mSystems最新文献

Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

Importance: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.

Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration on the composition of cellular RNA and metabolites are still poorly understood. Here, we describe how slow drying and rehydration with water vapor influence the composition of RNAs and metabolites in a soil Arthrobacter. While drying reduced cultivability relative to hydrated controls, water vapor rehydration fully restored it. Ribosomal RNA proportions remained constant throughout all treatments, and mRNA profiles showed stable composition during desiccation-changing only during transitions into and out of desiccation-induced dormancy. Six transcriptional modules displayed distinct expression patterns in desiccated-rehydrated samples relative to hydrated controls, including desiccation-rehydration responsive and rehydration-specific profiles. Targeted intracellular metabolomics revealed similarly static profiles during desiccation, with a cluster of ribonucleosides and nucleobases increasing in response to desiccation and returning to baseline levels upon rehydration with water vapor. These findings demonstrate that both mRNA and metabolite profiles remain essentially frozen in desiccated Arthrobacter, with dynamic changes occurring only during state transitions. These results have important implications for environments with frequent drying cycles where stable mRNA in dormant cells combined with intracellular RNA recycling may obscure interpretations of RNA-based environmental analyses that use RNA as a marker of microbial activity. Our results suggest that RNA-based activity assessments in periodically dry environments require careful consideration of dormancy-associated molecular preservation.IMPORTANCEMetabolic activity quickly ceases in drying bacteria as they enter desiccation-induced dormancy. We show that mRNA and metabolite profiles were variable during drying and rewetting but did not change while desiccated. Additionally, water vapor stimulated the shift from the static to active state when exiting desiccation-induced dormancy. These shifts coincided with increased cultivability, indicating water vapor resuscitated dry cells. Because RNAs are transient, labile molecules that are turned over rapidly in growing bacteria, the presence of RNA in the environment is used as a marker for microbial activity. Our research shows this assumption may not hold for desiccated cells, indicating reliance on RNA as a marker of activity in environments that experience drying may obscure estimates of in situ microbial activity.

Members of the genus Streptomyces are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salt supplementation as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives, as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including cation uptake, compatible solute production, and the phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the increased salinity. This response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolite biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salt supplementation were identified. Overall, our data show how S. coelicolor copes with the increased salinity and tailors the cellular metabolism toward secondary metabolism in a conserved and species-specific manner.IMPORTANCEPrecise control of cellular metabolism is critical to ensure directing cellular resources toward metabolic pathways required for the environment. Many Streptomyces species activate production of secondary metabolites upon exposure to environmental stimuli. This study reveals dynamic reprogramming of cellular metabolism in Streptomyces coelicolor under increased salinity, which induces production of various secondary metabolites. Notably, this model biological system redirects cellular resources toward various metabolic pathways required for proper activation of secondary metabolite biosynthesis, including precursor and energy supply and posttranslational modification of biosynthetic enzymes. Interestingly, some pathways are activated by phosphate limitation stress, presumably caused as a result of increased salinity. Certain aspects of this metabolic reprogramming are likely common in many Streptomyces species and may be controlled by rather complex regulatory pathways. Overall, this study unveils how Streptomyces species tailor the cellular metabolism toward secondary metabolism and paves the way for understanding metabolic regulation.

The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.

Listeria monocytogenes, as a significant foodborne pathogen, is not frequently encountered; however, when infections do occur, they can prove highly lethal to specific populations. Antibiotics are still regarded as the primary treatment option for Listeria infections. Nevertheless, under the global antibiotic crisis, there is an urgent demand for innovative and alternative strategies. In our study, we identified taurine, a sulfur-containing free amino acid that can be extracted from a wide variety of foods, as an effective inhibitor of Listeria growth. Furthermore, our findings revealed that taurine administration significantly reduced bacterial burden and concurrently mitigated host-derived inflammation in the mouse model. It was observed that taurine stimulated T-cell proliferation and inhibited pyroptosis via mitogen-activated protein kinase and NLRP3/caspase-1/GSDMD pathways. Our research outcomes position taurine as a promising therapeutic candidate for combating Listeria infections, with an inherent advantage of reduced likelihood for inducing antibiotic resistance compared to conventional antibiotic treatments.

Importance: Listeria monocytogenes infections are lethal to specific groups. With the antibiotic crisis, new treatments are needed. Taurine, a safe dietary compound, was found to inhibit Listeria growth. It targets both L. monocytogenes virulence and host immunopathology, stimulated T-cell proliferation, and inhibited pyroptosis. We establish taurine as the non-antibiotic agent that decouples bacterial cytotoxicity from inflammation-driven tissue damage, offering an immediately translatable strategy for high-risk infections amid the antibiotic resistance crisis.

