Search Results (5,746)

Odor emissions from animal manure present a significant environmental challenge in livestock farming, impacting air quality and farm sustainability. Traditional methods, such as chemical additives and manure treatment, can be costly, labor-intensive, and less eco-friendly. Therefore, this study investigated the effectiveness of microbial feed additives in reducing these odors. Conducted over three months in 2022 on a Korean beef cattle farm with 20 cattle, the experiment involved feeding a mixture of four microbial strains—Bacillus subtilis KNU-11, Lactobacillus acidophilus KNU-02, Lactobacillus casei KNU-12, and Saccharomyces cerevisiae KNU-06. Manure samples were collected from an experimental group (n = 9) and a control group (n = 11), with microbial community changes assessed through 16S ribosomal RNA gene amplicon sequencing. The results demonstrated significant reductions in specific odorous compounds in the experimental group compared to the control group: ammonia decreased by 64.1%, dimethyl sulfide by 81.3%, butyric acid by 84.6%, and isovaleric acid by 49.8%. Additionally, there was a notable shift in the microbiome, with an increase in the relative abundance of Ruminococcaceae and Prevotellaceae microbes associated with fiver degradation and fermentation, while the control group had higher levels of Bacteroidota and Spirochaetota, which are linked to pathogenicity. This study demonstrates that probiotics effectively alter intestinal microbiota to enhance microorganisms associated with odor mitigation, offering a promising and more sustainable approach to reducing odor emissions in livestock farming. Full article

Listeria monocytognes is an emerging pathogen responsible for the serious foodborne disease, listeriosis. The commensal gut microbiota is the first line of defense against pathogen internalization. The gut microbiome can be modified by prebiotic substrates, which are frequently added to food products and dietary supplements. Prebiotics should selectively support the growth of beneficial microbes and thus improve host health. Nevertheless, little is known about their effect on the growth of L. monocytogenes. The aim of this study was to evaluate the growth ability of four L. monocytogenes strains, representing the most common serotypes, on prebiotic oligosaccharides (beta-(1,3)-D-glucan, inulin, fructooligosaccharides, galactooligosaccharides, lactulose, raffinose, stachyose and 2′-fucosyllactose and a mixture of human milk oligosaccharides) as a sole carbon source. The results showed that only beta-(1,3)-D-glucan was metabolized by L. monocytogenes. These cell culture data suggest that beta-(1,3)-D-glucan may not be selectively utilized by healthy commensal bacteria, and its role in intestinal pathogen growth warrants further exploration in vivo. Full article

Itaconic acid (IA) is recognized for its potential application in treating intestinal diseases owing to the anti-inflammatory and antioxidant properties. Perfluorooctanoic acid (PFOA) can accumulate in animals and result in oxidative and inflammatory damages to multi-tissue and organ, particularly in the intestinal tract. This study aimed to explore whether IA could mitigate intestinal damage induced by PFOA exposure in laying hens and elucidate its potential underlying mechanisms. The results showed that IA improved the antioxidant capacity of laying hens and alleviated the oxidative damage induced by PFOA, as evidenced by the elevated activities of T-SOD, GSH-Px, and CAT, and the decreased MDA content in both the jejunum and serum. Furthermore, IA improved the intestinal morphological and structural integrity, notably attenuating PFOA-induced villus shedding, length reduction, and microvillus thinning. IA also upregulated the mRNA expression of ZO-1, Occludin, Claudin-1, and Mucin-2 in the jejunum, thereby restoring intestinal barrier function. Compared with the PF group, IA supplementation downregulated the gene expression of Keap1 and upregulated the HO-1, NQO1, SOD1, and GPX1 expression in the jejunum. Meanwhile, the PF + IA group exhibited lower expressions of inflammation-related genes (NF-κB, IL-1β, IFN-γ, TNF-α, and IL-6) compared to the PF group. Moreover, IA reversed the PFOA-induced imbalance in gut microbiota by reducing the harmful bacteria such as Escherichia-Shigella, Clostridium innocuum, and Ruminococcus torques, while increasing the abundance of beneficial bacteria like Lactobacillus. Correlation analysis further revealed a significant association between gut microbes, inflammatory factors, and the Keap1/Nrf2/HO-1 pathway expression. In conclusion, dietary IA supplementation could alleviate the oxidative and inflammatory damage caused by PFOA exposure in the intestinal tract by reshaping the intestinal microbiota, modulating the Keap1/Nrf2/HO-1 pathway and reducing oxidative stress and inflammatory response, thereby promoting intestinal homeostasis. Full article

