Search Results (1,221)

All forms of life on Earth are dependent on microbes. In vertebrates, the oral cavity and the gastrointestinal tract are colonized by large numbers of microorganisms, which includes species from many life forms: bacteria, fungi, archaea, and protozoa; this collection of microorganisms are commonly referred to as the microbiome. This article reviews the literature, providing a summary of oral and gastrointestinal microbial composition in health and during various disease states. Interactions are explored between microbes in the oral cavity and gastrointestinal tract. This study explores the influence of changed diet, lifestyle, and living conditions in order to examine the link between the oral and gastrointestinal microbiome and changes in their composition, and how this may affect human health. This study also investigates potential microbiome dysbiosis and disease causation in the space environment. The role of prebiotics, probiotics and postbiotics in oral health is discussed, with extension into the unexplored territory of probable oral and gastrointestinal bacterial population changes during long-duration (exportation class) space missions (ECSM). Full article

The human gastrointestinal tract hosts a complex ecosystem known as the gut microbiota, which plays a crucial part in digestion and immune system function. Among the clinically recognized manifestations of dysbiosis in this system are Small Intestinal Bacterial Overgrowth (SIBO), Intestinal Methanogen Overgrowth (IMO), Small Intestinal Fungal Overgrowth (SIFO), and Large Intestinal Bacterial Overgrowth (LIBO). This study aims to investigate the complex pathophysiological mechanisms underlying these syndromes and their diagnostics and therapeutic options, focusing primarily on the roles of methane-producing archaea and fungal overgrowth. The methods employed in this study involve a comprehensive analysis and synthesis of peer-reviewed articles, systematic reviews, clinical trials, and meta-analyses. This review summarizes that methane production by Methanobrevibacter smithii was linked to altered fermentation, reduced microbial diversity, and slowed intestinal transit. Fungal species were associated with increased intestinal permeability, inflammation, and biofilm formation. Targeted interventions addressing microbial imbalances demonstrated potential therapeutic value. This review highlights the complex and multifactorial nature of gut dysbiosis, revealing its impact beyond the gastrointestinal tract. While emerging therapies targeting methanogens, fungi, and biofilms show promise, further research is essential to optimize their clinical application. The findings emphasize the need for interdisciplinary collaboration to refine diagnostic and therapeutic strategies. Full article

Background/Objectives: The human skin provides a protective barrier composed of bacteria, fungi, viruses, and archaea that prevents the invasion of harmful organisms. Recent advancements in genomic sequencing have allowed for greater accuracy of species detection. This review aims to summarize the most up-to-date skin microbiome shifts in various dermatological diseases. Methods: A systematic search was conducted to examine microbiome shifts comparing lesional and nonlesional or diseased and healthy skin across various dermatological conditions. A literature search was conducted on PubMed, Web of Science, and Embase Databases from inception through April 2024, yielding 38 studies. Results: Staphylococcus aureus was reported unanimously in all skin conditions. Most studies in this review, except those investigating acne vulgaris, showed a decreased microbiome diversity in diseased skin. Finally, there was a greater shift in the proportion of pro-inflammatory bacterial and fungal strains. Conclusions: The skin microbiome is significantly altered in the progression of numerous dermatological diseases. Diversity of the skin microbiome is decreased, and there is an increased proportion of pro-inflammatory bacterial and fungal strains. The skin microbiome also provides a more comprehensive understanding of the development and progression of many inflammatory skin diseases. Prebiotic treatments may propose a much safer and cheaper alternative to antibiotics, which can have highly toxic side effects and negative implications for public health regarding antibiotic resistance. More research is required to fully understand both the microbiome changes and efficacy and viability of using probiotic treatments to restore the skin microbiome, thereby improving patient outcomes in all dermatological conditions. Full article

