Microbial Ecosystem Research Articles (Page 1)

The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples. Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3min for taxonomic analysis and 10min for strain-level analysis against the human microbial gene catalogue when processing 10M paired reads - operating within a modest 5GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results. These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.

Despite low temperatures and limited availability of water and nutrients, there is a high level of biological diversity hidden in the glaciers. Glacial microbial ecosystems are primarily composed of bacteria, algae, and fungi. However, knowledge about viruses in these extreme environments remains limited. To address this gap, we conducted virome analysis on two Slovenian glaciers: Triglavski ledenik (Triglav glacier) and ledenik pod Skuto (glacier below Skuta). From concentrated samples of melted glacial ice, we isolated ribonucleic acids (RNA), amplified them using random oligonucleotide primers, and performed untargeted sequencing using the Illumina platform. Through bioinformatic analyses, we identified viral sequences in the obtained data and classified them taxonomically. As expected, the proportion of reads classified as viral was low. Despite focusing on the description of RNA viral diversity, the most frequently detected viral reads in all glacier samples were those belonging to DNA bacteriophages, classified within the realm Duplodnaviria. Most of the viral sequences discovered in the Slovenian glacier samples showed low identity with known viral sequences in databases, indicating the presence of numerous novel viral species. Longer assembled viral sequences likely represent complete genomes of newly discovered RNA viruses (e.g., sequences related to toti-like and picorna-like virus groups). For these sequences, phylogenetic analyses revealed their closest known viral relatives and potential host organisms. This study represents the first insight into the presence of viruses in Slovenian glacier environments and reveals a large, previously unexplored diversity of these biological entities.

Cold environments, including glaciers, ice sheets, permafrost soils and sea ice, are common across the surface of the Earth. Despite the challenges of life at subzero temperatures, the global cryosphere hosts diverse microbial communities that support biogeochemical cycling and ecosystem functioning in areas where few other organisms can survive. However, the composition and function of cryosphere microbial communities, and the continued existence of cryosphere habitats, are threatened by ongoing climate change, which has disproportionate impacts in polar regions. In this Review, we survey the breadth of cryosphere habitats and the composition, function and unique adaptations of the microbial communities that inhabit them. We outline how climate change can affect these communities and the ecosystem services they provide through short-term changes in substrate availability, enzyme activity and redox potentials as well as longer-term changes in community composition. We also explore the wide-ranging consequences these changes may have for local ecosystems, human communities and the global climate. Finally, we outline the knowledge gaps in cryosphere microbial ecology that contribute to uncertainties about the future of these ecosystems in a warming world.

The intestinal barrier is a complex configuration that defends against external assaults and maintains intestinal health. Disruption of barrier function can lead to intestinal inflammation and various diseases. Mucins are the primary structural components of the intestinal barrier, and their extensive glycosylation is critical for their protective function. Mucin glycans enhance the physicochemical integrity of the mucus barrier, protect against enzymatic degradation, modulate host immune responses, and shape the gut microbiota by providing adhesion sites and selective nutrient sources. While proper glycosylation maintains barrier integrity, supports a balanced microbial ecosystem, and limits unnecessary immune activation, its disruption leads to compromised barrier function, microbial dysbiosis, increased intestinal permeability, and ultimately contributes to the development of chronic colitis and colorectal cancer. Therefore, mucin glycosylation plays a crucial role in preserving intestinal barrier integrity and preventing colonic diseases. This review summarizes the classifications and structural features of intestinal mucin glycosylation, elucidates their roles in maintaining barrier function and their pathological alterations in intestinal disorders, and highlights the implications of mucin glycosylation for precision diagnosis and targeted therapy of intestinal diseases.

The gut microbiota plays a vital role in intestinal homeostasis and the regulation of the immune system, thereby influencing overall well-being. Disruption of this microbial ecosystem, termed dysbiosis, has been implicated in the aetiology of a large number of human diseases, including inflammatory bowel diseases (IBD). IBD is classified into Crohn's disease (CD) and ulcerative colitis (UC). Several factors, such as genetic predisposition and gut microbiota, cause IBD. It has been suggested that there is a significant correlation between the development of IBD and alterations in the gut microbiome. This disproportion between healthy gut microbiota and their metabolites has recently been revealed by clinical studies, with the development of screening, sequencing, and multiomics technology. Therefore, gut microbiome dynamics studies and their interaction with the host can have essential results on the pathogenesis of IBD. Hence, this review highlights the recent findings on the role of the gut microbiota in IBD, the mechanisms by which microbial dysbiosis leads to inflammation, and the development of novel therapeutic strategies targeting the microbiome. In addition, we talked about potential interventions involving the microbiome, such as probiotics, prebiotics, and microbiome-directed therapies as well.

