mSystems最新文献

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller "active core" subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

Importance: Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.

The DPANN archaea comprise a major microbial lineage that appears to be primarily host dependent. Despite the relative ubiquity of DPANN archaea across the biosphere, our understanding of their ecological role is limited due to the absence of cultivated representatives for most DPANN lineages. The majority of cultivated DPANN species are characterized as mildly parasitic ectosymbionts due to reliance on physical interactions with host cells. However, Candidatus Nanohaloarchaeum antarcticus has been reported to adopt a predatory lifestyle, resulting in the lysis of large numbers of host cells. The factors influencing DPANN-host interactions that drive Ca. Nha. antarcticus to adopt an aggressive lifestyle, although other DPANN appear not to, remain unclear. Here, I present a framework for understanding the ecological pressures specific to the Ca. Nha. antarcticus-Halorubrum lacusprofundi system and why a more aggressive, predatory lifestyle improves population persistence compared with a lifestyle more similar to other DPANN.

Microbiome research focusing on late and moderate preterm infants (LMPT; 32 to 36 weeks gestation) is limited, despite rising LMPT births, large healthcare burdens, and increased risks of multiple morbidities, potentially microbially related. In this longitudinal cohort study, 16S rRNA gene sequencing was used to analyze 371 stool and 402 saliva samples from 160 LMPT infants, collected at five time points between birth and 12 months corrected age (CA), to describe spatial and temporal variability in gut and oral microbiomes. Paired stool and saliva samples (n = 337) were analyzed for potential microbial relationships. Early LMPT samples (up to 60 days of life; DOL) were also compared with data from seven extremely preterm infants (EP; <28 weeks gestation; stool n = 14, saliva n = 14). LMPT stool and saliva were composed of distinct microbial communities at each time point, and both sample types showed increasing alpha diversity over time. Stool was initially dominated by Escherichia/Shigella, Klebsiella, and Streptococcus, with Bifidobacterium becoming dominant from term equivalent age (TEA). Contrarily, saliva was dominated by Streptococcus throughout the first year, with early contributions from Staphylococcus and later Veillonella. LMPT infants had higher stool and lower saliva diversity compared with EP infants. Both sample types from EP infants were taxonomically distinct from LMPTs, with Escherichia/Shigella dominating both EP sample types throughout the first 60 DOL. The results highlight the unique trajectories of LMPT microbiomes and emphasize the role of gestational maturity in shaping microbial communities.IMPORTANCEThe oral and gut microbiome develops from birth and plays important roles in health. This has been well studied in extremely preterm infants (EP; born <32 weeks gestation) and term infants (born >38 weeks gestation), but there is a paucity of research describing oral and gut microbiome development in late and moderate preterm infants (LMPT; 32 to 36 weeks gestation). Our study analyzed microbiome development in 160 LMPT infants from birth to 12 months corrected age. The results showed distinct microbial communities in stool and saliva, with increasing alpha diversity and niche specification over time. LMPT infants' gut microbiome became dominated by Bifidobacterium by month 3, while the oral community was consistently dominated by Streptococcus. These results highlight that LMPT infants have gut and oral microbiome development that is more like term infants than EP infants, which has important implications for the care of LMPT infants.

Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation.

Importance: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba²⁺ and Ni²⁺, and biologically essential Mg²⁺. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba²⁺ and Ni²⁺) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.

Therapeutic elimination of high-grade cervical intraepithelial neoplasia (CIN) is widely implemented for cervical cancer prevention. Despite the demonstrated dysbiosis of vaginal microenvironment in high-grade CIN, its post-therapy restorations remain to be poorly understood, especially in functional aspects. This study aimed to characterize temporal changes in both vaginal microbiota (VM) and metabolome (VMeta) following therapeutic elimination of high-grade CIN. We conducted a longitudinal study of 32 HPV-positive women with high-grade CIN who underwent therapeutic procedures. Vaginal swabs were collected at baseline (pre-therapy) and at 6- and 12-month follow-up visits for integrated VM and VMeta analysis. We observed a gradual restoration of Lactobacillus crispatus levels from baseline to 12 months (P < 0.05). Concurrently, we detected significant decreases in dysbiosis-associated bacteria, including Prevotella bivia, Ureaplasma parvum, and Peptoniphilus sp. 6 months post-therapy compared to the baseline. VMeta analysis revealed distinct metabolic shifts across the follow-up periods. The early post-therapy phase (baseline to 6 months) was characterized by enrichment of glycerophospholipids and depletion of nucleotide metabolites, while the later phase (6-12 months) showed increases in flavonoids, lysophospholipids, bioactive amides, and amino acid metabolism. Integration of correlation and dynamic Bayesian network analysis indicated potential regulatory relationships and time-lag effects involving HPV infection, L. crispatus, Bifidobacterium sp., Streptococcus anginosus, Megasphaera sp., U. parvum, and those metabolites. This study enhances our understanding of a sequential restoration process post-therapy in the vaginal microenvironment.IMPORTANCETherapeutic elimination of high-grade CIN is routine, yet functional recovery of the vaginal ecosystem is poorly defined. In a 12-month longitudinal multi-omics study of 32 women, we show stepwise restoration: progressive L. crispatus dominance with sustained decreases in dysbiosis-associated taxa (P. bivia, U. parvum, Peptoniphilus). Metabolically, an early rise in glycerophospholipids and fall in nucleotide metabolites is followed by later enrichment of flavonoids, lysophospholipids, bioactive amides, and amino acid derivatives. Correlation and dynamic Bayesian network analyses reveal putative regulatory links, time-lag effects, and downstream impacts of HPV clearance. These findings deliver a functional roadmap of post-therapy recovery, nominate measurable microbial-metabolite milestones and candidate biomarkers for monitoring, and suggest targets for adjunct interventions to accelerate re-establishment of protective states. This work informs precision follow-up in cervical cancer prevention programs.

