Search Results (160)

Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of the natural product xanthohumol (XN) against SA infection in tilapia (Oreochromis niloticus). The results showed that XN could significantly reduce the bacterial loads of SA in different tissues (liver, spleen and brain) after treatment with different tested concentrations of XN (12.5, 25.0 and 50.0 mg/kg). Moreover, XN could improve the survival rate of SA-infected tilapia. 16S rRNA gene sequencing demonstrated that the alpha-diversity index (Chao1 and Shannon_e) was significantly increased in the XN-treated group (MX group) compared to the SA-infected group (CG group) (p < 0.05), and the Simpson diversity index significantly decreased. The Bray–Curtis similarity analysis of non-metric multidimensional scaling (NMDS) and principal coordinate analysis (PCA) showed that there were significant differences in microbial composition among groups. At the phylum level, the relative abundance of the phyla Actinobacteria, Proteobacteria and Bacteroidetes decreased in the MX group compared to the CG group, while the relative abundance of the phyla Fusobacteria, Firmicutes and Verrucomicrobia increased. Differences were also observed at the genus level; the relative abundance of Mycobacterium decreased in the MX group, but the abundance of Cetobacterium and Clostridium_sensu_stricto_1 increased. Metabolomics analysis revealed that XN changed the metabolic profile of the liver and significantly enriched aspartate metabolism, glycine and serine metabolism, phosphatidylcholine biosynthesis, arginine and proline metabolism, glutamate metabolism, urea cycle, purine metabolism, methionine metabolism, betaine metabolism, and carnitine synthesis. Correlation analysis indicated an association between the intestinal microbiota and metabolites. In conclusion, XN may be a potential drug for the prevention and treatment of SA infection in tilapia, and its mechanism of action may be related to the regulation of the intestinal microbiota and liver metabolism. Full article

Understanding the biodiversity of aquatic communities and the underlying mechanisms that shape biodiversity patterns and community dynamics is crucial for the effective conservation and management of freshwater ecosystems. However, traditional survey methods often fail to comprehensively capture species diversity, particularly for low-abundance taxa. Moreover, studies integrating both metazoan and fish communities at fine spatial scales remain limited. To address these gaps, we employed a multi-marker eDNA metabarcoding approach, targeting both the 12S and 18S rRNA gene regions, to comprehensively investigate the composition of metazoan and fish communities in the Yujiang River. A total of 12 metazoan orders were detected, encompassing 15 families, 21 genera, and 19 species. For the fish community, 32 species were identified, belonging to 25 genera, 10 families, and 7 orders. Among these, Adula falcatoides and Coptodon zillii were identified as the most prevalent and abundant metazoan and fish species, respectively. Notably, the most prevalent fish species, C. zillii and Oreochromis niloticus, are both recognized as invasive species. The Bray–Curtis distance of metazoa (average: 0.464) was significantly lower than that of fish communities (average: 0.797), suggesting higher community heterogeneity among fish assemblages. Beta-diversity decomposition indicated that variations in the metazoan and fish communities were predominantly driven by species replacement (turnover) (65.4% and 70.9% for metazoa and fish, respectively) rather than nestedness. Mantel tests further revealed that species turnover in metazoan communities was most strongly influenced by water temperature, while fish community turnover was primarily affected by water transparency, likely reflecting the physiological sensitivity of metazoans to thermal gradients and the dependence of fish on visual cues for foraging and habitat selection. In addition, a co-occurrence network of metazoan and fish species was constructed, highlighting potential predator-prey interactions between native species and Corbicula fluminea, which emerged as a potential keystone species. Overall, this study demonstrates the utility of multi-marker eDNA metabarcoding in characterizing aquatic community structures and provides new insights into the spatial dynamics and species interactions within river ecosystems. Full article

