Search Results (55)

Dynamic changes in gene and transcript expression represent a key factor in regulating the cyclical development of hair follicles. In this study, based on Nanopore sequencing (ONT-seq) data of skin tissue from three developmental stages (anagen (An), catagen (Cn), and telogen (Tn)) of Jiangnan cashmere goat hair follicles, this study presents a profile of candidate DETs implicated in cycle regulation by delineating their stage-specific expression patterns and dynamic expression trends from anagen to telogen. A large proportion of the candidate DETs were significantly enriched in functions related to fat synthesis, storage, or metabolism, with significance levels of p < 0.05 or p < 0.01. These significantly enriched DETs, which were generally upregulated from An to Cn or downregulated from Cn to Tn, support a model where accelerated intradermal fat deposition promotes the progression from An to Cn, while its subsequent decrease facilitates the transition from Cn to Tn. Concurrently, our results also suggest a potential role for dynamic changes in AS patterns in regulating the hair follicle cycle. This regulatory role of AS patterns is potentially mediated through affecting genes related to lipid synthesis/metabolism or cell structure/interaction. Notably, a broader range of fat synthesis, storage, or metabolism-related transcripts showed significant differential expression (p < 0.05) in the An vs. Cn group. Ultimately, by establishing this candidate DET profile, we aim to provide fresh perspectives for deciphering the complex molecular regulation of the hair follicle cycle and to identify new targets for genetically enhancing or molecularly breeding cashmere traits in cashmere goats. Full article

This study explored how top-dressed biogas slurry at winter wheat’s (Triticum aestivum L.) jointing stage (JS) and grain-filling period (GP) affects soil enzyme–microbe interactions, aiming to address nutrient supply–crop demand mismatches. A field experiment with five treatments (water [CK], chemical fertilizer [CF], and three biogas slurry topdressing regimes [S1–S3]) was conducted. Soil samples (0–20 cm) were collected at JS, flowering stage (FS), GP, and reaping period (RP) to analyze soil properties (total nitrogen [TN], available phosphorus [AP], available potassium [AK], soil organic matter [SOM], ammonium nitrogen [AN], pH), enzyme activities (urease [UE], neutral phosphatase [NP], sucrase [SC], catalase [CAT]), and microbial community abundance (via Illumina NovaSeq sequencing). Results showed biogas slurry altered enzyme activities, microbial structure (e.g., Actinomycetota, Ascomycota), and their interactions by regulating soil properties. JS application boosted Pseudomonadota and UE activity, GP application increased Ascomycota and CAT activity, and S3 had the most complex enzyme–microbe network, enhancing nutrient cycling. The analysis indicated that UE activity was strongly and positively correlated with several bacterial phyla (e.g., Planctomycetota, Verrucomicrobiota) (p < 0.01) and fungal phyla (e.g., Ascomycota) (p < 0.01). Full article

Background/Objectives: Actinobacillus pleuropneumoniae is an important respiratory tract pathogen of swine worldwide. Insertion sequences (ISs) play a major role in the transfer of antimicrobial resistance (AMR) among various porcine respiratory tract pathogens. In this study, three A. pleuropneumoniae genomes were investigated for the presence of a novel IS. Methods: Analysis of the draft genomes of three A. pleuropneumoniae serovar 8 isolates (AP_1, AP_120, AP_123) suggested the presence of a novel IS. A closed whole-genome sequence was generated for strain AP_123 by hybrid assembly of Oxford Nanopore MinION long-reads and Illumina MiSeq short-reads, followed by sequence analysis using standard online tools. Transfer was tested by natural transformation. Antimicrobial susceptibility testing was conducted by broth microdilution following Clinical and Laboratory Standards Institute standards. Results: A novel IS, designated ISApl4, was detected in all three genomes. ISApl4 is 712 bp in size and has a transposase gene (tnp) of 654 bp. Moreover, it has perfect terminal 14-bp inverted repeats and produces 8-bp direct repeats at its integration site. This IS was found in 39 copies in the AP_123 genome, two of which formed the 5,765-bp pseudo-compound transposon Tn7560. This transposon carries four AMR genes: sul2 (sulfonamide resistance), strA-strB (streptomycin resistance), and tet(Y) (tetracycline resistance). RT-PCR confirmed tnp gene expression and horizontal transfer of Tn7560 into A. pleuropneumoniae MIDG2331. Conclusions: This study identified the novel ISApl4 in porcine A. pleuropneumoniae and its association with the novel pseudo-compound transposon Tn7560, which proved to be an active element capable of disseminating multidrug resistance amongst A. pleuropneumoniae. Full article

