Search Results (4,976)

Sorghum genotypes differentially shape their rhizosphere microbiomes to cope with salt stress; however, the modulatory role of biochar in this genotype-specific plant–microbe interplay remains unclear. In this study, we investigated how salt-sensitive (Henong 16, HN16) and salt-tolerant (Jizaonuo 1, JZN) sorghum genotypes leverage biochar to assemble distinct functional rhizosphere microbiomes under salt stress (5 g kg⁻¹ NaCl). Biochar application (20 g kg⁻¹) alleviated ionic stress by reducing soil electrical conductivity (EC decreased by 46% in HN16) and enhanced soil fertility through increased organic matter (SOM increased by 26% in JZN). 16S rRNA gene sequencing revealed that biochar selectively enriched genotype-specific, stress-resistant taxa. The salt-sensitive HN16 primarily recruited Sporosarcina (a genus reported to exhibit salt tolerance and nitrogen-fixing capabilities) and Intrasporangiaceae, thereby rapidly establishing a rhizosphere barrier. In contrast, the salt-tolerant JZN consistently enriched Salinimicrobium (an extreme halophile) and the family LWQ8, forming more complex and stable co-occurrence networks with a higher proportion of positive correlations (81%). Plant genotype was the primary determinant of core microbiome assembly: Bacillus and Arthrobacter dominated in HN16, whereas Sphingomonas and Streptomyces prevailed in JZN. Biochar reinforced this genotype-specific assembly by modulating soil pH and SOM, which were identified as key drivers of microbial community divergence. Importantly, these biochar-shaped microbial modules showed significant positive correlations with increased plant biomass. Our findings demonstrate that biochar enhances salt tolerance not merely by improving soil properties, but primarily by facilitating the deterministic assembly of genotype-specific, functional rhizosphere microbiomes. This mechanistic insight shifts the paradigm of biochar from a universal soil amendment to a precision tool for rhizosphere engineering, providing a genotype-aware foundation for enhancing salinity resilience in sustainable agriculture. Full article

This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) on samples of feces (n = 58), soil (n = 35), and water (n = 35) collected from six typical regions. We systematically revealed the mechanisms by which soil properties influence the gut microbiome of wildlife in an arid desert ecosystem based on source tracking and Multiple Regression on distance Matrices (MRM) analysis. The results showed that soil total phosphorus (TP) was significantly positively correlated with the α-diversity of gut microbiota (coefficient = 0.4/0.23/0.332; p < 0.05), while soil organic carbon (SOC) was significantly negatively correlated (coefficient = −0.44/−0.436; p < 0.05), indicating that soil nutrients indirectly predict host microbial diversity by regulating vegetation productivity and forage quality. β-diversity analysis further demonstrated that spatial heterogeneity in soil pH (coefficient = 0.3083; p < 0.05) and TP (coefficient = 0.227; p < 0.05) significantly drove the structural differentiation of gut microbial communities. Source-tracking results based on FEAST revealed significant regional differences in the proportional contribution of environmental microorganisms to the gut microbiota, with individuals in resource-poor habitats (ALK region) exhibiting higher input from soil microbes (8.0672% ± 6.9291%; p < 0.05). In conclusion, this study clarifies the ecological mechanism by which soil physicochemical properties regulate the diversity and composition of herbivore gut microbiota through a “soil–plant–food–gut microbiota” cascading pathway, providing important empirical evidence for understanding animal–microbe–environment interactions and adaptive evolution in extreme environments. Full article

