Search Results (10,680)

Constructed wetlands (CWs) depend on plant–microbe associations for pollutant transformation, yet the processes linking macrophyte identity to rhizosphere microbiome assembly remain insufficiently resolved. We compared bacterial communities associated with C. articulatus (Ca) and T. geniculata (Tg) roots with an unplanted treatment (Up) in pilot-scale CWs on the Colombian Caribbean coast. Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Co-occurrence networks, taxon–environment correlations, and the phylogenetic bin-based null model iCAMP were used to assess community structure, potential associations and assembly mechanisms. CaS supported significantly greater bacterial diversity than TgS and Up, while each macrophyte recruited a distinct community. A shared core microbiome dominated by Rhodocyclaceae, Sphingomonadaceae, Chitinophagaceae, Pirellulaceae, and Xanthomonadaceae comprised taxa with putative roles in nutrient and organic matter transformations. Several bacterial families were significantly associated with PO₄³⁻, NH₄⁺, and dissolved oxygen. Assembly was predominantly stochastic, with dispersal limitation (45.2%) and ecological drift (33.2%) exceeding deterministic selection (16.5%). Nevertheless, planted treatments displayed higher network modularity and connectivity and inferred functional redundancy than Up, consistent with niche differentiation. These findings suggest that species-specific macrophyte configurations are associated with differences in root-associated microbial community composition, while assembly and network analyses provide exploratory insights into community organization. The limited replication precludes causal attribution to plant identity or conclusions regarding treatment performance. Future studies integrating controlled planting densities, increased replication, meta-omics, and root exudate characterization are needed to clarify plant–microbiome relationships and evaluate their potential relevance to constructed wetland functioning. Full article

Microbiome-based classification of multiple neurological conditions is challenged by sparse features, class imbalance, and heterogeneity between studies. We propose Multi-Stream Adaptive Feature Integration (MASFI), which combines CLR-transformed genus-level features, taxonomy-derived features, and self-supervised taxon-token Transformer representations in a Random Forest classifier with out-of-bag dynamic uncertainty sampling. We evaluated MASFI using 4049 faecal 16S rRNA gene amplicon sequencing samples from participants with Alzheimer’s disease (AD), autism spectrum disorder (ASD), Parkinson’s disease (PD), and healthy controls. Five-fold stratified cross-validation compared MASFI with conventional machine learning and supervised neural baselines. Ablation analyses assessed the contributions of the feature streams, while block- and taxon-level permutation analyses characterised the features used by the fitted classifier. Genera including Romboutsia, Prevotella, and Fusicatenibacter were highlighted as contributors to model predictions. These findings support multi-stream feature integration as an approach to microbiome-based multi-disease classification. Full article

Background: We revised the taxonomy and identification of the species of the genus Bothriocroton in light of entire mitochondrial genomes and nuclear rRNA genes, scanning electron microscopy, and light microscopy. Methods: (i) phylogenetic trees inferred from entire mitochondrial genomes and nuclear rRNA genes, (ii) species delimitation analyses (ABGD and bPTP), and (iii) the study of morphology by scanning electron microscopy (SEM) and light microscopy. Results: The most complete picture of the Bothriocroton ticks so far. Thirty-five new mitochondrial genomes and 27 partial 18S–28S rDNA sequences were generated. Phylogenetic analyses recovered seven well-supported clades corresponding to species-level lineages. Intraspecific genetic divergence ranged from 0.14 to 1.16%, whereas interspecific divergence ranged from 4.94 to 21.75%. Three new species were described, and the morphological diagnosis of other species was improved by redescribing two other species. In addition, we updated and improved the morphological dichotomous keys to male and female ticks. Conclusions and prospects: The routine genotyping of Bothriocroton ticks to identify species and to confirm provisional identifications of species from their morphology is an alternative to the morphological identification of closely related Bothriocroton ticks. Full article