Heterotrophic microorganisms derive energy by decomposing organic matter. Their composition and community structure are influenced by environmental factors and interactions. Soil heterotrophic respiration was assessed by establishing vegetation removal plots (Hr) and control plots (Sr). Soil physicochemical properties were analyzed, and the composition and biomass were evaluated using Illumina HiSeq sequencing and PLFA. The pH of Hr exhibited a significant increase (p < 0.05), whereas MC, MBC, SOC, DOC, TN, and AN all showed significant decreases (p < 0.05). PLFA analysis revealed that the biomass of bacteria, fungi, and total microorganisms in Hr was significantly lower than in Sr (p < 0.05). The predominant bacterial phyla were Acidobacteria, Verrucomycota, and Proteobacteria, with Verrucomycota significantly more abundant in Hr. The dominant fungal phyla were Ascomycota and Basidiomycota, both significantly more abundant in Hr. Community assembly was governed primarily by homogeneous selection in both Hr and Sr. The Hr co-occurrence network showed higher complexity, with >60% positive associations. Mantel tests confirmed significant links between soil properties (MC, pH, MBC, SOC, DOC, TN, and AN) and microbial composition. Vegetation removal induced soil heterogeneity and reduced microbial biomass with specific taxa shifts (Verrucomicrobia, Ascomycota, and Basidiomycota). Altered soil conditions and carbon resources reorganize microbial structure and function. Full article

Background/Objectives: Pasteurella multocida commonly colonizes the bovine respiratory tract and can occasionally cause intramammary infections. Here, eight P. multocida isolates from clinical cases of bovine mastitis were investigated for their molecular characteristics as well as phenotypic and genotypic antimicrobial resistance (AMR) properties. Methods: The isolates originated from quarter milk samples obtained in Germany for diagnostic purposes. Antimicrobial susceptibility testing (AST) by broth microdilution was performed according to the Clinical and Laboratory Standards Institute. Closed whole-genome sequences were generated by hybrid assembly of Illumina MiSeq short-reads and Oxford Nanopore MinION long-reads, followed by consecutive sequence analysis. Results: The P. multocida isolates belonged either to capsular:lipopolysaccharide type A:3 (n = 7) or A:6 (n = 1), and multi-locus sequence types 1 (n = 7) or 7 (n = 1). Seven isolates carried AMR genes, such as mef(C), mph(G), strA, strB, aphA1, aadA31, tet(H), tet(Y), floR, catA3, and sul2, as part of an integrative and conjugative element (ICE). These mobile genetic elements, 58,382–78,401 bp in size, were highly similar to the ICEs Tn7406 or Tn7407 that have been previously described in bovine Mannheimia haemolytica and P. multocida, respectively. Moreover, the isolates showed elevated minimal inhibitory concentrations corresponding to the identified AMR determinants. Conclusions: Molecular typing and ICE organization suggest the bovine respiratory tract as reservoir of the investigated mastitis-associated P. multocida. Horizontal cross-genus transfer of multidrug-resistance-mediating ICEs seems to occur under in vivo conditions among different pathogens from cattle in Germany, which underlines the importance of pathogen identification followed by AST for successful bovine mastitis therapy. Full article