The discovery of Asgard archaea has reshaped our understanding of eukaryotic origins, supporting a two-domain tree of life in which eukaryotes emerged from Archaea. Building on this revised framework, we propose the Pre-prokaryotic Organismal Lifeforms Existing Today (POLET) hypothesis, which suggests that relic pre-prokaryotic life forms—termed POLETicians—may persist in deep, anoxic, energy-limited environments. These organisms could represent a living bridge to the RNA world and other origin-of-life models, utilizing racemic oligoribonucleotides and peptides, non-enzymatic catalysis, and mineral-assisted compartmentalization. POLETicians might instead rely on radical-based redox chemistry or radiolysis for energy and maintenance. These biomolecules may be racemic or noncanonical, eluding conventional detection. New detection methods are required to determine such life. We propose generalized nanopore sequencing of any linear polymer—including mirror RNAs, mirror DNAs, or any novel genetic material—as a potential strategy to overcome chirality bias in modern sequencing technologies. These approaches, combined with chiral mass spectrometry and stereoisomer-resolved analytics, may enable the detection of molecular signatures from non-phylogenetic primitive lineages. POLETicians challenge the assumption that all life must follow familiar biochemical constraints and offer a compelling extension to our search for both ancient and extant forms of life hidden within Earth’s most extreme environments. Full article

Phylogenetic studies of the pyruvate kinase family reveal two clusters: the K⁺-dependent and -independent enzymes. Thermoplasma acidophilum pyruvate kinase belongs to the latter but possesses the conserved signature of those K⁺-dependent. Recently, we found two distinct ways for these groups to catalyze. It is interesting to elucidate how the T. acidophilum enzyme achieves its active conformation. A structural model of this enzyme revealed the presence of an extra C-terminal sequence (ECTS). To understand its role, an enzyme lacking this sequence from T. acidophilum was constructed. We then compared the kinetic parameters, far-UV CD spectra, thermal stability, molecular dynamics simulations, and oligomeric states of both the wild-type and truncated enzymes. We found that the truncated enzyme is aggregated and almost inactive, with residual 20% of the total interactions, and it exhibits a soluble fraction of smaller oligomeric states than the wild-type enzyme. These findings suggest that ECTS plays a crucial role in maintaining its active tetrameric state. This sequence is the first reported in an archaeal pyruvate kinase and is also found in other archaea and bacteria. Phylogenetic analysis of ECTS in pyruvate kinases exhibits a sparse distribution that might be explained if ECTS represents an ancient domain prone to loss. Full article

The black soil region of Northeast China is crucial for agricultural productivity. Ammonia-oxidizing archaea (AOA) are key indicators of soil nitrification in this region, yet it remains unclear whether this process is driven by the entire community or by specific clusters. Here, we investigated the AOA community across a long-term fertilization Brown Soil Experimental Station and 15 sites in the Typical Black Soil Zone. Using Illumina MiSeq sequencing of the AOA amoA gene and cluster-specific primers, 14 OTUs were selected as core clusters based on relative abundance >0.1% and strong correlations (r > 0.7) with soil properties or PNR, and were further grouped into five distinct clusters according to phylogenetic analysis. Compared to the overall AOA community, core clusters responded more precisely to fertilization, straw addition, and spatial variation, with contrasting environmental responses reflected in their relationships with soil nitrification dynamics. Clusters G1 and G2 had positive correlations with soil PNR, while Clusters G4 and G5 had negative correlations. Moreover, AOA core clusters demonstrated stronger correlations with soil properties, including pH, C/N ratio, and NH₄⁺/NO₃⁻ ratio. These findings demonstrate that AOA core clusters are reliable microbial indicators of soil nitrification, and monitoring their abundance changes under nitrogen input can provide early insights into potential inhibition, informing predictive models and guiding more precise nitrogen management to support sustainable agricultural practices. Full article