Oral Squamous Cell Carcinoma (OSCC) is often diagnosed at advanced stages despite the oral cavity’s anatomical accessibility, highlighting the need for molecular adjuncts that can identify disease-associated changes before overt morphological progression. This review evaluates the biological roles and salivary diagnostic potential of microRNA-21 (miR-21) and miR-31, two miRNAs repeatedly associated with OSCC pathogenesis and progression. We examine current clinical evidence supporting their use as salivary biomarkers and discuss major sources of methodological variability, including differences in saliva collection, RNA recovery, normalization, and diagnostic thresholds. We pay particular attention to the transition from laboratory-based RT-qPCR to Recombinase Polymerase Amplification (RPA) for decentralized detection. Although RPA offers rapid, low-temperature amplification with reduced hardware requirements, mature miRNAs present a key technical challenge because their short length requires prior target extension or conversion. Successful chairside translation will depend on standardized sample processing, robust target-specific amplification, contamination control, and validation in clinically relevant early-stage and comparator populations. Full article

Production of functional exopolysaccharides (EPS) by lactic acid bacteria (LAB) is a promising strategy for the value-added utilization of beet molasses. This study aimed to isolate high-sucrose-tolerant LAB strains from beet molasses and evaluate their potential for crude EPS production. A total of 13 LAB strains were initially isolated from beet molasses, among which seven isolates were selected as high-sucrose-tolerant candidates based on their growth performance under high-sucrose conditions. Further crude EPS-production screening showed that two isolates, Leuconostoc mesenteroides C4 and Pediococcus pentosaceus T1, produced relatively high crude EPS yields. These two isolates were then identified by 16S rRNA gene sequence analysis. Further, L. mesenteroides C4 was selected as a candidate, and preliminary OFAT screening followed by Box–Behnken response surface methodology (RSM) was employed to optimize the conditions for crude EPS production. The antioxidant activity and antibiofilm activity of the crude EPS-C4 fraction were also evaluated. The RSM-predicted optimal conditions for crude EPS production by L. mesenteroides C4 were 350 g/L of beet molasses, an initial pH of 6.0, a fermentation time of 30 h, a fermentation temperature of 37 °C, an inoculum size of 2.3%, a loading volume of 85%, and a shaking speed of 108 r/min. Under these optimal conditions, a maximum crude EPS yield of 16.99 ± 0.22 g/L was obtained, which was approximately 5.0-fold higher than the yield obtained under the initial fermentation condition (3.40 g/L). Furthermore, crude EPS-C4 exhibited in vitro free-radical-scavenging activity against DPPH and ABTS⁺ radicals, with scavenging rates of 97.00% and 67.35% at 6.0 mg/mL, respectively. The crude EPS-C4 fraction also inhibited biofilm formation by Escherichia coli and Staphylococcus aureus, with inhibition rates of 60.68% and 68.69% at 8.0 mg/mL, respectively. These findings provide preliminary evidence that beet molasses can be used as a substrate for LAB-EPS production and suggest that crude EPS-C4 is a promising candidate for further purification, structural characterization, safety assessment, and application-oriented evaluation. Full article

A study was carried out to identify the nematodicidal bacteria in ruminant dung and assess their efficacy against gastrointestinal nematodes of small ruminants. A total of 10 bacteria were isolated from ruminant dung and their nematodicidal activity was determined. Evaluation of nematodicidal efficacy of all the isolates through larval feeding assay revealed 0.00 ± 0.00 to 100.00 ± 0.00% efficacy with varying time. However, of the 10 bacterial isolates from the dung, three bacterial isolates showed 100.00 ± 0.00% nematodicidal activity in 4 h of incubation. The bacterial isolates were preliminarily classified based on cultural and Gram-staining characteristics and were subsequently identified by 16S rRNA gene sequencing. Molecular analysis confirmed that the three isolates exhibiting the highest nematodicidal activity in the larval feeding assay were Citrobacter amalonaticus, Shigella flexneri, and Klebsiella aerogenes. The isolate Citrobacter amalonaticus (5.5 × 10⁸ CFU per mL) caused 100% larval mortality at 10 and 7.5% culture broth concentrations in 4 and 6 h of incubation, respectively in a dose-dependent larval assay. In the simulation pasture model study, compared to the control tray, the pasture tray treated with the bacterium Citrobacter amalonaticus (5.6 × 10⁸ CFU per mL) showed a reduction in larval recovery of 87.50%. The present work using bacteria isolated from animal origin against nematodes affecting small ruminants is the first of its kind in India. The results of this seminal work will go a long way in developing an alternative strategy for chemical control of the worm problem in animals. Full article