Background/Objectives: Septic cardiomyopathy (SCM) is a severe cardiac complication of sepsis, characterized by cardiac dysfunction with limited effective treatments. This study aimed to identify repurposable drugs for SCM by integrated multi-omics and network analyses. Methods: We generated a mouse model of SCM induced by lipopolysaccharide (LPS) and then obtained comprehensive metabolic and genetic data from SCM mouse hearts using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) and RNA sequencing (RNA-seq). Using network proximity analysis, we screened for FDA-approved drugs that interact with SCM-associated pathways. Additionally, we tested the cardioprotective effects of two drug candidates in the SCM mouse model and explored their mechanism-of-action in H9c2 cells. Results: Network analysis identified 129 drugs associated with SCM, which were refined to 14 drug candidates based on strong network predictions, proven anti-infective effects, suitability for ICU use, and minimal side effects. Among them, acetaminophen and pyridoxal phosphate significantly improved cardiac function in SCM moues, as demonstrated by the increased ejection fraction (EF) and fractional shortening (FS), and the reduced levels of cardiac injury biomarkers: B-type natriuretic peptide (BNP) and cardiac troponin I (cTn-I). In vitro assays revealed that acetaminophen inhibited prostaglandin synthesis, reducing inflammation, while pyridoxal phosphate restored amino acid balance, supporting cellular function. These findings suggest that both drugs possess protective effects against SCM. Conclusions: This study provides a robust platform for drug repurposing in SCM, identifying acetaminophen and pyridoxal phosphate as promising candidates for clinical translation, with the potential to improve treatment outcomes in septic patients with cardiac complications. Full article

In this study, we investigated the changes in the communities of arbuscular mycorrhizal fungi (AMF) and their driving factors across eight vegetation succession stages in the Sanjiang Plain, Northeast China, original natural wetland (NW), wetland edge (EW), shrub-invaded wetland (IW), shrub-dominated wetland (DW), young-Betula forest (YB), mature-Betula forest (MB), Populus and Betula mixed forest (PB), and conifer forest (CF), using Illumina MiSeq sequencing. As this research has revealed, significant differences exist in soil physicochemical indicators, including moisture content (MC), pH, soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP). As vegetation succession progresses, the diversity and structure of AMF communities also undergo changes, with the Simpson diversity index being highest in coniferous forests (CF) and the Abundance-based Coverage Estimator (ACE) and Chao1 indices being elevated in shrub-dominated wetlands (PB). Non-metric multidimensional scaling (NMDS) analysis reveals distinct differences in AMF communities across various succession stages. Furthermore, stacked bar charts indicate that the genus Glomus dominates in most wetland and forest succession stages but is nearly absent in CF, where it is replaced by the genus Paraglomus. Canonical correspondence analysis (CCA) demonstrates that SOC has a more significant impact on AMF communities during the EW stage of succession, while AP and TP exert greater influence during the CF stage as well as the MB and YB stages. AN, on the other hand, plays a more prominent role in shaping AMF communities during the IW and NW stages. PICRUSt2 predictions reveal that enzymes such as alcohol dehydrogenase and L-aminoadipate-semialdehyde dehydrogenase are most abundant in YB, whereas pathways like 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis are most enriched in IW. These findings uncover the close interplay between soil physicochemical properties and AMF community dynamics, aiming to deepen our understanding of the relationships among soil physicochemical properties, AMF community changes, and succession dynamics in wetland and forest ecosystems. Full article