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems. Full article

Bacterial vaginosis (BV) affects 30% of women annually, but many face barriers to in-person care. Here we present real-world outcomes of remote BV diagnosis and management through self-collected vaginal microbiome (VMB) testing and telemedicine visits, focusing on symptom resolution, recurrence, and overall microbial shifts. Among the 1159 study participants, 75.5% experienced symptom resolution at four weeks when managed with our algorithm-guided treatment protocol. At a median follow-up of 4.4 months after the initial visit, 30.0% of patients experienced recurrent BV, which is lower than the typical recurrence rates seen in historical in-person cohorts. Across the entire cohort, metagenomic data demonstrated a significant increase in Lactobacillus abundance (mean of 32.9% to 48.4%, p < 0.0001) and a corresponding decrease in BV-associated taxa such as Gardnerella, Prevotella, and Fannyhessea. A PERMANOVA of pairwise Bray–Curtis distances showed significant separation between pre-and post-treatment samples (pseudo-F = 37.6, p < 0.0001), driven by an increase in Lactobacillus-dominated samples. Treatment adherence was high (a total of 78% reported perfect or near-perfect adherence), and adverse events were generally mild (in total, 22% reported vaginal irritation, and 13% reported abnormal discharge). These results demonstrate that Evvy’s at-home metagenomic platform, paired with telemedicine and a smart treatment algorithm, delivers robust clinical and microbial outcomes. This work offers a novel approach to managing bacterial vaginosis, a challenging condition characterized by persistently high recurrence rates. Full article

Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray–Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia–Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat’s gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host’s energy balance and health under seasonal contexts. Full article

Background: Cow-milk-induced allergic proctocolitis (CMIAP) is a non-IgE-mediated food hypersensitivity that often resolves spontaneously but may predispose infants to IgE-mediated allergies and eosinophilic gastrointestinal disorders. Understanding its pathophysiology is crucial for microbiota-based interventions. Methods: We enrolled 32 exclusively breastfed infants—16 with confirmed cases of CMIAP and 16 age-matched healthy controls. The cohorts were sex-balanced (8 F/8 M), term-born (gestational age ± SD: 40 ± 1.2 vs. 39 ± 1.3 weeks), vaginally delivered, and sampled at a mean age of 2.0 ± 0.44 months (range 1.5–3.0) vs. 2.4 ± 0.66 months (range 1.5–3.5). Faecal samples underwent 16S rRNA gene sequencing on the Illumina NovaSeq platform, with diversity and differential abundance analyses. Results: The maternal dairy intake was similar (total dairy: 250 ± 80 vs. 240 ± 75 mL/day; yoghurt: 2.3 ± 1.0 vs. 2.5 ± 1.2 days/week; p = 0.72). Bray–Curtis dissimilarity assessments revealed distinct microbiota in infants with CMIAP. Infants with CMIAP had a lower abundance of Bifidobacterium (log₂FC−2.27; q = 0.022; ANCOM-BC), Collinsella (−29.35; padj < 0.0001; DESeq2), and Limosilactobacillus (−8.01; padj = 0.0285; DESeq2; q < 0.0001; ANCOM-BC) compared with controls. In contrast, Hungatella (+24.99; padj < 0.0001; DESeq2), Veillonella (+4.73; padj = 0.0221; DESeq2), Citrobacter (+10.44; padj = 0.0124; DESeq2), and Ruminococcus gnavus (+2.69; q < 0.0001; ANCOM–BC) were more abundant in the CMIAP group. Conclusions: Infants with CMIAP exhibit gut dysbiosis, which is characterised by the depletion of beneficial commensals and the enrichment of potential pathogens, independent of maternal dairy intake. Further studies should establish whether these microbiota alterations are causal or consequential in CMIAP. Full article

This study investigates the feeding behavior of the European brown hare on Pianosa Island, Italy, focusing on seasonal dietary preferences in coastal and inland areas. We quantified plant species frequencies in vegetation and fecal pellets, assessed α and β diversity, compared diets via Bray–Curtis matrices, and evaluated selection preferences using the Resource Selection Ratio. During spring, the coastal diet was predominantly composed of grasses, particularly Dactylis glomerata, while non-leguminous forbs like Hedypnois rhagadioloides were prominent inland. Fabaceae, including Lotus ornithopodioides, were highly preferred. In autumn, non-leguminous forbs, such as Crepis foetida, were favored on the coast, while grasses like Bromus hordeaceus dominated inland. Fabaceae, particularly Trifolium species, remained a key component of the diet. Plant diversity peaked in spring and decreased markedly in autumn. Dietary overlap between seasons was moderate, with higher similarity observed in the coastal area. The study underscores the importance of Fabaceae and seasonal vegetation changes in shaping the hare’s diet. These findings provide valuable insights for conservation, emphasizing the need to preserve key plant species and habitats to support isolated hare populations in Mediterranean ecosystems. Full article