Desert plants host specialized microbiomes that contribute to their survival under extreme conditions; yet, niche and specific microbial dynamics remain poorly understood. In this study, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with Leptadenia pyrotechnica, which is a desert-adapted shrub. Five representative sample types were analyzed: rhizospheric soil from a non-arid adjacent location (control; S1); rhizospheric soil from the arid site (S4); and stem endosphere from the arid site (S5, S6, and S7). For each sample type, three biological replicates were collected from different healthy plants to ensure independence. Sequencing yielded high-quality datasets (89,000–134,000 reads/sample) with ASV retention ratios of 68–80%, confirming their sufficient depth for diversity profiling. Alpha diversity indices revealed a markedly greater richness in rhizospheric samples (e.g., S1 Shannon: 3.04; 530 ASVs) than in endosphere samples (Shannon < 1.0; ASVs ≤ 33), consistent with known gradients in desert plant microbiomes. Rarefaction curves confirmed the completeness of sampling. Beta diversity analyses, including PCoA and hierarchical clustering, showed clear segregation between rhizospheric and endophytic communities, indicating strong compartment-specific structuring. The rhizosphere was dominated by Actinobacteria (48%), Proteobacteria (32%), and Firmicutes (10%), whereas the stem endosphere was enriched in Proteobacteria (45%) and Actinobacteria (40%). Taxonomic profiling revealed that Bacillota and Actinomycetota dominated rhizospheric soils, including Bacillus licheniformis, while stem tissues were enriched in Cyanobacteriota and Alphaproteobacteria, suggesting host-driven filtering. Genera such as Cupriavidus, Massilia, and Noviherbaspirillum were exclusive to the rhizosphere, while Paracholeplasma appeared uniquely in stem sample S6. Archaea and rare phyla were nearly absent. The current findings indicate that L. pyrotechnica harbors distinct microbial assemblages in rhizospheric and endophytic niches, reflecting microhabitat-driven selection. These microbial communities may contribute to host resilience by harboring taxa with potential stress-tolerance traits, offering insights for microbiome-informed strategies in arid land restoration. Full article

High-altitude wetland holds unique peatland ponds subjected to extreme diel environmental condition changes. Herein, we evaluate the response of photoautotrophic and nitrification activities and compare it with bacteria and archaea composition shifts in sediment and water changes during key hours of the day. Results indicate the presence of photo-inhibition, including ammonia oxidizers, but a high recovery of photosynthetic activities in the microbial mat and of potential specific functional groups towards the afternoon. The microbial community was composed of 45 phyla, mainly proteobacteria from Alpha-, Delta-, and Gammaproteobacteria and Bacteroidota in the water and sediments, and these later groups were notoriously enriched during the afternoon. The microbial community composition changes were associated with chlorophyll a, nutrients, and greenhouse gases reservoir variability, including methane potential release towards the atmosphere at hours of high radiation. Peatland pond microbial communities and their biogeochemical contribution change in a complex interplay coupled by time to environmental conditions predominantly driven by the extreme solar radiation. Full article

The biotechnological conversion of CO₂ to biomethane represents an energy-efficient, environmentally friendly, and sustainable approach within the waste-to-energy cycle. This process, in which CO₂ and H₂ are converted to biomethane in anaerobic bioreactors, is referred to as hydrogenotrophic biomethane production. While several studies have investigated hydrogenotrophic biomethane production, there is a lack of research comparing flocculent and granular sludge inoculum in continuously operated systems fed with a gas substrate. Both granular and flocculent sludge possess distinct advantages: granular sludge offers higher density, stronger microbial cohesion, and superior settling performance, whereas flocculent sludge provides faster substrate accessibility and more rapid initial microbial activity. In this study, two UASB (Upflow Anaerobic Sludge Blanket) reactors operated under mesophilic conditions were continuously fed with synthetic off-gas composed of pure H₂ and CO₂ in a 4:1 ratio and were compared in terms of microbial community shifts and their effects on hydrogenotrophic biomethane production. Biomethane production reached 75 ± 2% in the granular sludge reactor, significantly higher than the 64 ± 1.3% obtained with flocculent sludge. Although hydrogen consumption did not differ significantly, the granular sludge reactor exhibited higher CO₂ removal efficiency. Microbial analyses further revealed that granular sludge was more effective in supporting methanogenic archaea under conditions of gas substrate feeding. These findings offer advantageous suggestions for improving biogas production, enhancing waste gas management, and advancing sustainable energy generation. Full article