Pseudomonas cannabina pv. alisalensis (Pcal) causes bacterial blight on cabbage. In a previous study, we screened for reduced virulence using Tn5 transposon mutants and identified a LysR-type transcriptional regulator (LTTR) as a potential virulence factor in Pcal. However, the role of LTTR in Pcal virulence has not been thoroughly investigated. In this study, we demonstrated that the Pcal NN14 mutant (with Tn5 insertion in the LTTR-encoding gene) showed reduced disease symptoms and bacterial populations in cabbage, indicating that LTTR contributes to Pcal virulence. RNA-seq analysis identified 39 LTTR-dependent genes. Genes associated with 13 of the type three secretion system (T3SS), two of flagellar apparatus, ABC transporters, and transcription factors were expressed at lower levels in the NN14 mutant compared to the wild type. Conversely, tssH and hcp, type six secretion system (T6SS)-related genes, showed higher expression in NN14. Furthermore, these differences in gene expression were observed in minimal medium, but not in nutrient-rich medium, suggesting that LTTR acts as a global regulator responsive to nutrient conditions. Additionally, LTTR activated the expression of T3SS-related genes during Pcal infection. We also demonstrated that NN14 showed a reduced ability to induce hypersensitive reaction (HR) cell death in non-host plants. Collectively, these results suggest that LTTR contributes to Pcal virulence by regulating T3SS in response to environmental changes. Full article

Lycium barbarum is a plant of considerable economic importance in China. However, root rot poses a significant threat to its yield and quality, leading to substantial economic losses. The disparities in rhizosphere soil fungal communities between healthy and root-rot-affected L. barbarum have not been thoroughly explored. Delving into the dynamics between these fungal communities and the onset of root rot may provide pivotal insights for the biological control of this disease in L. barbarum, as well as aid in identifying fungi associated with the condition. In this study, we utilized rhizosphere soil samples from Ningqi No. 1, a distinguished cultivar of L. barbarum, as our experimental material. We assessed the composition and diversity of fungal communities in both diseased (D) and healthy (H) samples using Illumina MiSeq sequencing technology. The study’s findings revealed that the mean concentrations of total nitrogen (TN) and soil organic matter (SOM) were significantly higher in the healthy specimens when contrasted with the diseased ones, while the pH levels were notably increased in the latter group. Additionally, the alpha-diversity of fungal communities was observed to be greater within the healthy samples as opposed to the diseased samples. Marked distinctions in fungal diversity were discerned between the healthy (H) and diseased (D) samples. Ascomycota was identified as the predominant fungal phylum in both groups. In the healthy samples, beneficial fungi such as Plectosphaerella and Mortierella were prevalent, in contrast to the diseased samples, the relative abundances of Embellisia and Alternaria demonstrated remarkable increases of 89.59% and 87.41%, respectively. Non-metric Multidimensional Scaling (NMDS) illustrated clear distinctions in the composition of fungal communities between the healthy and diseased samples. Redundancy Analysis (RDA) indicated total nitrogen (TN), organic matter (SOM), total phosphorus (TP), Available Potassium (AK), pH, and Total Potassium (TK). Notably, pH showed a stronger correlation with the diseased samples, while TN and SOM were more significantly associated with the healthy samples. Full article

Meloidogyne causes a devastating disease known as root-knot that affects tomatoes and other cash crops worldwide. Conversely, Paraburkholderia tropica has proven beneficial in mitigating the effects of various pathogens in plants. We aimed to unravel the molecular events that underlie the beneficial effects of the bacterium and the detrimental impacts of the nematode when inoculated separately or together in tomato plants. The transcriptional responses induced by P. tropica (TB group (tomato-bacteria group)), Meloidogyne spp. (TN group (tomato-nematode group)) or by the two agents (TBN group (tomato-bacteria-nematode group)) in tomato were assessed by RNA-seq. We implemented a transcript discovery pipeline which allowed the identification of 2283 putative novel transcripts. Differential expression analysis revealed that upregulated transcripts were much more numerous than downregulated ones. At the gene ontology level, the most activated term was ‘hydrolase activity acting on ester bonds’ in all groups. In addition, when both microbes were inoculated together, ‘hydrolase activity acting on O-glycosyl compounds’ was activated. This finding suggests defense responses related to lipid and carbohydrate metabolism, membrane remodeling and signal transduction. Notably, defense genes, transcription factors and protein kinases stood out. Differentially expressed transcripts suggest the activation of a multifaceted plant defense response against the nematode occurred, which was exacerbated by pre-inoculation of P. tropica. Full article

