; presents the variety of interfaces, workflow managers, and package managers they feature; and describes the typical modular structure. Also, it provides a compacted technical overview of 41 publicly available pipelines or platforms to build MAGs starting from short and/or long sequences. Moreover, recognizing the overwhelming number of factors to consider when selecting an appropriate pipeline, we introduce an interactive decision-support web application, 2Pipe, that helps users to identify a suitable workflow based on their input data characteristics, desired outcomes, and computational constraints. The tool presents a question-driven interface to customize the recommendation, a pipeline gallery to offer a summarized description, and a pipeline comparison based on key factors used for the questionnaire. Beyond this and foreseeing the release of novel pipelines in the near future, we include a quick form and detailed instructions for developers to append their workflow in the application. Altogether, this review and the application equip the researchers with a general outlook of the growing metagenomics pipeline landscape and guide the users toward deciding the workflow that best fits their expectations and infrastructure.

Endoplasmic reticulum (ER) stress-related mucin depletion could be involved in the pathogenesis of ulcerative colitis (UC). Akkermansia muciniphila (A. muciniphila) uses mucin as its sole energy source and shows potential in the treatment of colitis. However, the effects and underlying mechanisms of A. muciniphila on colonic epithelial ER stress in colitis are largely unknown. Colitis was induced by adding 2.5% dextran sulfate sodium (DSS) in drinking water. Mice were orally administered A. muciniphila (3*10^{^}7, 3*10^{^}8 cfu/day) once daily for 10 days during DSS intervention. Ultra high performance liquid chromatography q-exactive orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS)-based metabolomic analyses were performed on feces. 16S rRNA sequencing was used to quantify and characterize the gut microbiota of mice. Metabolomic analysis showed that P-hydroxyphenyl acetic acid (p-HPAA), the metabolite with the highest variable importance in projection (VIP) score that was elevated by A. muciniphila, was negatively correlated with acetic acid levels and exhibited a potential inhibitory effect on ER stress. Additionally, A. muciniphila supplementation decreases the abundance of Parasutterella, a genus implicated in bile acid homeostasis. By restoring the levels of deoxycholic (DCA) and ursodeoxycholic acid (UDCA), A. muciniphila administration normalized the bile acid pool size and composition altered by colitis. A. muciniphila supplementation protected colon shortening and histological injury in wild-type (WT) mice, but not in farnesoid X receptor-null (FXR^-/-) mice. Mechanistically, our results demonstrate that A. muciniphila alleviates DSS-induced colitis by targeting inositol requiring enzyme 1α(IRE1α) and unspliced XBP1 (XBP1u) within the ER stress pathway, with the regulation of XBP1u being FXR-dependent. Supplementation with A. muciniphila at appropriate doses may, thus, offer a promising therapeutic strategy for Ulcerative colitis (UC).

Importance: UC is a chronic inflammatory disease in which inflammation begins in the rectum and extends proximally throughout the colon. A.muciniphia is significantly reduced in UC patients and shows promise as a next-generation probiotic. However, the mechanisms behind its protective effects are not fully understood. Our study reveals that A. muciniphila alleviates experimental colitis by reshaping the gut microbiome and correcting imbalances in bile acid metabolism. Crucially, we identify a novel mechanism where A. muciniphila acts through the host bile acid receptor FXR to suppress a specific ER stress pathway (XBP1u) in colon cells, thereby helping to restore the intestinal barrier. These findings provide a scientific basis for using A. muciniphila as a targeted therapeutic strategy for UC.

Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.

Staphylococcus aureus clonal complex 59 (CC59) has emerged as a significant public health threat in Asia, yet the mechanisms driving its host adaptation and global evolutionary success remain poorly understood. Here, we performed a comprehensive genomic analysis of 3,994 global CC59 isolates, which included 549 isolates associated with bloodstream infections from China. Our analysis revealed three phylogenetically distinct lineages exhibiting region-specific distribution patterns, tracing their origins to the USA, Australia, and China. Notably, high-risk CC59 clones circulating in Taiwan likely diverged from mainland Chinese strains during the 1940s-1960s, coinciding with historical population migration following the Chinese civil war around 1949. Among China-associated CC59 strains, respiratory tract colonization was related to high cross-source linkage across multiple ecological niches, suggesting its role as a dissemination hub, particularly for bloodstream infection (BSI). Additionally, we observed significant enrichment of Clf-Sdr family proteins in human isolates, especially in BSI cases. Functional characterization using ΔclfB and ΔsdrD knockout strains demonstrated impaired biofilm formation, recapitulating findings in USA300. These findings establish an evolutionary framework for CC59 surveillance and highlight promising potential targets for anti-virulence therapeutics.