An in-depth study of the phylogenetic relationships of Xylaria species associated with nutshells of fruits and seeds within the genus Xylaria and related genera of Xylaceaecea was conducted in China. The multi-gene phylogenetic analyses were carried out based on ITS, RPB2, and TUB sequences of 100 species of 16 known genera in Xylariaceae around the world. Based on molecular phylogenetic analyses, morphological observations, and ecological habitats, a new genus, Heteroxylaria, is established to accommodate four new species, viz. H. cordiicola, H. juglandicola, H. meliicola, and H. terminaliicola, and four new combinations, viz. H. oxyacanthae, H. palmicola, H. reevesiae, and H. rohrensis. The genus is characterized by cylindrical stromata with conspicuous to inconspicuous perithecial mounds, surface black, having brown to dark brown ascospores with a germ slit, and it grows on nutshell of fruits. The combined ITS+RPB2+TUB sequence dataset of representative taxa in the Xylariaceae demonstrate that Heteroxylaria is grouped with Hypocreodendron but forms a monophyletic lineage. All novelties described herein are morphologically illustrated and compared to similar species and phylogeny is investigated to establish new genera and species. Full article

The SnTox1 effector is a virulence factor of the fungal pathogen Stagonospora nodorum (Berk.), which interacts with the host susceptibility gene Snn1 in a gene-for-gene manner and causes necrosis on the leaves of sensitive wheat genotypes. It is known that salicylic acid (SA), jasmonic acid (JA) and ethylene are the key phytohormones involved in plant immunity. To date, effectors of various pathogens have been discovered that can manipulate plant hormonal pathways and even use hormone crosstalk to promote disease development. However, the role of SnTox1 in manipulating hormonal pathways has not been studied in detail. We studied the redox status and the expression of twelve genes of hormonal pathways and two MAPK genes in six bread wheat cultivars sensitive and insensitive to SnTox1 with or without treatment by SA, JA and ethephon (ethylene-releasing agent) during infection with the SnTox1-producing isolate S. nodorum 1SP. The results showed that SnTox1 controls the antagonism between the SA and JA/ethylene signaling pathways. The SA pathway was involved in the development of susceptibility, and the JA/ethylene pathways were involved in the development of wheat plants resistance to the Sn1SP isolate in the presence of a SnTox1-Snn1 interaction. SnTox1 hijacked the SA pathway to suppress catalase activity, increase hydrogen peroxide content and induce necrosis formation; it simultaneously suppresses the JA and ethylene hormonal pathways by SA. To do this, SnTox1 reprogrammed the expression of the MAPK genes TaMRK3 and TaMRK6 and the TF genes TaWRKY13, TaEIN3 and TaWRKY53b. This study provides new data on the role of SnTox1 in manipulating hormonal pathways and on the role of SA, JA and ethylene in the pathosystem wheat S. nodorum. Full article

Stevia rebaudiana (Bertoni) is a valuable sweetener plant whose sweetness primarily derives from steviol glycosides (SGs), especially rebaudioside A (RA). Polyploidization has the potential to enhance the content of active ingredients in medicinal plants, making this strategy a promising avenue for genetic improvement. However, the underlying regulatory mechanisms that contribute to the fluctuating SGs content between autotetraploid and diploid stevia remain unclear. In this study, we employed metabolic analysis to identify 916 differentially accumulated metabolites (DAMs), with the majority, specifically terpenoids, flavonoids, and lipids, exhibiting upregulation due to polyploidization. Notably, the content of stevia’s signature metabolite SGs (including RA, steviolbioside, and rebaudioside C), along with their precursor steviol, increased significantly after polyploidization. Furthermore, a comprehensive analysis of the transcriptome and metabolome revealed that the majority of differentially expressed genes (DEGs) involved in the SG-synthesis pathway (ent-KAH, ent-KS1, UGT73E1, UGT74G1, UGT76G1, UGT85C2, and UGT91D2) were upregulated in autotetraploid stevia, and these DEGs exhibited a positive correlation with the polyploidization-enhanced SGs. Additionally, multi-omics network analysis indicated that several transcription factor families (such as five NACs, four WRKYs, three MYBs, eight bHLHs, and three AP2/ERFs), various transporter genes (four ABC transporters, three triose-phosphate transporters, and two sugar efflux transporters for intercellular exchange), as well as microorganisms (including Ceratobasidium and Flavobacterium) were positively correlated with the accumulation of RA and steviol. Overall, our results indicate the presence of a regulatory circuit orchestrated by polyploidization, which recruits beneficial rhizosphere microbes and modulates the expression of genes associated with SG biosynthesis, ultimately enhancing the SG content in stevia. This finding will provide new insights for promoting the propagation and industrial development of stevia. Full article