Streptococcus pyogenes, or Group A Streptococcus (GAS), is responsible for over 500,000 deaths per year. Approximately 15% of these deaths are caused by necrotizing soft-tissue infections. In 2008, we isolated an M5 GAS, named the LO1 strain, responsible for the nosocomial transmission of necrotizing fasciitis between a baby and a nurse in Belgium. To understand this unusual transmission route, the LO1 strain was sequenced. A comparison of the LO1 genome and transcriptome with the reference M5 Manfredo strain was conducted. We found that the major differences were the presence of an additional DNase and a Tn916-like transposon in the LO1 and other invasive M5 genomes. RNA-seq analysis showed that genes present on the transposon were barely expressed. In contrast, the DNases presented different expression profiles depending on the tested conditions. We generated knock-out mutants in the LO1 background and characterized their virulence phenotype. We also determined their nuclease activity on different substrates. We found that DNases are dispensable for biofilm formation and adhesion to both keratinocytes and pharyngeal cells. Three of these were found to be essential for blood survival; Spd4 and Sdn are implicated in phagocytosis resistance, and Spd1 is responsible for neutrophil extracellular trap (NET) degradation. Full article

Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for functions such as virulence, immunity, stress survival, and antibiotic resistance. Transposon-directed sequencing (Tn-Seq) has emerged as a powerful method for identifying both essential and conditionally essential genes. In this review, we explored Tn-Seq workflows, focusing on eubacterial species and some yeast species. A comparison of 14 eubacteria species revealed 133 conserved essential genes, including those involved in cell division (e.g., ftsA, ftsZ), DNA replication (e.g., dnaA, dnaE), ribosomal function, cell wall synthesis (e.g., murB, murC), and amino acid synthesis (e.g., alaS, argS). Many other essential genes lack clear orthologues across different microorganisms, making them specific to each organism studied. Conditionally essential genes were identified in 18 bacterial species grown under various conditions, but their conservation was low, reflecting dependence on specific environments and microorganisms. Advances in Tn-Seq are expected to reveal more essential genes in the near future, deepening our understanding of microbial biology and enhancing our ability to manipulate microbial growth, as well as both the primary and secondary metabolism. Full article

Intercropping is widely utilised in agricultural production to enhance land use efficiency because of its benefits, such as heightened crop productivity and optimised resource utilisation. We investigated the effects of Pinto peanut/sisal (HST), Stylo/sisal (strT) and Grona styracifolia/sisal (JqT) intercropping systems on soil bacterial communities compared with sisal continuous cropping (CK) by using Illumina MiSeq high-throughput sequencing technology. The intercropping system significantly increased the total nitrogen (TN), soil pH and soil moisture levels and decreased the levels of available phosphorus (AP) and available potassium (AK). Minimal variations were observed in Shannon’s and Simpson’s diversity indices between the monoculture and intercropping systems as well as among different intercropping systems. The most abundant phyla observed within the four groups were Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes. At the phylum level, the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes were 37.37–54.35%, 10.54–21.21%, 3.46–20.43% and 2.15–5.67%, respectively. Compared with ZCK, StrT, JqT and HST treatments led to higher abundance of Cyanobacteria (from 3.46% to 20.43%, 11.37% and 16.58%, respectively) and Bacteroidetes (from 2.15% to 5.67%, 5.21% and 5.10%, respectively). The results of the linear discriminant analysis of effect sizes demonstrated notable variations in the relative abundance of bacterial taxa among various intercropping systems. The dominant categories of the genus in strT and JqT groups were Blastocatellia and Blastocatellaceae-Subgroup4, while Firmicutes was the dominant category of the genus in the HST group. The structure of bacterial communities did not vary between intercropping and monoculture systems. The findings indicated that the impact of the intercropping system on the bacterial community structure was not contingent on the specific intercropping patterns employed. Full article