Chlamydia trachomatis, an intracellular pathogen, is recognized as the most common sexually transmitted bacterial infection among women worldwide. Chlamydia infections can lead to undesirable clinical outcomes, including pelvic inflammatory disease and infertility. Recently, the gut has been identified as a niche for Chlamydia colonization in human gut-derived organoids. However, despite the biological impact on the host remaining under investigation, oral inoculation of Chlamydia as a whole-organism vaccine has been reported as a promising strategy for preventing genital Chlamydia infections in mice. Few studies have evaluated the impact of oral Chlamydia vaccination on the gut microbiome and metabolite changes. In this study, we assessed time-series alterations in the gut microbiome and metabolites following oral Chlamydia muridarum inoculation in a mice model, and we analyzed the composition and correlation between serum immune parameters and the sequencing profiles in the host. We identified 129 microbial changes and 186 differentially abundant metabolites in the gut across various vaccination approaches during the 30-day immunization process. Additionally, we discussed the potential influence of live Chlamydia on gut epithelium and the biomarkers of effective immunization based on correlation analysis.IMPORTANCEChlamydia infections primarily lead to morbidity rather than mortality. Consequently, in developing and implementing a Chlamydia vaccine, the utmost priority is evaluation of safety. As a promising yet controversial approach, live oral vaccination for Chlamydia raises concerns regarding its impact on the host's gut environment. Our study not only investigates changes in the gut microbiome and metabolites during vaccination but also identifies changes in gut epithelium during vaccination and potential biomarkers during immunization. These findings are crucial for the development of whole-organism oral Chlamydia vaccines and provide valuable insights into the long-term colonization of Chlamydia in the gut.

High-throughput chemical genomics uses phenotypic profiling of strain libraries under defined chemical and environmental conditions to identify gene functions. This approach enables the mapping of biological pathways and can potentially highlight drug targets. Chemical genomic data sets have been springboards for numerous hypothesis-driven research projects, with direct implications for antimicrobial resistance and clinical outcomes. High-throughput phenotypic profiles are valuable tools for enriching microbial sequence data with functional annotations and benefiting the broader scientific community. This work provides a step-by-step guide for conducting chemical genomics screens from start to finish.IMPORTANCEChemical genomic screening is a powerful systems biology approach for linking gene function to phenotype under diverse chemical and environmental stressors. However, its broader use in microbial research has been limited by the lack of standardized, reproducible workflows. Our study introduces a scalable, end-to-end protocol that integrates experimental, imaging, and computational steps into a cohesive framework for high-throughput screening across a range of microbial species. This enables researchers to generate consistent, high-quality phenotypic data suitable for large-scale analyses. The protocol supports systematic exploration of gene-environment interactions, microbial stress responses, and antimicrobial resistance. Its adaptability and troubleshooting guidance make it especially useful for groups working in microbiome research, synthetic biology, and microbial community studies. By bridging benchwork and computational analysis, this workflow expands the technical toolkit available to microbial systems biologists. Our work contributes to the development of robust methods for functional genomics and supports the core mission of mSystems to advance microbial systems biology.

Gut microbiota often influence host defense against infection, but this relationship is incompletely understood in wild bumblebees. These critical pollinators host a characteristic core gut microbiota, yet field studies have offered conflicting insights into its association with Crithidia bombi, a prevalent trypanosomid parasite. To address this gap in our knowledge, we conducted an 3 year field survey, profiling the gut microbiota of 638 bumblebees from 9 sympatric species across diverse sites in Maine using 16S rRNA amplicon sequencing and qPCR for C. bombi detection. We confirmed a robust core bumblebee microbiota, identifying novel host-specific phylogenetic associations of bacterial amplicon sequence variants even among closely related host species. C. bombi infection was common and showed significant seasonal increases. We also found spatial variation, with higher prevalence in coastal regions. Crucially, increasing C. bombi infection load was consistently associated with microbiome dysbiosis. This dysbiosis was characterized by a depletion of core bumblebee-associated microbial taxa, notably Apibacter and Gilliamella (previously shown to be protective), and a corresponding increase in opportunistic, environmentally derived microbes like Entomomonas. While the core microbiota's association with initial pathogen transmission appears minor, its depletion in severe infections strongly supports a correlation to host health in wild bumblebees.