Background: Sepsis-induced organ dysfunction poses a significant clinical challenge with limited therapeutic options. This study investigated the therapeutic potential of the glucagon-like peptide-1 receptor agonist (GLP-1RA) liraglutide in sepsis and its underlying mechanisms, focusing on modulation of the gut microbiota-derived metabolome. Methods: Public transcriptomic data analysis identified overlapping targets between liraglutide and sepsis-related genes. In a murine cecal ligation and puncture (CLP) model, liraglutide treatment was evaluated for its effects on survival, systemic inflammation, and organ injury. The gut microbiota composition and fecal metabolome were assessed via 16S rRNA sequencing and UPLC-MS. We also measured plasma GLP-1 in sepsis patients and examined the microbiota-dependency of liraglutide’s effects using antibiotic-depleted mice and fecal microbiota transplantation (FMT) from liraglutide-treated mice. Additionally, citrulline, a key identified metabolite, was functionally validated both in vitro and in a clinical cohort. Results: Liraglutide significantly improved survival, reduced pro-inflammatory cytokines, and alleviated lung, liver, and colon damage in septic mice. It partially restored sepsis-induced gut dysbiosis and modulating associated metabolites, including increasing citrulline. The survival benefit of liraglutide was abolished in microbiota-depleted mice, while FMT from liraglutide-treated mice conferred protection against sepsis, confirming the gut microbiota as a critical mediator. Furthermore, citrulline exhibited direct anti-inflammatory properties in cellular assays, and its plasma levels were negatively correlated with sepsis biomarkers (PCT and CRP) in patients. Conclusions: Taken together, our findings indicate that liraglutide mitigates sepsis by modulating the gut microbiota and regulating associated metabolic pathways. Citrulline may represent a potential microbial mediator or exploratory biomarker within this axis, warranting further mechanistic investigation. Full article

Rural black-odorous waterbodies (RBOWBs) represent a critical environmental challenge in China, yet the vertical stratification of sedimentary bacterial communities and its underlying drivers remain poorly understood. This study combined 16S rRNA gene amplicon sequencing across five sediment depths (0–125 cm) with shotgun metagenomic analysis of surface sediments to investigate bacterial diversity, composition, and functional potential in typical rural black-odorous systems of Dongming County, Shandong Province. Results showed a clear decline in bacterial richness with increasing sediment depth, with the surface layer (0–25 cm) exhibiting 1.2–1.9 times higher diversity than deeper strata. Community composition displayed distinct vertical zonation: Chloroflexi and Thiobacillus dominated surface layers and were linked to carbon hydrolysis and desulfurization, whereas Bacillus and nitrifying bacteria prevailed in deeper anoxic layers. Metagenomic analysis revealed high genetic potential for carbohydrate metabolism, amino acid biosynthesis, and sulfur-nitrogen cycling, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) being particularly abundant. Statistical correlations identified total phosphorus (TP₁), dissolved oxygen (DO), and pH of the overlying water—rather than sediment intrinsic nutrients—as the primary environmental factors associated with microbial functional stratification. These findings provide a mechanistic understanding of vertical microbial zonation in rural black-odorous sediment and offer a microbiological basis for developing depth-resolved sustainable remediation strategies. Full article

Pistachio skin is a by-product that is considered a promising novel feed ingredient for ruminants; however, its role in shaping the lamb gastrointestinal tract microbiota is poorly studied. The present study aimed to investigate, through a metagenomics approach, the effects of integrating pistachio skin into the diet on the faecal and ruminal microbiota of healthy lambs. Faecal samples, collected at the beginning (d0) and 58 days after the start of the dietary treatment (d58), and ruminal samples, collected after slaughter, were subjected to Illumina MiSeq analysis of the 16S rRNA gene. The results revealed that, although temporal variations were observed, the supplementation of pistachio skin did not markedly affect the overall faecal microbiota structure. Conversely, specific rumen taxa were selectively modulated by the experimental diet. In conclusion, the use of pistachio skin as a feed ingredient can be considered a suitable and sustainable dietary strategy that modulates specific rumen microbial groups, thereby preserving the stability of the gut microbiota in lambs. Full article