Foodborne diseases are major public health problems globally. Metagenomics has emerged as a widely used tool for pathogen screening. In this study, we conducted an updated Tn5 transposase-assisted RNA/DNA hybrid co-tagmentation (TRACE) library construction approach. To address the detection of prevalent known foodborne viruses and the discovery of unknown pathogens, we employed both specific primers and oligo-T primers during reverse transcription. The method was validated using clinical samples confirmed by RT-qPCR and compared with standard RNA-seq library construction methods. The mapping-based approach enabled the retrieval of nearly complete genomes (>95%) for the majority of virus genome segments (86 out of 88, 97.73%), with a mean coverage depth of 21,494.53× (ranging from 77.94× to 55,688.58×). Co-infection phenomena involving prevalent genotypes of Norovirus with Astrovirus and Human betaherpesvirus 6B were observed in two samples. The updated TRACE-seq exhibited superior performance in viral reads percentages compared to standard RNA-seq library preparation methods. This updated method has expanded its target pathogens beyond solely Norovirus to include other prevalent foodborne viruses. The feasibility and potential effectiveness of this approach were then evaluated as an alternative method for surveilling foodborne viruses, thus paving the way for further exploration into whole-genome sequencing of viruses. Full article

Forest fires are among the most influential drivers of changes in forest soil bacterial diversity. Nevertheless, little is known regarding the effects of forest fires on maintaining the complex interactions that preserve forest ecosystem stability. Therefore, this study characterized alterations in soil bacterial community composition and diversity within taiga forests subjected to varying disturbance intensities. Particularly, this study examined the bacterial community within a Larix gmelinii fire-burnt site in Daxinganling, analyzing the changes in bacterial community structure and function across light, moderate, and heavy fire-burnt sites, as well as a control sample site, utilizing Illumina MiSeq technology. Through an assessment of bacterial community diversity and soil physicochemical properties (moisture content (MC), pH, microbial biomass carbon (MBC), organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AP)), we explored the influence of the soil microenvironment on the soil bacterial community structure at the burnt site under different disturbance intensities. Our findings demonstrated that (1) there was no significant change in the Chao index of soil bacteria in the burnt site under different disturbance intensities, whereas the Shannon index decreased significantly (p < 0.05) and the Simpson index increased significantly (p < 0.05) in the burnt site under light and moderate disturbance. (2) The relative abundance of dominant phyla, such as Proteobacteria, Proteobacteria, and Actinobacteriota, did not change significantly in the fire-burnt site under different disturbance intensities, whereas rare species, such as Acidipila, Occallatibacter, and Acidibacter, experienced a significant increase in relative abundance at the genus level. (3) The results of principal coordinates analysis (PCoA) and canonical correlation analysis (CCA) revealed significant differences in the Beta diversity of soil bacteria in the fire-burnt site under varying interference intensities. The Beta diversity of soil bacteria exhibited significant differences (p = 0.001), with MC, pH, TN, AN, and AK identified as significant influencing factors. (4) FAPROTAX functional prediction analyses were conducted to assess the changes in soil bacteria involved in Cellulolysis, Chemoheterotrophy, and Aerobic_Chemoheterotrophy in the fire-burnt site, with the relative abundance of bacteria involved in Chemoheterotrophy being significantly increased (p < 0.05) under different disturbance intensities. Collectively, our findings demonstrated that different disturbance intensities caused by fires significantly affected the Alpha diversity, Beta diversity, and functional abundance of soil bacterial communities in taiga forests, with MC, pH, TN, AN, and AK being identified as key influencing factors. Additionally, the presence of numerous rare species suggests their role as pioneer communities in the succession of soil bacterial communities. Full article