Importance: The community of microorganisms in close association with an animal, its microbiota, can be important to its health. Understanding how microbiota composition relates to health and disease is an important goal with broad potential implications. Like most animals, bumblebees have a characteristic core gut microbiota. We have conducted a broad survey of bumblebees over 3 years to examine the interactions of microbiota composition with infection by an endemic trypanosomatid parasite. We found that the relative abundances of core microbes were inversely related to infection load, and that increased pathogen load was associated with the prevalence of novel microbes. These results are evidence of strong associations between bumblebees and their core microbiota and suggest a role in providing resistance to severe parasitism.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products with wide-ranging structural and functional diversity. Central to many RiPP biosynthetic pathways is the RiPP Recognition Element (RRE), a structurally conserved peptide-binding domain that enables class-independent genome mining. Bioinformatic tools, such as RRE-Finder, have leveraged this domain to identify novel RiPPs, but accuracy has been limited by high false-positive rates. To improve accuracy, we assessed whether structure-based searching of the AlphaFold database with the rapid tertiary structure alignment tool Foldseek could reduce false-positive rates and identify previously unretrievable, sequence-divergent RREs. We used these divergent RREs to build 11 new Foldseek-derived Hidden Markov Models (HMMs) and refined existing models through improved seed alignments, domain excision, bit score thresholds, and Pfam filters. Improved precision mode HMMs retrieved nearly twice as many RREs from the UniProt database as the original models, including novel domain fusions. In total, the updated workflow identified >90,000 high-confidence RREs. To further characterize these RREs and assess their functional relevance, we used a combined bioinformatic and AlphaFold 3 approach to predict over 8,000 RRE-peptide complexes. This enabled the mapping of 13 distinct recognition sequences across known RiPP classes. We further validated the ability of AlphaFold to predict precursor peptide interactions with their cognate RRE domains through binding assays to streamline recognition sequence and putative substrate identification. Together, these improvements enhance the accuracy and scope of RRE-Finder, improving access to previously hidden RRE-dependent biosynthetic pathways.

Importance: Genome mining relies heavily on sequence similarity searches, which severely limit the discovery potential for sequence-divergent proteins. To mitigate this challenge for RRE domain discovery, we employed structure-based alignments to predict sequence-divergent RREs using Foldseek. The newly identified RRE domains were then used to build new HMMs for use by RRE-Finder. This process identified 5,000 previously unidentified but high-confidence RRE domains. Representatives in this sequence-divergent group retain the canonical RRE fold but display new domain fusions, offering additional bioinformatic handles for genome mining. In parallel, AlphaFold 3 modeling of RRE-precursor peptide interactions enabled the identification of 13 distinct recognition sequence motifs, spanning many RiPP biosynthetic pathways. These approaches have significantly expanded the RRE-dependent RiPP biosynthetic landscape.

Large sex hormonal fluctuations are thought to influence vaginal microbiota, but little is known about the impact of small, physiological variations. Here, we tracked changes in vaginal microbiota during four key menstrual cycle phases in 61 healthy, naturally menstruating Italian women from the Women4Health cohort. The microbiota, characterized using a high-depth 16S rRNA amplicon sequencing approach covering four hypervariable regions, was primarily composed of Lactobacillus species, with Lactobacillus iners being the most abundant (average relative abundance: 40%) and the most prevalent (prevalence: 98%). Individual microbiota were generally stable, but beta diversity was higher during the follicular phase (P = 0.007). Only 11 women exhibited compositional shifts, mostly occurring between the follicular and ovulatory phases. Finally, using linear mixed models, we assessed the association between taxa relative abundance and five sex hormones along the menstrual cycle. Among these, 17-beta estradiol showed the largest number of significant associations, linking its increase to a decrease in the relative abundance of taxa that are more common after menopause. Our study highlights specific features of the Italian population and points to the resilience of the vaginal microbiota to physiological hormonal changes. Noteworthy, the observed high abundance of L. iners contrasts with previous studies in European populations, challenging its proposed pathogenic role and suggesting distinct microbiota profiles within Europe.IMPORTANCEThe vaginal microbiota plays an important role in women's health, yet we know little about how it responds to normal hormonal fluctuations. In this study, we followed 61 healthy Italian women over a natural menstrual cycle to explore microbiota changes across different hormonal phases. We found that Lactobacillus iners was the most common species, unlike previous findings in Northern Europe, suggesting population-specific patterns. The common hypothesis that L. iners is invariably linked with poor health is called into question by our findings. They emphasize the importance of considering population context and hormonal status when assessing vaginal health. The vaginal microbiota was generally stable, with only a few changes observed between the follicular and ovulatory phases. When evaluating the association between five sex hormones and taxa abundances, we found that 17-beta estradiol levels had the largest number of significant associations. These highlight an association between increased levels of 17-beta estradiol and increased relative abundance of rare bacterial taxa rather than dominant species like Lactobacillus. Our findings help define what constitutes a "healthy microbiota" in generally healthy Italian women of reproductive age and may inform future strategies for diagnosing or preventing women's health conditions.