This study explores the taxonomic diversity, metabolic profile, and bioactivity of marine-derived actinomycetes isolated from sediments collected off the coast of Lisbon and Setúbal Peninsula, Portugal. The combined use of two sediment pre-treatments (heat shock and dry overnight) and four growth media with varying nutrient concentrations revealed that formulations 10% A1 and SWA were most effective for recovering diverse actinomycetes, including rare Actinomadura, resulting in a total of 142 cultivable strains closely related to 47 phylogenetic distinct species dominated by Streptomyces and Micromonospora. Antimicrobial screening against methicillin-resistant Staphylococcus aureus (MRSA, COL) and Escherichia coli (K12) identified 22 bioactive strains, with strain PTS-083 exhibiting the strongest activity against MRSA (MIC = 1.95 µg/mL) and a 98.30% 16S rRNA gene identity to S. chumphonensis, highlighting it as a strong candidate for further metabolite and genomic studies. Cytotoxicity assays against HCT-116 human colorectal adenocarcinoma cells revealed eight bioactive strains with potent anticancer activity for extracts from strains related to S. sundarbansensis, S. violaceorubidus, and S. aculeolatus (IC₅₀ < 0.005–5.08 µg/mL). Untargeted LC-MS/MS metabolomic analysis uncovered a wide array of secondary metabolites, including macrolides, siderophores, fatty acids, and cyclic peptides. Comparative analyses with other Portuguese coastal studies revealed both shared and distinctive metabolomic profiles, emphasizing the importance of exhaustive sampling, even at nearby locations, as their localized environmental conditions can influence metabolic diversity. These findings highlight Portugal’s coastal sediments as a rich and underexplored source of novel actinomycetes and bioactive compounds with promising pharmaceutical applications. Exhaustive sampling of marine sediment actinomycete communities, even at nearby locations, is crucial for discovering unique metabolites with potential biotechnological value. Full article

Background: This study aimed to assess the presence of thermotolerant Campylobacter resistant to ciprofloxacin and erythromycin in poultry slaughterhouses and retail markets, as well as to characterize their multidrug resistance profiles, genetic determinants, and clonal relationships. Methods: Samples were collected at slaughterhouses from cecal content (n = 270), neck skin (n = 270), and wastewater (n = 9), and at retail markets from breast skin (n = 241). Isolates were obtained from mCCDA agar supplemented with ciprofloxacin (2 μg/mL) and identified as C. jejuni or C. coli by PCR. The agar microdilution test was used to determine the minimum inhibitory concentration for ciprofloxacin and erythromycin, and other critical antibiotics. Point mutations in gyrA (Thr86Ile) and 23S rRNA (A2075G), virulence genes (flaA, flhA, cadF, and cdt), and clonal relationships were assessed by PCR and PFGE. Results: At the slaughterhouses, thermotolerant Campylobacter spp. resistant to erythromycin and ciprofloxacin were detected in 48.55% (107/549) of the samples, whereas 4.56% (11/241) of retail samples were positive. The Thr86Ile substitution in gyrA and the A2075G mutation in the 23S rRNA gene were detected in 92.97% and 89.84% of the isolates, respectively. Most isolates (>80%) were multidrug resistant and harbored key virulence genes (flaA, flhA, and cadF). C. jejuni exhibited the highest prevalence of cdt genes (76.19%). There was substantial genotypic diversity among isolates, with broad distribution across the sampled matrices and sites. Conclusions: These findings highlight the circulation of multidrug-resistant and potentially virulent thermotolerant Campylobacter spp. in the later stages of the poultry meat supply chain. Full article