Microplastic-associated biofilms (plastisphere) have been proposed as potential reservoirs of antibiotic resistance genes (ARGs), potential pathogens, and opportunistic microorganisms. However, information on freshwater ecosystems remains limited. In this study, the occurrence and distribution of selected ARGs, predicted resistance-associated functional profiles, and potentially pathogenic bacterial taxa were investigated in the plastisphere and planktonic communities of four Italian lakes. Quantitative PCR was used to quantify four ARGs (blaCTX-M, tetA, sul2 and ermB), while 16S rRNA gene datasets were analyzed to identify potentially pathogenic bacterial genera and reconstruct predicted resistance-associated functional profiles. ARGs were detected more frequently and at higher relative abundance in the plastisphere than in surrounding waters, although their distribution was highly heterogeneous among lakes and sampling sites. In particular, blaCTX-M was frequently detected on microplastics (MPs) but only rarely in planktonic communities. Predicted resistance-associated functional profiles showed a clear separation between plastisphere and planktonic communities, with MP-associated biofilms characterized by a higher contribution of resistance- and stress-associated functions. No consistent enrichment of potentially pathogenic bacterial genera was observed on MPs. Overall, freshwater plastisphere communities may represent distinct microbial microhabitats in which ARGs and resistance-associated functions accumulate more frequently than in surrounding waters, although local ecological conditions appear to strongly influence their distribution. Full article

Objective: We aim to assess gut and endometrial microbiota simultaneously in women with unexplained recurrent implantation failure (RIF) and explore the hypothesis of a gut–endometrium microbial axis. Study design: This monocentric observational pilot study included women aged 38 years or younger with a history of RIF. Paired fecal and endometrial samples were collected on the same day and analyzed by 16S rRNA gene sequencing. Relative abundances of major phyla and alpha-diversity indices were compared between compartments. Results: Twenty-one women were included. Chronic endometritis was documented through hysteroscopy in all cases. Gut dysbiosis was observed in 20/21 patients (95.2%), whereas endometrial dysbiosis was found in 16/21 (76.2%); crude agreement between compartments was 71.4% (Gwet’s AC1 0.62, 95% CI 0.25–0.90). The intestinal microbiota was dominated by Bacteroidetes (52.8% ± 14.9%) and Firmicutes (33.3% ± 11.0%), whereas the endometrial microbiota was enriched in Firmicutes (64.5% ± 33.5%) and Proteobacteria (30.9% ± 32.3%). Bacteroidetes were significantly more abundant in fecal than endometrial samples (p < 0.001), while Firmicutes were significantly enriched in the endometrium (p = 0.001). All alpha-diversity indices were significantly higher in feces, indicating greater microbial richness and complexity in the gut. Conclusions: In this pilot cohort of women with unexplained RIF, gut and endometrial dysbiosis frequently co-occurred. These findings support a potential gut–endometrium microbial axis and highlight the possible interplay between gut and endometrial microbiota in recurrent implantation failure. Further studies are warranted to better elucidate the clinical and biological implications of this relationship. Full article