Gut microbiota composition plays a crucial role in host health and may be influenced by age and disease conditions. This study investigates the gut microbiota diversity of 175 dogs across three age groups (Junior (20–46 months, 43 dogs), Adult (47–92 months, 58 dogs), and Senior (93–168 months, 74 dogs), and examined the impact of osteoarthritis on microbial composition. Alpha diversity analysis using the Shannon and Chao1 indices were significant (p < 0.05) in Senior dogs Beta diversity analysis based on Bray–Curtis dissimilarity indices demonstrated substantial overlap in gut microbiota composition across age groups, with no significant clustering observed (p > 0.05). A second analysis compared the microbiota of 69 healthy dogs and 81 dogs affected by osteoarthritis (OA) in the three classes of age. No significant differences were shown for alpha diversity and beta diversity between healthy and OA dogs. This indicates that aging and osteoarthritis do not induce significant shifts in microbial beta diversity, although high inter-individual variability was noted. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis identified distinct bacterial taxa associated with different age groups. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis identified distinct bacterial taxa associated with different age groups. Junior dogs exhibited enrichment in Blautia, Erysipelotrichaceae, and Clostridium, while Adult dogs were characterized by higher abundances of Prevotella, Streptococcus, and Ruminococcaceae. Senior dogs had increased representation of Prevotella and Ruminococcus. In OA dogs, Peptococcus, Peptostreptococcus, Clostridiaceae, and Coprobacillus were significantly enriched in comparison to healthy dogs, suggesting potential microbiota shifts associated with osteoarthritis. Overall, these findings indicate that gut microbiota diversity varies across different life stages, specific bacterial taxa were differentially enriched in relation to age and OA. This study enhances our understanding of gut microbiota dynamics in dogs and provides insights into potential age- and disease-related microbial signatures. Full article

The elevational patterns of plant β diversity and their underlying drivers are known to be scale-dependent, but pinpointing the spatial scales at which different ecological processes occur remains challenging using traditional field inventory methods. Remote sensing has emerged as a promising alternative, providing continuous spatial data for monitoring plant diversity. In this study, we used field inventory data and corresponding Sentinel-2 images from a subtropical mountain to simulate pooled assemblages and assess the potential of using multispectral satellite images in predicting tree β diversity. We further examined the scale-dependent elevational gradient of the spectral β diversity and identified primary topographic variables across different spatial extents (0.16–64 ha). The spectral β diversity showed a consistently positive relationship with the inventory β diversity calculated using various indices (average pairwise Sørensen, Jaccard, and Bray–Curtis dissimilarities, as well as multi-community differentiation measures based on Hill numbers), with the strongest correlation observed for abundance-weighted indices and images from early spring and late autumn (R²_max = 0.63). However, a null model-derived β deviation showed only a weak correlation between remote sensing and field-based measures. A declining trend in the spectral β diversity with an increasing elevation was observed and became more pronounced at larger extents. The topographic heterogeneity, represented by the slope and northness, explained the elevational gradients at spatial extents >4 ha, attesting the significant role of environmental filtering in shaping plant diversity patterns, even at fine scales. While the northness was more influential at smaller spatial extents (<4 ha), the slope had a stronger impact at broader spatial extents (>4 ha). This study showcases the potential of using readily available remote sensing data to address difficult questions in plant diversity research. Full article