The escalating global demand for large-scale, cost-effective, and sustainable high-quality protein has positioned single-cell protein (SCP) production from one-carbon (C1) gases as a highly promising solution. In this study, eight chemolithoautotrophic hydrogen-oxidizing bacteria (HOB) were isolated from mangrove sediments. Based on the 16S rRNA gene sequence analysis, they belonged to genera Sulfurimonas, Sulfurovum, Thiomicrolovo, and Marinobacterium. Among these, Thiomicrolovo sp. ZZH C-3 was identified as the most promising candidate for SCP production based on the highest biomass and protein content, and was selected for further characterization. Strain ZZH C-3 is a Gram-negative, short rod-shaped bacterium with multiple flagella. It can grow chemolithoautotrophically by using molecular hydrogen as an energy source and molecular oxygen as an electron acceptor. Genomic analysis further confirmed that ZZH C-3 harbors a complete reverse tricarboxylic acid (rTCA) cycle gene set for carbon fixation, and diverse hydrogenases (Group I, II, IV) for hydrogen oxidation. Subsequently, its cultivation conditions and medium composition for SCP production were systematically optimized using single-factor experiments and response surface methodology (RSM). Results showed that the optimal growth conditions were 28 °C, pH 7.0, and with 1 g/L (NH₄)₂SO₄ as the nitrogen source, 5–10% oxygen concentration, 9.70 mg/L FeSO₄·7H₂O, 0.17 g/L CaCl₂·2H₂O, and 1.90 mg/L MnSO₄·H₂O. Under the optimized conditions, strain ZZH C-3 achieved a maximum specific growth rate of 0.46 h⁻¹. After 28 h of cultivation, the optical density at 600 nm (OD₆₀₀) reached 0.94, corresponding to a biomass concentration of 0.60 g/L, and the protein content ranked at 73.56%. The biomass yield on hydrogen (Y_H2) was approximately 3.01 g/g H₂, with an average H₂-to-CO₂ consumption molar ratio of about 3.78. Compared to the model HOB Cupriavidus necator, strain ZZH C-3 exhibited a lower H₂/CO₂ consumption ratio, superior substrate conversion efficiency, and high protein content. Overall, this study not only validated the potential of mangrove HOB for SCP production but also offers new insights for future metabolic engineering strategies designed to enhance CO₂-to-biomass conversion efficiency. Full article

Background: The human gut microbiota plays a pivotal role in maintaining health throughout the lifespan, and age-related alterations in its composition and diversity have been implicated in numerous chronic and neurodegenerative conditions. However, the combined effects of aging, dementia, and shared living environments on gut microbial communities remain incompletely understood. Methods: This study included 56 older adults residing in a nursing home, of whom 29 had been diagnosed with dementia. Gut microbiota composition was characterized by 16S ribosomal RNA (rRNA) gene sequencing. Microbial diversity was assessed using alpha- and beta-diversity metrics, and differences in amplicon sequence variants (ASVs)/features were determined. Analyses adopted some covariates as potential confounders variables including age, sex, frailty status, drug use, and time spent in the nursing home. Results: Alpha diversity was significantly higher in older adults compared with younger, while beta-diversity analyses revealed distinct microbial community structures between age groups. In older individuals, Bacteroidota and Proteobacteria were the most abundant phyla, whereas Firmicutes and Actinobacteriota declined with advancing age. Notably, older adults exhibited an increased relative abundance of Euryarchaeota, a phylum encompassing Archaea, predominantly methanogens involved in anaerobic carbon dioxide reduction to methane. In subjects with dementia, marked compositional shifts were detected, resulting in a distinct microbial signature. Dementia was associated with a significant enrichment of Actinobacteriota, Euryarchaeota, and Proteobacteria, alongside a depletion of Bacteroidota and Firmicutes. Overall, different bacterial genera mostly belonging to the Firmicutes phylum were associated both with aging and dementia. Conclusions: Results show age-related remodeling of the gut microbiota, with a stable core of common taxa and distinct individual-specific signatures. These shifts reflect both host factors and life-long environmental conditions. Dementia-related changes seem to correlate with increased inflammatory species, thus suggesting the effect of vulnerability in microbiota changes in subjects sharing living environment and diet. Full article