Clostridium thermocellum is a leading candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels due to its native cellulolytic capabilities. Beyond ethanol, C. thermocellum is being developed as a platform for producing higher-chain alcohols such as isobutanol and n-butanol. However, its physiological adaptations to alcohol stress remain poorly understood. Here, we investigate how C. thermocellum remodels its membrane lipid composition in response to exogenous ethanol, n-butanol, isobutanol, and butyrate. Exposure to linear alcohols such as n-butanol or to organic acids like butyrate increased the proportion of straight-chain fatty acids in the membrane at the expense of branched-chain species, whereas exposure to the branched alcohol isobutanol produced the opposite effect. Isotope tracer experiments demonstrated that C. thermocellum directly incorporates the carbon backbones of exogenous alcohols and acids into fatty acids, providing a mechanistic basis for these contrasting shifts. We show that the bifunctional aldehyde/alcohol dehydrogenase AdhE is essential for the assimilation of exogenous alcohols into fatty acids, acting through its oxidative activity by first oxidizing alcohols to aldehydes and then converting them to acyl-CoA intermediates. Deletion of the pyruvate:ferredoxin oxidoreductase isozyme pfor4 abolished branched-chain fatty acid synthesis, but supplementation with isobutanol restored production, indicating that Pfor4 substitutes for the canonical branched-chain α-keto acid dehydrogenase complex. These findings reveal two distinct routes for branched-chain fatty acid production in C. thermocellum: a Pfor4-dependent pathway from α-keto acid intermediates derived from amino acid synthesis, and an AdhE-dependent salvage pathway that assimilates exogenous branched-chain alcohols.

Importance: This study identifies key mechanisms of Clostridium thermocellum membrane remodeling under alcohol stress, showing that AdhE mediates incorporation of exogenous alcohols into fatty acids, while Pfor4 drives branched-chain fatty acid synthesis in the absence of the canonical Bkd complex. These findings highlight actionable targets for metabolic engineering to enhance solvent tolerance and improve the robustness and productivity of C. thermocellum as a biofuel-producing platform.

Indigenous high-altitude populations maintain relatively normal brain function despite chronic hypoxia, yet the underlying neurophysiological mechanisms and the potential role of gut-brain interaction remain unclear. This study combined 16S rRNA gut microbiota profiling in 211 high-altitude indigenous populations at 2, 3, and 4 km altitudes with resting-state and task-based electroencephalography recordings in 135 of them. Residents at 4 km showed enhanced delta (1-4 Hz) power across most brain regions along with increased frontal-occipital functional connectivity (FC) during resting state. During a cognitive oddball task, the 4 km group exhibited elevated P3 amplitude in response to oddball stimuli, together with larger parietal delta power. In parallel, the 4 km group displayed higher species richness and an elevated abundance of short-chain fatty acid-producing genera such as Roseburia, Blautia, and Coprococcus. Furthermore, the abundance of Blautia was positively associated with resting-state FC, a relationship that may further influence anxiety and sleep quality. Our findings demonstrate a coordinated gut-brain interaction adaptation to high altitude, highlighting the homeostatic role of microbial pathways.IMPORTANCEIndigenous high-altitude populations maintain normal cognitive function under chronic hypoxia, a process potentially involving the gut microbiota. Our study added evidence that the neural activity patterns and gut microbiota structure may work in coordination to assist the host in adapting to extreme environments.

Bacterial pathogens vary markedly from species to species in their capacity to cause different types of infection. A recent study by Penaranda and colleagues in mSystems shows that the genetic backgrounds of Pseudomonas aeruginosa isolates do not dictate whether they infect the lungs, blood, urine, or other body sites (C. Penaranda, E. P. Brenner, A. E. Clatworthy, L. A. Cosimi, et al., mSystems 11:e01362-25, 2026, https://doi.org/10.1128/msystems.01362-25). These findings suggest that each P. aeruginosa strain is versatile and has the potential to infect a variety of tissues and organs.

Conjugation, the exchange of genetic material between different bacterial species, is an important process underlying adaptation. The reason for this is that conjugative elements carry additional genes potentially providing adaptive benefit to the host, such as antibiotic resistance or pathways for degradation of environmental contaminants. However, there is increasing evidence that the conjugative process itself is also responsive to cellular or environmental cues and may, thus, be under rate-dependent selection. Here, we investigate the integrative and conjugative element ICEclc as a model for both metabolic pathway "engrafting" (i.e., how a Pseudomonas putida-encoded benzoate pathway is expanded to 3-chlorobenzoate; 3-CBA) and understanding how metabolic cues or states may lead to ICE activation. We compared differences in gene expression of P. putida with or without ICEclc grown on 3-CBA, benzoate, and succinate, both in exponential and stationary phase conditions. Mutants were constructed in the 3-CBA metabolic pathway, and effects on ICE-transfer were examined. We further deleted parts of a seemingly redundant methyltetrahydrofolate (mTHF) biosynthesis operon that was highly expressed during 3-CBA growth and studied its effects on ICE-activation. Our results demonstrate that 3-CBA metabolism is necessary for ICE activation and reveal an unexpected connection between mTHF pathway induction and ICEclc activation and transfer. These findings show how metabolic states may arise that are perceived by the ICE and lead to an increase in its transfer frequency, thereby mobilizing the very genes that partly caused this state to appear.

Importance: Bacterial conjugation is widely appreciated for its diversity, its molecular details, and evolutionary consequences. However, the regulation of the onset of the conjugative process in or by the host cell is frequently taken for granted, whereas any influence of environmental or cellular cues on the rates of conjugation can have drastic consequences on both positive and negative outcomes of conjugation-dependent adaptation (e.g., the distribution of genes for antibiotic resistance). We study here a particular case of an integrative and conjugative element (ICEclc), representative of a widely distributed family of elements pervasive in pseudomonads, which has a modulable conjugation rate in donor populations that is dependent on the proportion of transfer-competent cells arising in stationary phase. Transfer-competent cell appearance permits to quantify and understand conditions favoring ICE activation and transfer, and we show here how the ICE reacts to differences in the physiological states of the host cell under influence of its metabolism of aromatic compounds.