Abstract The intratumoral microbiome is an emerging hallmark of cancer, yet its multi‐kingdom host–microbiome ecosystem in colorectal cancer (CRC) remains poorly characterized. Here, we conducted an integrated analysis using deep shotgun metagenomics and proteomics on 185 tissue samples, including adenoma (A), paired tumor (T), and para‐tumor (P). We identified 4057 bacterial, 61 fungal, 108 archaeal, and 374 viral species in tissues and revealed distinct intratumor microbiota dysbiosis, indicating a CRC‐specific multi‐kingdom microbial ecosystem. Proteomic profiling uncovered four CRC subtypes (C1–C4), each with unique clinical prognoses and molecular signatures. We further discovered that host‐microbiome interactions are dynamically reorganized during carcinogenesis, where different microbial taxa converge on common host pathways through distinct proteins. Leveraging this interplay, we identified 14 multi‐kingdom microbial and 8 protein markers that strongly distinguished A from T samples (area under the receiver operating characteristic curve (AUROC) = 0.962), with external validation in two independent datasets (AUROC = 0.920 and 0.735). Moreover, we constructed an early‐ versus advanced‐stage classifier using 8 microbial and 4 protein markers, which demonstrated high diagnostic accuracy (AUROC = 0.926) and was validated externally (AUROC = 0.659–0.744). Functional validation in patient‐derived organoids and murine allograft models confirmed that enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum promoted tumor growth by activating Wnt/β‐catenin and NF‐κB signaling pathways, corroborating the functional potential of these biomarkers. Together, these findings reveal dynamic host–microbiome interactions at the protein level, tracing the transition from adenoma to carcinoma and offering potential diagnostic and therapeutic targets for CRC.

Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting and drought associated microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five populations of Oreocharis mileensis , a resurrection plant, during hydrated and dehydrated states to examine population-level microbiome differences or affinity, identify microorganisms that may assist during plant desiccation, and assess their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, and endosphere) but exhibited only moderate drought-induced changes, suggesting that O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa varied relatively between populations, reflecting niche specialization and host genotype. Drought increased bacterial alpha diversity while reducing beta diversity, indicating homogenization driven by stress-tolerant taxa such as Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (e.g., Microlunatus, Rubrobacter) and other drought-resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought conditions. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. Overall, this study expands our understanding of microbiome assembly in resurrection plants and highlights candidate microbes for microbiome engineering to enhance crop stress tolerance.

The oral cavity harbors one of the most diverse microbial ecosystems in the human body, second only to the gut. Periodontitis, a chronic inflammatory disease arising from oral microbiota dysbiosis, has been increasingly associated with systemic disorders such as diabetes mellitus, atherosclerosis, rheumatoid arthritis, inflammatory bowel disease, and neurodegenerative conditions. Although hematogenous dissemination of oral pathogens and inflammatory mediators has long been proposed as a mechanistic link, emerging evidence identifies the oral–gut axis as a novel bidirectional pathway. Swallowed oral pathobionts, such as Porphyromonas gingivalis and Fusobacterium nucleatum, can colonize the gut, disrupt the intestinal barrier, and induce dysbiosis, immune imbalance, and metabolic alterations that aggravate systemic inflammation and disease progression. In contrast, gut dysbiosis, especially in obesity or high-fat-diet models, can exacerbate periodontal tissue destruction through hyperuricemia, altered bone metabolism, and Th17/Treg immune imbalance. Experimental and clinical studies further support this reciprocal relationship, implicating microbial, metabolic, and immune crosstalk in both oral and systemic pathology. Understanding this oral–gut–systemic axis offers a paradigm shift in diagnostics and therapeutics, focusing on precision interventions such as microbiome modulation, probiotics, and integrated oral care to mitigate systemic inflammatory burden and improve overall health outcomes.