Mafic mine tailings are highly resistant to bioleaching due to their silicate-rich composition, low sulfide content, and strong buffering capacity. This study aimed to assess the potential use of heterotrophic bioleaching to promote the release of metals from mafic tailings by evaluating the organic acid production and leaching capabilities of indigenous bacterial isolates and a known lactic acid producer, Lactiplantibacillus plantarum ATCC 8014. Indigenous acid-producing heterotrophic bacteria were isolated from a vanadium-titanium-bearing magnetite tailings in Québec, Canada, and screened for organic acid production in various culture media. The most active bacteria were L. plantarum and two isolates identified by their 16S rRNA gene as Enterococcus (CBGM-1C) and Acetobacter (BL-F) sp. They produced significant quantities of lactic acids, followed by acetic, citric, and gluconic acids during glucose metabolism, through fermentative or oxidative pathways. A two-step bioleaching process was implemented, consisting of an initial organic acid production phase followed by tailings leaching at 5% pulp density over 10 days at 30 °C. Metal solubilization and mineralogical analyses demonstrated strain-dependent and metal-specific mobilization, with zinc being the only element efficiently leached (up to ~74% recovery by L. plantarum). XRD analyses confirmed partial dissolution and reduced crystallinity of key silicate phases without secondary mineral formation. These findings indicate that heterotrophic leaching can selectively mobilize more labile metals such as Zn from alkaline, silicate-rich tailings, although its overall efficiency for refractory elements remains limited under the tested conditions. Full article

Cyanobacteria of the genus Tychonema are common inhabitants of freshwater bodies in a temperate zones. In Lake Baikal, Tychonema sp. was first reported in 2014. It grows excessively on the bottom on almost all substrates types, forming epiphytic and epizoic biofilms, and its role in the mass mortality events affecting of endemic Baikal sponges is discussed. The cyanobacterial strain BBK16 (=IPPAS B-2063^T), isolated from a biofilm on a log pier in the Bolshiye Koty settlement in 2016, was used for further taxonomic characterization. Key morphological features of strain BBK16 include its growth as a creeping mat, highly motile trichomes that are sometimes narrowed and hooked at the ends, and the presence of rounded-conical apical cells with a calyptra. Strain ultrastructure (fascicular parietal thylakoids and type D cell division) differs from Tychonema species with radial thylakoids but aligns with other genera in the Microcoleaceae family. A comprehensive analysis, including 16S rRNA gene phylogeny, conserved protein phylogeny, and whole-genome comparisons, confirmed its placement within the genus Tychonema. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain BBK16 and T. bourrellyi FEM GT703 were 90.7%, 91.1% and 43.3%, respectively, indicating values below the standard thresholds for species delineation. Based on combined morphological, genomic, and ecological evidence, we propose the name Tychonema litorale sp. nov. for strain BBK16, a novel species described in accordance with the International Code of Nomenclature for Algae, Fungi, and Plants. Full article

The ponyfish genus Nuchequula is presents taxonomic challenges within Leiognathidae due to morphological complexities and a lack of genomic resources. However, the absence of a complete mitochondrial genome for Nuchequula longicornis has hindered comprehensive phylogenetic comparisons. Here, we employed an integrative approach combining detailed morphology with molecular validation via 16S rRNA gene sequencing to confirm the identity of specimens from the Beibu Gulf. Furthermore, we present the first complete mitogenome of N. longicornis. This circular 16,514 bp molecule exhibits a typical gene order, a moderate AT bias (54.8%), and strong purifying selection across all protein-coding genes. Phylogenomic analysis based on the complete mitogenome reliably resolved the position of N. longicornis within Leiognathidae, contributing to the discussion on the phylogenetic relationships and potential monophyly of Nuchequula and contributing to the understanding of intra-familial relationships. Our study provides an essential mitogenomic resource for N. longicornis and offers insights into mitochondrial evolutionary patterns within this family. Full article