Expansion and intensification of agricultural land in the tropics increasingly raises environmental concerns and questions about sustainability of production systems. A key parameter to consider when assessing the sustainability of production systems is soil fertility, and of particular interest are macronutrients, pH, electrical conductivity, and microbial communities. To understand which environmental factors influence soil fertility, we studied the abovementioned key parameters in two agroforestry systems (rustic and polyculture) in Bali, Indonesia. Via Generalized Linear Models, we found that agroforestry system, canopy cover, crop richness, tree richness, and yields had differing effects on topsoil (0–5 cm) and subsoil (10–15 cm) properties, including C:N ratios, conductivity, K, organic C, P, and total microbes. We found a higher C:N ratio in topsoil (p = 0.027), higher organic carbon content in topsoil (p = 0.009) and subsoil (p < 0.001), higher total microbes in subsoil (p = 0.001), and lower phosphorus levels in topsoil (p < 0.001) in rustic than in polyculture systems. Rustic systems may foster conditions conducive to soil fertility, and in our study, canopy cover (p < 0.001) and tree richness (p < 0.001) emerge as a key positive drivers of the total number of microbes in topsoil. The positive associations observed between crop and tree richness with electrical conductivity and total microbe counts underscore the importance of biodiversity in enhancing soil fertility, emphasizing the need for diversified agricultural systems to promote soil fertility. With soil fertility declining across the world due to global investments in agricultural intensification, it is vital that food production systems divert to the use of systems such as agroforestry in order to ensure soil sustainability and food security for future generations. Full article

Networks are widely used to represent relationships between objects, including microorganisms within ecosystems, based on high-throughput sequencing data. However, challenges arise with appropriate statistical algorithms, handling of rare taxa, excess zeros in compositional data, and interpretation. This work introduces a novel Slope-Matrix-Graph (SMG) algorithm to identify microbiome correlations primarily based on slope-based distance calculations. SMG effectively handles any proportion of zeros in compositional data and involves: (1) searching for correlated relationships (e.g., positive and negative directions of changes) based on a “target of interest” within a setting, and (2) quantifying graph changes via slope-based distances between objects. Evaluations on simulated datasets demonstrated SMG’s ability to accurately cluster microbes into distinct positive/negative correlation groups, outperforming methods like Bray–Curtis and SparCC in both sensitivity and specificity. Moreover, SMG demonstrated superior accuracy in detecting differential abundance (DA) compared to ZicoSeq and ANCOM-BC2, making it a robust tool for microbiome analysis. A key advantage is SMG’s natural capacity to analyze zero-inflated compositional data without transformations. Overall, this simple yet powerful algorithm holds promise for diverse microbiome analysis applications. Full article