Importance: The prevalence and propagation of Staphylococcus aureus clonal complex 59 (CC59) in Asia are serious public health concerns. To understand its adaptation to hosts and worldwide evolutionary success, we analyzed the genomic population structure of all CC59 isolates and traced their evolutionary history. Our research indicates that CC59 lineages developed through unique evolutionary routes that vary across time and space, highlighting their adaptation to diverse ecological environments. This study presents a comprehensive genomic epidemiology framework that integrates extensive metadata analysis with evolutionary assessment. It serves as a model for future S. aureus monitoring and provides insights into potential targets for interventions focused on reducing virulence.

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) infection is gradually increasing globally. Phage therapy is a viable application as an alternative to antibiotics. However, clinical application of phage therapy is restricted by phage resistance. To further explore the mechanism underlying phage resistance, particularly the difference observed between in vivo and in vitro, we employed a mouse intra-abdominal infection model to assess the antibacterial properties of two lytic phages and further isolate and characterize phage-resistant mutants. We identified that the majority of the mutation sites in the phage-resistant K. pneumoniae mutants were located in the capsular polysaccharide (CPS) gene cluster, as determined through genomic and transcriptomic analysis. However, some K. pneumoniae phage-resistant mutants, including RM01, RM02, and RM12, developed phage resistance by downregulating CPS and the respective transcriptional regulators without any mutations in the CPS gene. In summary, these findings provide further evidence supporting phage therapy, particularly addressing the issue of CR-hvKP infections.IMPORTANCEThe global rise in antibiotic resistance has rekindled interest in utilizing bacteriophage therapy as a potential solution. In this study, we explored the therapeutic potential of two novel bacteriophages, with a focus on their in vivo efficacy using mouse models, and analyzed the probable mechanisms of phage resistance in bacteria. Our results indicated that in a murine infection model, phages JLBP1001 and JLBP1002 for Klebsiella pneumoniae were highly effective, significantly improving mouse survival. We further characterized and analyzed phage-resistant K. pneumoniae isolated from the mice and found that the resistance mechanisms in an in vivo environment are primarily concentrated in the capsular polysaccharide gene cluster. In RM01, RM02, and RM12, putA contributes to phage resistance through point mutations. These insights are important for optimizing phage-based therapies, particularly in the context of multidrug-resistant bacterial infections.

The gut microbiome undergoes dynamic age-related changes shaped by diet and maternal factors. Here, we present a species-level, long-read 16S rRNA survey of the developing gut microbiome in a translational canine model, profiling 89 purebred Hungarian Pumis across early-life and reproductive stages. We collected 456 fecal samples longitudinally: 60 puppies followed from birth to 81 weeks, their mothers sampled during pregnancy and lactation, and adult controls from six kennels. We recorded detailed dietary metadata and reproductive status throughout the study. Age was the strongest determinant of alpha diversity, with a rapid increase during weaning and stabilization by 6 months of age. Beta diversity analyses revealed structured compositional transitions from early developmental phases to adulthood, including a shift toward more uniform, adult-like communities. Within-kennel variation was modest, consistent with shared environmental exposures. Mixed-effects models showed robust associations between specific taxa and age, diet, and kennel, while SparCC-inferred co-occurrence networks indicated increasing ecological complexity with age. We also demonstrated that the delivery mode-vaginal versus cesarean-impacted early-life microbiome composition: Lactobacillus spp. were significantly more abundant in cesarean-born puppies than in vaginally delivered littermates during the 8-10-week window. We also observed reproducible maternal microbiome shifts during pregnancy and lactation, with potential implications for vertical microbial transfer. Taken together, our results show that domestic dogs follow a reproducible, age-structured trajectory of microbial maturation that parallels human development, including delivery-mode effects and diet-responsive taxa.IMPORTANCEMicrobiome research is among the fastest-moving areas in biomedicine driven by major global efforts to understand how microbial communities shape human health and disease. Dogs provide an ideal translational model because their gut microbiota more closely resembles that of humans than that of other studied animals; moreover, breeds show high within-breed genetic homogeneity; diets can be tightly regulated; and longitudinal sampling across the lifespan is feasible. Mapping shifts driven by diet and maternal factors-from early-life events through later life, including senior stages-is essential to leverage microbial plasticity for prevention, with implications for inflammation, metabolic disease, and neurodegeneration. Here, we advance this goal by providing a longitudinal, high-resolution data set and demonstrating that full-length 16S rRNA sequencing is a powerful tool for resolving fine-scale patterns of gut colonization and maturation.