Probiotics, especially Bacillus species, have gained attention for their potential to improve growth and strengthen disease resistance in cultured shrimp. This study evaluated the effects of native Bacillus strains on growth performance, disease resistance and gut microbiota of Penaeus vannamei through the rearing water. Bacillus subtilis (BS) and Bacillus cereus (BC) group strain were isolated from pond sediment collected in Chanthaburi, Thailand, in April 2025. Both strains were identified by 16S rRNA gene sequencing, and the sequence data were deposited in the NCBI database under BioProject accession no. PRJNA1513981 (SRX34829739 for B. cereus BUUC2501 and SRX34829740 for B. subtilis BUUC2502). The shrimp were reared in water supplemented with one of four treatments: (a) a negative control (no bacterial addition), (b) a commercial Bacillus spp. product (positive control), (c) B. subtilis, and (d) B. cereus group strain. Treatments were applied every 7 days as three applications on days 7, 14, and 21, with each strain added to the rearing water at a final concentration of approximately 1 × 10⁵ CFU/mL per application; shrimp were then reared until day 28. Shrimp reared with the B. cereus group strain showed numerically higher specific growth rate (SGR) and average daily gain (ADG) than the control; however, after adjusting for a lower initial weight in this group by ANCOVA, these differences were not statistically robust. There was no significant difference in final body weight and feed conversion ratio among groups (p > 0.05). After Vibrio parahaemolyticus (VP_AHPND) challenge, the survival rate was the highest in the B. cereus-treated group, showing the highest disease resistance. Alpha diversity of the gut microbiota was not significantly different among groups, whereas beta-diversity analysis (PERMANOVA) showed significant differences in gut microbial community structure among groups, and LEfSe identified the genus Bacillus as a biomarker of the B. cereus group. These results provide proof-of-concept evidence that water-based supplementation with a native B. cereus group strain can enhance disease resistance and increase the relative abundance of Bacillus in the shrimp gut. However, because the B. cereus group includes potentially toxigenic strains, a strain-level safety assessment is required before this approach can be applied in shrimp aquaculture. Full article

Prebiotics are widely used to modulate gut microbial communities, but their effects on the honey bee gut microbiota remain poorly understood. Xylo-oligosaccharides (XOS) are recognized as potential prebiotic substrates in humans and livestock, whereas their effects in honey bees have rarely been investigated in vivo. In this study, we evaluated the effects of dietary XOS supplementation on the gut microbiota of Apis mellifera. Total bacterial load and the absolute and relative abundances of five core bacterial groups (Lactobacillus Firm-5, Bombilactobacillus, Bifidobacterium, Gilliamella, and Snodgrassella alvi) were quantified using spike-in-based absolute 16S rRNA gene sequencing. Microbial diversity and community structure were further assessed using alpha-diversity indices and beta-diversity analyses. XOS supplementation did not significantly affect total bacterial abundance or the abundance of the five core bacterial groups (p > 0.05). No significant differences were detected in alpha diversity (p > 0.05), and the control and XOS groups exhibited largely overlapping community structures based on unweighted and weighted UniFrac analyses. However, PICRUSt2 analysis identified differences in several predicted microbial functional pathways between the two groups (p < 0.05). These results indicate that dietary XOS supplementation had limited detectable effects on the abundance, diversity, and structure of the established honey bee gut microbiota under the tested conditions, although changes in its predicted functional potential were observed. Our findings suggest that the efficacy of prebiotics in honey bees may depend on host-specific microbial ecology, and that prebiotic responses observed in mammalian systems may not be directly applicable to honey bees. These results highlight the importance of validating commercial prebiotic products using bee-specific in vivo evidence before their widespread application. Full article

We report an adult male Chinese water deer Hydropotes inermis repeatedly observed at Jiamusi University, Heilongjiang Province, northeastern China (130°22′02″ E, 46°46′56″ N). Clear photographs documented diagnostic external characters, and fecal samples collected from the same campus area were independently assigned to H. inermis by mitochondrial 16S rRNA sequencing. The locality lies approximately 208 km north of the Wuchang record in terms of latitudinal displacement and represents the northernmost currently confirmed occurrence of the species in its native Northeast Asian range. Repeated use of a university campus with regular pedestrian and vehicle activity suggests apparent tolerance of routine human presence within a human-modified setting, although the observations do not demonstrate urban adaptation, local population establishment, or the provenance of the individual. Full article