SSB proteins play essential roles in DNA replication, recombination, and repair in bacteria, archaea, and eukarya. This study investigates the transcript levels, identification, expression and purification, subcellular localization, and immune protective potential of the SSB-like proteins of Eimeria necatrix (EnSSB), exploring its role in the development of E. necatrix and its potential as a candidate antigen for a subunit vaccine against avian coccidiosis. The level of EnSSB gene transcription was highest in unsporulated oocysts (UO), followed by gametocytes (GAM) (p < 0.05). The gene consisted of an open reading frame of 1488 nucleotides encoding a protein of 495 amino acid residues with a predicted molecular weight of 53.31 kDa. EnSSB contained a SSB domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. The molecular mass of the native protein, as determined by Western blot analysis, was ~58 kDa in second-generation merozoites (MZ-2) and UO. In addition to the 58 kDa band, four other bands (~98 kDa, ~82 kDa, ~36 kDa and ~28 kDa) were detected in GAM. No bands were detected in MZ-3. Indirect immunofluorescence and immuno-electron microscopy localized EnSSB in the cytoplasm of macrogametocytes but not in wall-forming bodies and oocyst wall. Animal challenge experiments demonstrated that rEnSSB elicited robust IgY responses, increased splenic T lymphocytes and body weight gain, reduced intestinal lesion scores and oocyst shedding, and presented anticoccidial index (ACI) more than 160. These findings not only offer a foundation for understanding the role of EnSSB protein in regulating the development of E. necatrix, but also present a potential protective antigen of E. necatrix for the development of a subunit vaccine against avian coccidiosis. Full article

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation. Full article

The impact of long-term organic (ECO) versus conventional (CON) agricultural management on subsurface soil microbiota diversity and soil physicochemical properties remains unclear in Mediterranean vineyards. This study evaluated long-term ECO and CON effects in the Alt Penedès terroir (Spain), focusing on subsurface soil microbial diversity and soil characteristics. ECO increased the fungal-to-bacterial ratio and ammonium-oxidizing bacteria but reduced total subsurface soil bacterial populations and soil organic carbon. While ECO did not enhance annual yield production in the vineyard, fungal abundance, and ammonium-oxidizing archaea, it slightly increased the overall alpha diversity (Shannon and Inverse Simpson indexes) and significantly altered taxa composition in subsurface soil with a more robust and modular community. Crop management, soil texture, training system, and rootstock, but not vine variety, significantly influenced beta diversity in subsurface soil. The Mantel test revealed subsurface soil texture, Ca²⁺/Mg²⁺ ratio, and salinity as the main key soil drivers shifting the microbial community (beta diversity), while C/N and topsoil organic matter significantly correlated with bacterial abundance; NH₄⁺ correlated with fungal abundance; and N-Kjeldahl, pH, and Mg²⁺/K⁺ correlated with alpha diversity. Integrating soil microbiota and physicochemical monitoring allowed us to confirm the positive effect of long-term agroecological practices on subsurface soil health and to identify the critical factors shaping their microbial communities in Mediterranean vineyards. Full article

The submerged petrified forest in Sozopol Bay, located along Bulgaria’s southeastern coast in the Black Sea, is an extraordinarily rare natural phenomenon that has remained unexplored in terms of microbial diversity until now. This study focuses on characterizing the microbial communities associated with this unique habitat. Ancient petrified tree remnants located at depths of 18–20 m were sampled in August–September 2024, targeting four tree trunks from different sites within the bay. The quantitative assessment of selected bacterial groups, essential for nutrient cycling, organic matter degradation, and marine ecosystem health, revealed distinct community profiles. 16S rDNA sequencing of cultivated isolates identified a diverse microbial community predominantly composed of γ-Proteobacteria, with key representatives such as Vibrio aestuarianus, Vibrio orientalis, Pseudoalteromonas, and Cobetia sp. The culture-independent approach confirmed the dominance of Proteobacteria, along with other prevalent phyla like Bacteroidetes, Planctomycetes, and Actinobacteria. The most abundant taxa included Woeseia oceani, Ilumatobacter coccineus, Halioglobus maricola, and Vibrio breoganii. Archaea made up about 3% of classified reads. Fungal sequences accounted for less than 2% of the total reads, indicating a low fungal prevalence. These results provide essential baseline data for future monitoring and the conservation of this unique habitat and its diverse microbial communities. Full article