Xanthohumol (XN), a polyphenol from hops (Humulus lupulus), exhibits antioxidant, anti-inflammatory, antihyperlipidemic, and chemo-preventive activity. Preclinical evidence suggests gut microbiota are critical to mediating some of these bioactivities. Nevertheless, its precise impact on human gut microbiota, particularly at supplemental doses, remains poorly characterized. We evaluated 200 mg/day XN for 3 weeks on human gut microbiota in a eubiotic and dysbiotic model using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Functional assessments of microbiota included quantification of XN metabolites, short-chain fatty acids (SCFAs), and untargeted metabolomics of the digestive metabolome. Bacterial composition was assessed by 16S rRNA gene sequencing. XN reduced alpha-diversity and short-chain fatty acid production in both models, as well as altered taxa abundance variably between models. XN disrupted bile acid metabolism through inhibition of microbial bile salt hydrolase (BSH). The modulation of bile acid metabolism has important implications for host-level bioactivity of XN.

The global prevalence of inflammatory bowel disease (IBD) has been increasing in recent years, paralleling a growing recognition of gut dysbiosis as a pivotal etiological factor. Emerging evidence reveals intricate crosstalk between the oral and gut microbial ecosystems, with oral-derived microbiota potentially translocating to the intestinal tract through hematogenous or enteral routes. This microbial crosstalk has crystallized into an "oral-gut axis" pattern, providing novel mechanistic insights into the pathogenesis of IBD. In this review, we summarize currently available studies on the oral-gut axis and the relationship between the oral-gut axis and IBD to evaluate the role of the axis in the pathogenesis of IBD development.

Tire wear particles drive size-dependent loss of freshwater bacterial biofilm diversity.

Dual-functional probiotic hydrogel with puerarin integration for microbiota-neuroimmune regulation in antibiotic-free periodontitis therapy.

Synthetic microbial community mimicking kefir for investigating community dynamics and interspecies interactions.

Modulation of butyrate-induced stress responses in Bacteroides by lotus seed resistant starch and its sugar degradation products.

Application of integrated in vitro fecal cultivation and 16S rRNA gene sequencing for optimizing beneficial gut microbiota combinations.

Late preterm prelabor rupture of membrane (>33 weeks): the risk of intraamniotic inflammation and fetal inflammation is influenced by the cervical microbial ecosystem and cervical inflammation.

Fumigation-driven restructuring of soil microbial ecosystems enhances endangered Fritillaria cirrhosa productivity and secondary metabolite biosynthesis: Insights from metabolomics and microbiome profiling

Ideal dietary fiber model: Personalized gut microbiota modulation based on structure-function relationships.

Mastitis represents one of the most economically devastating diseases in dairy production, causing billions of dollars in annual losses through reduced milk quality and quantity. Recent advances in microbiome research have unveiled a critical gut–mammary axis that fundamentally influences mastitis susceptibility and pathogenesis in dairy cattle. Through comprehensive analysis of microbial communities across multiple anatomical sites, we demonstrate that mastitis development involves systematic disruption of both mammary and gastrointestinal microbiomes, characterized by reduced beneficial bacterial populations and increased pathogenic species. Healthy animals maintain balanced microbial ecosystems dominated by protective taxa including Firmicutes, Bacteroidetes, and beneficial Lactobacillus species, while mastitis-affected animals exhibit dysbiotic shifts toward Proteobacteria dominance, elevated Streptococcus and Staphylococcus populations, and compromised microbial diversity. Mechanistic investigations reveal that gut microbiota disruption compromises systemic immune competence, alters metabolite production including short-chain fatty acids and bile acids, and influences inflammatory mediators that circulate to mammary tissue. Therapeutic interventions targeting this axis, including probiotics, prebiotics, and plant-derived compounds, demonstrate significant efficacy in restoring microbiome homeostasis and reducing mastitis severity. These findings establish the gut–mammary axis as a fundamental regulatory mechanism in mastitis pathogenesis, opening new avenues for microbiome-based prevention and treatment strategies that could significantly enhance dairy health management while addressing antimicrobial resistance concerns.

BackgroundKhecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake’s microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.ResultsICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.ConclusionThis first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04450-1.