In ex situ conservation, gut bacteria and fungi play a crucial role in maintaining the intestinal microecological balance of the gut, and disruptions in this system may negatively impact host health. The South China tiger (Panthera tigris amoyensis) is a critically endangered tiger subspecies currently surviving under human-managed care and captive breeding programs, with only a small number of individuals remaining. Disruption in the gut microbiota, particularly the proliferation of pathogenic bacteria, can be fatal for cubs. This study analyzed the composition and seasonal changes of the gut bacterial and fungal communities of South China tigers in captive and semi-released environments during the winter of 2023 and the summer of 2024, using 16S rRNA and ITS high-throughput sequencing. The results showed that the dominant gut bacteria were Bacillota, Actinomycetota, Fusobacteriota, Pseudomonadota, and Bacteroidota. The abundance of Bacillota decreased in summer and was slightly lower in captive tigers than in semi-released tigers. Fungal communities were dominated by Ascomycota, with a negative correlation observed between Ascomycota and Basidiomycota. The abundance of Ascomycetes was lower in summer but significantly higher in semi-released tigers than in captive ones. Diversity analysis revealed no significant effects of the season or the environment on bacterial α-diversity, and fungal α-diversity was also not significantly affected by seasonal variation. However, microbial diversity increased under semi-free-range conditions, with fungal richness significantly higher than in captive environments (p < 0.01). Principal coordinate analysis (PCoA) based on Bray–Curtis distances revealed significant differences in the community structures of both bacterial (Adonis, R² = 0.2364, p = 0.001) and fungal (Adonis, R² = 0.1542, p = 0.001) communities across different seasons and environments. These findings provide valuable insights into the health management strategies and ecological adaptation of South China tigers. Full article

Background: Gut microbiome composition may influence the risk of intracranial aneurysm rupture. Methods: This study analyzed the gut microbiota of 48 patients—24 with ruptured aneurysms (RA) and 24 with unruptured intracranial aneurysms (UIA)—using next-generation sequencing. Results: While alpha diversity was similar between groups, beta diversity revealed significant taxonomic differences (Bray–Curtis: p = 0.02; unweighted UniFrac: p = 0.0291). Both groups were dominated by the phyla Bacillota, Bacteroidota, and Proteobacteria, but genus- and family-level differences were observed. RA patients showed higher abundances of Anaerotruncus, Coprobacillus, Sellimonas, Hungatella, and Ruthenibacterium, whereas UIA patients exhibited greater levels of Faecalibacterium, Brotolimicola, Clostridiaceae, Roseburia, and Agathobaculum. Linear discriminant analysis identified one class, 10 genera, and 17 species that differed significantly between groups. Notably, Faecalibacterium prausnitzii and Agathobaculum butyriciproducens—bacteria known for their anti-inflammatory and neuroprotective properties—were enriched in UIA patients. Conclusions: These findings suggest that gut microbiota, particularly short-chain fatty acid–producing bacteria, may contribute to vascular protection and aneurysm pathophysiology. Microbiome-based therapeutic strategies could offer new avenues for the prevention of cerebrovascular disease. Full article

The present study aimed to characterize the benthic macroinvertebrate community of the Jabal Ali Marine Sanctuary (JAMS), the sole marine protected area in the Emirate of Dubai, during the summer and winter seasons of 2017. Limited research on the biological quality of the JAMS prompted this investigation, which involved 10 sampling stations to assess macroinvertebrate diversity and community composition in relation to abiotic factors such as sediment granulometry, trace metals, salinity, and temperature. Collected sediment samples were analyzed for macroinfauna, and their abundance was measured, revealing an average abundance of 2150 ind/m² in summer and 2132 ind/m² in winter without a significant difference between both seasons. Univariate indices, including the Margalef diversity index and Pielou evenness index, indicate a range of diversity values across sampling sites. Community composition was assessed through SIMPROF and Bray–Curtis similarity clustering, further elucidating the relationship between community structures and environmental gradients. The dominant macroinvertebrate species varied across seasons and stations, providing insights into seasonal variations in community dynamics. These findings contribute to the understanding of benthic community structures and biodiversity in the JAMS and serve as a baseline for future monitoring and management efforts aimed at preserving the ecological integrity of this important marine sanctuary. Full article