Neonatal calf diarrhea caused by intestinal microbial dysbiosis severely restricts rearing efficiency, and fecal microbiota transplantation (FMT) emerges as a promising antibiotic-free strategy for regulating gut homeostasis. Nevertheless, to the best of our knowledge, the effects of colostrum-period FMT and the functional differences between colonic and colostrum delivery routes remain poorly characterized in pre-weaned dairy calves. We hypothesized that colostrum-period FMT would accelerate gut microbiota maturation, improve immune status and reduce diarrhea incidence in pre-weaned calves, with delivery-route-dependent effects. This study aimed to investigate how two colostrum-phase FMT delivery routes shape growth performance, serum immune profiles and gut microbiota in neonatal Holstein calves. Sixty newborn calves were randomly assigned to three groups (n = 20 per group): control (no FMT), colon-FMT (colonic perfusion), and colostrum-FMT (FMT mixed with colostrum). Donor feces were homogenized with sterile saline at a 1:9 ratio for FMT suspension preparation, and the trial lasted 56 days. For growth performance, the colon-FMT calves exhibited significantly higher average daily gain from D29 to D56 (p < 0.05). In terms of intestinal health, the colostrum-FMT group exhibited lower diarrhea incidence during D15-28 (p < 0.05) but markedly higher diarrhea rates during D29-56 (p < 0.01). For serum immunity, colon-FMT calves had elevated serum IgG at D14 (p < 0.05). At D56, the concentrations of IL-2 (p < 0.01) and IL-4 (p = 0.05) were significantly lower in the colostrum-FMT group than the colon-FMT group; no intergroup differences were detected for other serum cytokines and immunoglobulins. 16S rRNA gene sequencing of D28 fecal samples revealed that the colon-FMT group possessed a significantly higher relative abundance of Lactobacillus compared with the other two treatments (p < 0.05). Collectively, colonic FMT is associated with remodeling intestinal microbiota by enriching beneficial Lactobacillus, improved late-stage growth and sustained long-term intestinal health in pre-weaned calves, whereas colostrum-mediated FMT only provides transient protection against early diarrhea. Full article

Traditional fermented dairy products of Kazakhstan represent potential sources of indigenous lactic acid bacteria (LAB). However, the cultivable LAB associated with these products remain insufficiently characterised. This study aimed to isolate and taxonomically characterise cultivable LAB recovered from traditional dairy products of Kazakhstan using a culture-dependent workflow combined with MALDI-TOF MS, 16S rRNA gene sequencing, phylogenetic analysis, and whole-genome sequencing (WGS) of selected isolates. A total of 102 samples, including kumis, shubat, raw mare’s milk, raw camel’s milk, and freshly prepared soft camel milk cheese, were analysed. Samples were cultured on MRS agar under aerobic conditions at 30 °C for 48 h, and colonies were collected from randomly selected sectors of the plates and purified for further analysis, irrespective of their morphology. In total, 315 bacterial isolates were recovered, of which 79 were confirmed as LAB and retained for further taxonomic analysis. Eight LAB species belonging to four genera were identified, with Leuconostoc mesenteroides being predominant among the recovered LAB isolates (48/79, 60.8%), followed by Lactococcus lactis (19/79, 24.1%). Lentilactobacillus hilgardii, Lentilactobacillus kefiri, and Lentilactobacillus diolivorans were detected only among isolates recovered from fermented products, whereas Lacticaseibacillus paracasei was detected at low frequency. Five representative isolates, including both frequently and less frequently recovered species, were selected for WGS. WGS supported the taxonomic assignments and yielded draft genome assemblies ranging from 1.68 to 2.69 Mb, with GC contents of 34.8–43.1%. OrthoANI analysis further supported their species-level assignments and enabled subspecies-level resolution for selected isolates. Overall, the study establishes a culture-based collection of indigenous LAB recovered from traditional dairy products of Kazakhstan, representing the genera Leuconostoc, Lactococcus, Lentilactobacillus, and Lacticaseibacillus. The observed LAB species composition reflects the cultivable fraction recovered under the applied cultivation and colony-selection conditions and should not be interpreted as a comprehensive representation of LAB diversity in the investigated products. The resulting strain collection and genome sequences provide a basis for subsequent comparative genomic, physiological, and technological studies of selected indigenous LAB. Full article