Streptococcus pyogenes (group A Streptococcus, GAS) causes various clinical complications and invasive diseases. Our previous studies have shown that GAS survives inside endothelial cells due to the insufficient acidification of lysosomes, which fuse with reactive oxygen species (ROS)-induced phagosomes of LC3-associated phagocytosis. For catalase-deficient peroxide-producing GAS to survive in hosts, GAS uses a peroxide response regulator (PerR) to modulate ROS-induced oxidative stress and metal ion regulation. However, it remains unclear whether PerR regulates zinc homeostasis during infections. We generated the GAS ΔperR isogenic mutant and conducted dual RNA-seq analysis, an endothelial cell infection model, computational predictions, and phenotypic characterization to demonstrate the protective role of PerR in GAS survival in endothelial cells. The ΔperR mutant's vulnerability to zinc deprivation demonstrated that PerR coordinates iron and zinc homeostasis, likely using PmtA's iron efflux, iron and zinc-chelating ferritin-like Dpr, the AdcR regulon (adcA, adcAII, and phtD), and zinc efflux (czcD). We also demonstrated that the wild-type strain and ΔperR mutant encounter zinc restriction inside the phagolysosome GAS-containing vacuoles of endothelial cells. This host zinc starvation severely reduces the survival of the ΔperR mutant. These results suggest that the PerR-mediated iron and zinc modulation through Dpr is more important than had been previously thought. Consequently, PerR enhances GAS fitness during its invasions of human endothelial cells.

Importance: Our study combines dual RNA-seq analysis, an endothelial cell infection model, computational predictions, and phenotypic characterization to discover the impact of group A Streptococcus (GAS) PerR on the coordination of iron and zinc homeostasis during infection. We found that PmtA's iron efflux, iron and zinc-chelating ferritin-like Dpr, the AdcR regulon, and zinc efflux are delicately modulated by PerR. We also determined that zinc limitation inside the phagolysosome GAS-containing vacuoles of endothelial cells causes host zinc starvation, resulting in reduced survival of the ΔperR mutant. Consequently, PerR enhances GAS fitness through Dpr during its invasions of human endothelial cells. Our novel findings offer new insights into how GAS combats iron-mediated oxidative stress and zinc homeostasis that may help develop new anti-GAS treatments.

Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.

Importance: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.

Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese-rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese-rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface with Brachybacterium alimentarium. Integration of liquid chromatography-tandem mass spectrometry and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with B. alimentarium, and experiments with purified penicillic acid showed inhibition in a dose-dependent manner against this rind bacterium. These findings show that A. westerdijkiae deploys a context-dependent suite of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.IMPORTANCEThis study identifies the chemical mechanisms underlying the negative impacts of Aspergillus westerdijkiae on cheese-rind development, revealing how specialized metabolites like penicillic acid and ochratoxin B influence rind bacterial communities. By integrating biosynthetic gene cluster analyses with mass spectrometry, we demonstrate how chemical communication shapes microbial interactions, with possible implications for food safety and cheese quality. Understanding these interactions is essential for assessing the risks of fungal-driven spoilage and mycotoxin production in cheese-rind maturation. Beyond cheese, these findings contribute to broader microbiome ecology, emphasizing how secondary metabolites mediate microbial competition in natural and fermented food environments.