Next-Generation Sequencing (NGS) technology was applied to evaluate Food Safety Management System (FSMS) performance in seafood-processing factories by exploring microbiome diversity alongside traditional methods for detecting foodborne pathogens. A total of 210 environmental swabs collected from processing zones in six factories underwent 16S rRNA amplicon sequencing. FSMS-certified factories exhibited significantly higher species richness, with alpha diversity p-values of 0.0036 for observed ASVs, 0.0026 for Faith’s PD and 0.032 for Shannon. Beta diversity analysis also revealed significant differences, with p-values of 0.001 for Bray–Curtis, unweighted UniFrac and Jaccard. Pathogens like Listeria monocytogenes, Salmonella spp. and Bacillus cereus were present in “uncertified” factories but absent in the “certified” factories. The “certified” factories had a significantly higher proportion of lactic acid bacteria (LAB) genera (70.22%) compared to “uncertified” factories (29.78%). The LAB genera included Streptococcus, Lactococcus, Lactobacillus and others. NGS has demonstrated superior capability by providing comprehensive microbiome detection, including the unculturable microorganisms and insights into microbial diversity, so it lacks the limitations that come with traditional culturing. These findings highlight the potential for leveraging beneficial microbes in bioremediation and pathogen control to enhance FSMS effectiveness in seafood-processing environments. Full article

The effect of agricultural practices on soil bacterial communities is not constant and depends a lot on the climatic context, changes in the soil characteristics, land use, and agricultural strategy. Thus, knowledge about how different land use systems in the Cerrado influence the diversity and taxonomic structure of microbial communities under the same soil type remains limited. In this context, the objective of this work was to analyze and compare the bacterial communities of Cerrado soil under two different land use systems (cover crop and potato cultivation) and in a neighboring native Cerrado area. For this, we used high-throughput amplicon sequencing of 16S rRNA genes (metabarcoding) to characterize the bacterial community at different taxonomic levels in a native Cerrado area, in a potato crop area, and in an area with cover crops. Our data indicated significant impacts on soil physicochemical properties and enzymatic activity, which directly reflect the dynamics of bacterial communities. The three bacterial phyla with the highest relative abundance in the three areas were Proteobacteria, Actinobacteriota, and Acidobacteriota. At the taxonomic class level, small variations were observed among areas, while at the amplicon sequence variant (ASV) level, these variations were more pronounced. The alpha diversity indices showed that the bacterial communities among the areas are rich and diverse. Bray–Curtis and Jaccard distance-based PCoA demonstrated an overlap of bacterial communities present in the cover crop area with the native Cerrado area and separation from the potato cultivation area. The in silico prediction demonstrated that the native Cerrado area presented the highest values of functional diversity of the soil bacterial community compared to the others. Thus, our results provide a holistic view of how different land use systems in the Cerrado can influence the taxonomic and functional diversity of soil bacterial communities. Full article

Understanding soil microbial community assembly in endangered mangrove ecosystems is crucial for ecological conservation. This study investigated the diversity and drivers of soil microbiomes across Barringtonia racemosa communities (pure: T1; associated: T2, T3) in China’s Leizhou Peninsula, using SMRT sequencing and phospholipid fatty acid analysis. The results reveal that pure B. racemosa communities (T1) harbored the highest microbial diversity (Chao1: 2980 bacteria, 14,378 fungal OTUs), with Pseudomonadota (37.6%) and Ascomycota (52.6%) as dominant phyla. Fungal communities exhibited 3.2-fold higher β-diversity variability than bacteria across communities (Bray–Curtis; p < 0.01). Redundancy analysis identified soil organic carbon (SOC), available nitrogen (SAN), and leaf manganese as primary drivers, collectively explaining 72.4% of microbial variation (p = 0.003). Notably, pure communities showed an elevated SOC (74.3 mg/kg) and fungal: bacterial ratio (0.19 vs. 0.13–0.14 in associated communities), indicating fungal dominance in carbon-rich sediments. Conversely, rice field controls displayed distinct SAP/SAK patterns reflecting agricultural impacts. These findings demonstrate that the B. racemosa community structure differentially regulates fungal assemblages more strongly than bacterial communities, providing critical insights for mangrove restoration through microbial-informed management. Full article