Heyndrickxia coagulans (formerly Bacillus coagulans) has been increasingly utilized as an immunomodulatory probiotics. Oral administration of H. coagulans HOM5301 significantly boosted both innate and adaptive immunity in mice, particularly by increasing the phagocytic capacity of monocytes/macrophages. Lipoteichoic acid (LTA), a major microbe-associated molecular pattern (MAMP) in Gram-positive bacteria, exhibits differential immunomodulatory effects due to its structural heterogeneity. We extracted, purified, and characterized LTA from H. coagulans HOM5301. The results showed that HOM5301 LTA consists of a glycerophosphate backbone. Its molecular weight is in the range of 10–16 kDa. HOM5301 LTA induced greater productions of nitric oxide, TNFα, and IL-6 in RAW 264.7 macrophages compared to Staphylococcus aureus LTA. Comparative transcriptome and proteome analyses identified the differentially expressed genes and proteins triggered by HOM5301 LTA. KEGG analyses revealed that HOM5301 LTA transcriptionally and translationally activated macrophages through two immune-related pathways: cytokine–cytokine receptor interaction and phagosome formation. Protein–protein interaction network analysis indicated that the pro-inflammatory response elicited by HOM5301 LTA was TLR2-dependent, possibly requiring the coreceptor CD14, and is mediated via the MAPK and NF-kappaB pathways. Our results demonstrate that LTA is an important MAMP of H. coagulans HOM5301 that boosts immune responses, suggesting that HOM5301 LTA may be a promising immunoadjuvant. Full article

Virulencefactors (VFs) are key molecules that enable pathogens to evade the immune systems of the host. These factors are crucial for revealing the pathogenic processes of microbes and drug discovery. Identification of virulence factors in microbes become an important problem in the field of bioinformatics. To address this problem, this study proposes a novel model DTVF (Deep Transfer Learning for Virulence Factor Prediction), which integrates the ProtT5 protein sequence extraction model with a dual-channel deep learning model. In the dual-channel deep learning model, we innovatively integrate long short-term memory (LSTM) with convolutional neural networks (CNNs), creating a novel integrated architecture. Furthermore, by incorporating the attention mechanism, the accuracy of VF detection was significantly enhanced. We evaluated the DTVF model against other excellent-performing models in the field. DTVF demonstrates superior performance, achieving an accuracy rate of 84.55% and an AUROC of 92.08% on the benchmark dataset. DTVF shows state-of-the-art performance in this field, surpassing the existing models in nearly all metrics. To facilitate the use of biologists, we have also developed an interactive web-based user interface version of DTVF based on Gradio. Full article

Ecosystems that experience elevated CO₂ (eCO₂) are crucial interfaces where intricate interactions between plants and microbes occur. This study addressed the impact of eCO₂ and a N supply on faba bean (Vicia faba L.) growth and the soil microbial community in auto-controlled growth chambers. In doing so, two ambient CO₂ concentrations (aCO₂, daytime/nighttime = 410/460 ppm; eCO₂, 550/610 ppm) and two N supplement levels (without a N supply—N0—and 100 mg N as urea per kg of soil—N100) were applied. The results indicated that eCO₂ mitigated the inhibitory effects of a N deficiency on legume photosynthesis and affected the CO₂ assimilation efficiency, in addition to causing reduced nodulation. While the N addition counteracted the reductions in the N concentrations across the faba beans’ aboveground and belowground plant tissues under eCO₂, the CO₂ concentrations did not significantly alter the soil NH₄⁺-N or NO₃⁻-N responses to a N supply. Notably, under both aCO₂ and eCO₂, a N supply significantly increased the relative abundance of Nitrososphaeraceae and Nitrosomonadaceae, while eCO₂ specifically reduced the Rhizobiaceae abundance with no significant changes under aCO₂. A redundancy analysis (RDA) highlighted that the soil pH (p < 0.01) had the most important influence on the soil microbial community. Co-occurrence networks indicated that the eCO₂ conditions mitigated the impact of a N supply on the reduced structural complexity of the soil microbial communities. These findings suggest that a combination of eCO₂ and a N supply to crops can provide potential benefits for managing future climate change impacts on crop production. Full article

Microeukaryotes are a diverse and often overlooked group of microbes that are important in food webs and other ecological linkages. Little is known about microeukaryotes associated with aquatic invertebrates, although filter feeders such as mussels are likely to take in and potentially retain microeukaryotes in their gut while feeding. Microeukaryotes such as apicomplexans have been reported in marine mussel species, but no studies have examined the presence of these microorganisms in freshwater mussels or how they relate to mussel host species or environmental conditions. In this study, microbial community DNA was extracted from the gut tissue of over 300 freshwater mussels, representing 22 species collected from rivers in the southeastern USA. Microeukaryote DNA was detected using PCR amplification, followed by the sequencing of positive amplicons. Microeukaryotes were found in 167 individual mussels (53%) of those tested. Amplicons included dinoflagellates/algae that differed between mussel species and are likely food sources that were distinct from those found in water and sediment samples analyzed concurrently. A total of 5% of the positive amplicons were non-photosynthetic alveolates that could represent parasitic microeukaryotes. Understanding the distribution of microeukaryotes in the freshwater mussel gut microbiome could further our understanding of the ongoing decline of mussel populations. Full article