Background/Objectives: Serratia liquefaciens is a bacterium commonly found in the rhizosphere and may possess PGPR capabilities. The present study aimed to elucidate the genomic, phylogenomic, and metabolic characteristics of S. liquefaciens strain UNJFSC002 to determine whether it is an effective PGPR. Methods: The genome of strain UNJFSC002 was obtained from NCBI and annotated using Prokka. Functional genome prediction, phylogenetic reconstruction, and comparative genomics were performed using bioinformatics tools. A GEM model was reconstructed to simulate metabolic fluxes associated with nitrogen fixation, phosphate solubilization, and phytohormone biosynthesis. Computational phenotyping and in silico functional validation were also performed. Results: The draft genome (5.19 Mb, GC 55.33%) contained 4792 protein-coding genes, 4 rRNAs, and 81 tRNAs, with 100% completeness. ANI and core genome phylogeny confirmed its taxonomic position within S. liquefaciens, with an identity higher than 98.8%. Pangenome analysis of 25 Serratia genomes revealed an open and highly dynamic pangenome (30,515 orthologous groups), indicating extensive genetic plasticity. Functional annotation identified key genes associated with nitrogen and phosphate acquisition, as well as the biosynthesis of IAA and GABA, findings that were supported by GEM simulations, reinforcing its potential as a biofertilizer. Conclusions: The genomic approach confirmed that strain UNJFSC002 harbors multiple active genes and metabolic pathways associated with plant growth promotion and environmental resilience. Full article

Pesticide use in agriculture can have negative collateral effects on the environment. In this study, two groups of treatments (G1 and G2) based on active substances (ASs) with different mobility were evaluated in order to determine pesticide residues in the soil and their impact on soil microbial populations in two vineyards located in two Denominations of Origin (D.O.). Soil samples were collected in July, October, and the following March over two consecutive years. Pesticide residues were analyzed by liquid chromatography–tandem mass spectrometry (LC-MS/MS) after QuEChERS extraction. Microbial genera were identified by the amplification of the fungal ITS regions with the universal primers ITS86F and ITS4R, and the bacterial 16S rRNA gene (V4 region) with primers 515F and 806R. Although G1 consistently showed higher residues, primarily attributable to azoxystrobin, no significant differences were observed between the two pesticide groups in the total pesticide residues or diversity of microbial communities. The factors D.O., campaign, and sampling month influenced the concentration of residues. Several ASs exhibited different dissipation dynamics depending on the D.O. Azoxystrobin and metrafenone were the most persistent in soil. The LEfSe analysis associated four beneficial fungal genera with the G2 group. The judicious selection of ASs can help to minimize the pesticide residues in soil and their harmful effects on beneficial genera. Full article

Vultures are extraordinarily adapted to feed on carrion, providing them with a constant microbiologically hostile environment. This peculiar ecological position has influenced the evolution of their gut microbiota, potentially conferring its uncommon antimicrobial traits and resistance to stress. In this study, we report on the isolation and comprehensive characterization of a lactic acid bacterium strain, identified as Ligilactobacillus agilis, from vulture feces via 16S rRNA gene sequencing. This strain exhibited potent antagonistic activity against several clinically relevant bacterial pathogens, including Salmonella enterica Typhimurium (25.26 ± 0.26 mm), Escherichia coli (23.5 ± 0.88 mm), Staphylococcus aureus (23.1 ± 1.8 mm), and Listeria monocytogenes (24.88 ± 0.61 mm), as demonstrated by agar well diffusion assays. Remarkably, it also demonstrated considerable resilience in simulated gastrointestinal conditions, with survival rates of 52.5 ± 7.4% in artificial gastric juice and 61.1 ± 3.7% in intestinal fluids. Antimicrobial susceptibility profiling confirmed its sensitivity to a broad range of commonly used antibiotics, including gentamicin, streptomycin, clindamycin, and penicillin. Whole-genome sequencing further revealed a complete repertoire of core genes associated with genetic information processing, robust carbohydrate metabolism, and nutrient assimilation, underscoring its adaptability and probiotic potential. It is important to note that the analysis of the assembled genome against VFDB did not show the presence of any known virulence factor according to the given criteria, which is preliminary evidence of safety-related aspects that are to be followed with the help of guideline-based analyses. Taken together, the unique ecological origin and in vitro inhibitory activity against the tested pathogens, gastrointestinal robustness, genomic features, and safety credentials position this L. agilis strain as a promising probiotic candidate for mitigating enteric infections in animal production systems, warranting further functional validation and in vivo efficacy studies. Full article