Global agricultural intensification has exacerbated soil compaction and nitrogen (N) inefficiency, thereby threatening sustainable crop production. Sub-soiling, a tillage technique that fractures subsurface layers while preserving surface structure, offers potential solutions by modifying soil physical properties and enhancing microbial-mediated N cycling. This study investigated the effects of subsoiling depth (0, 20, and 40 cm) on soil microbial communities and N transformations in a semi-arid maize system in China. The results demonstrated that subsoiling to a depth of 40 cm (D2) significantly enhanced the retention of nitrate-N and ammonium-N, which correlated with improved soil porosity and microbial activity. High-throughput 16S rDNA sequencing revealed subsoiling depth-driven reorganization of microbial communities, with D2 increasing the abundance of Proteobacteria (+11%) and ammonia-oxidizing archaea (Nitrososphaeraceae, +19.9%) while suppressing denitrifiers (nosZ gene: −41.4%). Co-occurrence networks indicated greater complexity in microbial interactions under subsoiling, driven by altered aeration and carbon redistribution. Functional gene analysis highlighted a shift from denitrification to nitrification-mineralization coupling, with D2 boosting maize yield by 9.8%. These findings elucidate how subsoiling depth modulates microbiome assembly to enhance N retention, providing a mechanistic basis for optimizing tillage practices in semi-arid agroecosystems. Full article

Background/Objectives: Inteins are mobile genetic elements invading highly conserved genes across all domains of life and viruses. Five active intein insertion sites (MCM-a through e) had previously been identified and studied in the archaeal replicative helicase minichromosome maintenance (MCM) subunit gene mcm, making MCM an ideal system for dissecting the dynamics of multi-intein genes. However, work in this system thus far has been limited to particular archaeal groups. To better understand the dynamics and diversity of these inteins, MCM homologs spanning all archaeal groups were extracted from NCBI’s non-redundant protein sequence database, and the distribution and structural architectures of their inteins were characterized. Methods: The amino acid sequences of 4243 archaeal MCM homologs were retrieved from NCBI’s non-redundant protein sequence database. These sequences were systematically assessed for their intein content through within-group multiple sequence alignments. To characterize the inteins present at each site, extensive intein structure predictions and comparisons were performed. Phylogenetic analyses were used to investigate intein relatedness between and within sites, as well as the distribution of different MCM inteins in geographically overlapping populations of archaea. Results: In total, 11 active MCM intein insertion sites were identified, expanding on the previously known five. The insertion sites have varied invasion activity levels across archaeal groups, with Nanobdellati (DPANN) being the only group with all 11 sites active. In all but two (Methanonatronarchaeia and Hadarchaeota) of the archaeal groups studied where inteins were present, at least one MCM homolog was invaded by more than one intein. With respect to intein structure, within-intein insertions bearing semblance to DNA-binding domains were identified, with varied presence between inteins. Additionally, a study of archaeal MCM sequences of samples collected from the Atacama Desert in June 2013 revealed high MCM intein diversity levels. Conclusions: We identified six new active intein insertion sites in archaeal MCM, more than doubling the five previously known sites. All eleven intein insertion sites were either close to the ATP binding site, or the lined the channel through which the single-stranded DNA is pulled during the catalytic cycle of the helicase. Many of the analyzed inteins contained insertions bearing similarity to DNA-binding helix-turn-helix domains suggesting potential involvement in the intein homing process. Additionally, the high levels of MCM intein diversity observed in archaea from the Atacama Desert provide novel and strong support for a co-existence model of intein persistence. Full article