The changing notion of “companion animals” and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences. Full article

As one of the most important fertilizers in agriculture, the fate of urea-derived nitrogen (urea-N) in agricultural ecosystems has been well documented. However, little is known about the function of urea-derived carbon (urea-C) in soil ecosystems, especially which soil microorganisms benefit most from the supply of urea-C and whether the utilization of urea-C by the rhizosphere and bulk soil microorganisms is affected by irrigation regimes. To address this, a soil pot experiment was conducted using ¹³C-labeled urea to investigate changes in the composition of the rhizosphere and bulk soil microbial communities and differences in the incorporation of urea-derived C into the rhizosphere and bulk soil phospholipid fatty acids (PLFA) pool under flooded irrigation (FI) and water-saving irrigation (CI). Our results suggest that the size and structure of the rhizosphere and bulk soil microbial communities were strongly influenced by the irrigation regime. The CI treatment significantly increased the total amount of PLFA in both the rhizosphere and bulk soil compared to the FI treatment, but it only significantly affected the abundance of Gram-positive bacteria (G+) in the bulk soil. In contrast, shifts in the microbial community structure induced by irrigation regimes were more pronounced in the rhizosphere soil than in the bulk soil. Compared to the FI treatment, the CI treatment significantly increased the relative abundances of the G+ and Actinobacteria in the rhizosphere soil (p < 0.05). According to the PLFA-SIP, most of the labeled urea-derived C was incorporated into 16:1ω7c, 16:0 and 18:1ω7c under both treatments. Despite these general trends, the pattern of ¹³C incorporation into the PLFA pool differed between the treatments. The factor loadings of individual PLFAs suggested that 18:1ω7c, 16:1ω7c and 16:1ω5c were relatively enriched in urea-C in the bulk soil, while 17:1ω8c, i16:0 and 16:0 were relatively enriched in urea-C in the rhizosphere soil under different irrigation regimes. The loadings also confirmed that 10-me16:0, cy17:0 and cy19:0 were relatively enriched in urea-C under the CI treatment, whereas 14:0, a15:0 and 15:0 were relatively enriched in urea-C under the FI treatment. These results are helpful not only in revealing the interception mechanism of urea-C in soil but also in understanding the functions of key microbes in element cycles. Full article

Toll-like receptors (TLRs) are pattern recognition receptors expressed in immune cells, including neutrophils, macrophages, and dendritic cells. Microbe-associated molecular patterns, including bacterial components, membranes, nucleic acids, and flagella are recognized by TLRs in inflammatory immune responses. Periodontal disease is an inflammatory disease known to cause local infections associated with gingival inflammation, subsequently leading to alveolar bone resorption. Prostaglandin E2 (PGE2) is a key mediator of TLR-induced inflammatory bone resorption. We previously reported that membrane-bound PGE synthase (mPGES-1)-deficient mice failed to induce bone resorption by lipopolysaccharide (LPS), a major pathogenic factor involved in periodontal bone resorption. Further experiments exploring specific pathogen-promoting osteoclast differentiation revealed that various TLR ligands induced osteoclast differentiation in a co-culture model. The ligands for TLR2/1, TLR2/6, TLR3, and TLR5, as well as TLR4, induce osteoclast differentiation associated with the production of PGE2 and the receptor activator of nuclear factor-kappa B ligand (RANKL), an inevitable inducer of osteoclast differentiation in osteoblasts. In vivo, local injection of TLR ligands, including TLR2/1, TLR2/6, and TLR3, resulted in severe alveolar bone resorption. This review summarizes the latest findings on TLR-mediated osteoclast differentiation and bone resorption in inflammatory diseases, such as periodontal diseases. Full article