Background/Objectives: Gastric cancer (GC) is associated with depletion of short-chain fatty acid (SCFA)-producing gut commensals, and the same taxa are consistently reduced in type 2 diabetes (T2D). Co-existing metabolic disease might therefore be expected to compound GC-associated dysbiosis, but this has not been examined within a single cohort alongside tumor characteristics. Methods: Fecal microbiota of 97 Korean adults (63 with GC, 34 controls) were profiled by 16S rRNA gene sequencing. Composition, α-diversity, and β-diversity were compared between groups, and within the GC cohort by T2D status, H. pylori status, tumor stage, and lesion location. The summed relative abundance of significantly depleted SCFA-producing genera was analyzed as an aggregate measure of SCFA-producer abundance. Comparisons used Mann–Whitney U tests with Benjamini–Hochberg correction; community-level differences were tested by PERMANOVA. Results: SCFA-producer abundance fell from 26.7 ± 16.9% of the fecal community in controls to 6.6 ± 8.3% in patients with GC (p < 0.001; Cliff’s δ = +0.76, 95% CI +0.61 to +0.89). Enriched genera were predominantly oral and opportunistic, accompanied by expansion of Proteobacteria. Community-level separation was confirmed by PERMANOVA (R² = 0.088, p = 0.001) with homogeneous dispersions. Within the GC cohort, SCFA-producer abundance did not differ by T2D status, H. pylori status, tumor stage, or lesion location (p = 0.125–0.332), though confidence intervals were wide. Conclusions: Depletion of SCFA-producing commensals in gastric cancer extends across the guild rather than individual genera and was not detectably modified by co-existing T2D or tumor characteristics. Within the limits of this cohort, the signature therefore appears to reflect the presence of disease rather than its clinical or metabolic heterogeneity. Full article

This study aims to explore the shaping mechanism of habitat heterogeneity on its gut microecology and to clarify the structural differences and functional succession patterns of gut microbiota of an earthworm Amynthas aspergillum under artificial breeding versus natural habitats. A total of 175 A. aspergillum specimens and their corresponding soil samples were collected from seven typical habitats in Guangxi: fertile farmland, barren farmland, plantation forest, primary forest, artificial grassland, wasteland slope, and a breeding farm. 16S rRNA high-throughput sequencing was employed to analyze the gut microbiota structure. PICRUSt2 was used to predict metabolic functions, and the correlation between soil physicochemical factors and community characteristics was analyzed. There were only 25 core shared OTUs found across the seven habitats, indicating a strong habitat specificity of the gut microbiota in A. aspergillum. The fertile farmland group exhibited the highest species richness (Chao1) and diversity (Shannon) among all groups (p < 0.05). Although rich in organic matter, the breeding farm group showed the highest Simpson dominance index. Actinomycetota, Pseudomonadota, Chloroflexota, and Bacillota were the dominant shared phyla in all groups. LEfSe analysis revealed that the wasteland slope habitat specifically enriched the stress-tolerant genus Mycobacterium, while the breeding farm was dominated by the anaerobic fermentation-capable genus Clostridium. Functional prediction indicated that the primary forest group had the most complex microbial metabolic network, while the breeding farm group exhibited a “functional simplification” trend focused on basic carbohydrate metabolism, which was significantly correlated with the soil C/N ratio. Soil physicochemical factors, particularly the intensity of anthropogenic disturbance and the composition of organic matter, are the key forces driving the assembly of A. aspergillum gut microbiota through environmental filtering. Artificial monoculture breeding leads to the functional degradation of the gut microecology. Full article