Search Results (2,619)

Intestinal diseases are one of the diseases that affect the growth and immunity of deer. Currently, more lactic acid bacteria (LAB) are available as feed additives to improve the intestinal ecological balance of ruminants in production practices. In this study, Enterococcus faecalis was supplemented in the feed of fallow deer for 170 d, and body weights, blood indices and immune levels of fallow deer were counted at 35, 65 and 170 d. The effects of Enterococcus faecalis on the intestinal microbiota and the metabolism of fallow deer were analysed using 16S rDNA and UPLC-MS/MS methods. The results showed that the addition of Enterococcus faecalis to the diet improved body weight and immune function and increased the aggregation of gut microbiota in fallow deer. The addition of Enterococcus faecalis altered the community structure of intestinal microorganisms in fallow deer and increased the number of beneficial bacteria. In addition, combined with metabolomics analysis, it was found that supplementation with Enterococcus faecalis significantly altered the metabolites of fallow deer, mainly regulating lipid metabolism, carbohydrate metabolism and phospholipid metabolism. In conclusion, this study presents, for the first time, evidence that the LAB strain Enterococcus faecalis can be used as a potential probiotic for deer and points to a new direction for the treatment of intestinal disorders in the deer family. Full article

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3–0.8 µm in diameter and 1.5–2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with “Fibrivirga algicola JA-25” (99.2%) and Fibrella forsythia HMF5405^T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO₂ fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture. Full article

Tuber aestivum, commonly known as the summer truffle, is typically found in various parts of Europe where it grows naturally. However, its presence in Portugal was not confirmed until now. The first fruit bodies were collected in April 2024 at stone pine stands (Alenquer and Arruda dos Vinhos, Lisbon) and in June at holm oak stands (Salir, Faro). These specimens are characterized by hypogeous, subglobose, black ascomata with a peridium surface covered with pyramidal warts. Ascopores are subglobose-to-broadly ellipsoid, distinctively ornamented, usually 1–6 per asci. According to the results of the internal transcribed spacer (ITS) rDNA sequence analysis, these specimens form a well-supported group within the Aestivum clade, with T. aestivum being the closest phylogenetic taxon. This remarkable discovery opens up new opportunities for truffle exploitation in Portugal thanks to the summer truffle’s gastronomical value and high market prices. Full article

To tease apart differences between conventional cage (CC) and cage-free (CF) housing systems, this study focuses on the effects of excreta exposure and age by comparing microbial communities, intestinal permeability, and corticosterone in hens in enriched colonies (EC) and CF housing systems during early- and late-lay. Hens were randomly selected from two rooms of CF (n = 20) and EC (n = 20) at 35 and 76 weeks of age. One hour following an oral gavage of fluorescein isothiocyanate dextran (FITC-D), hens were euthanized, and ileal contents and blood were collected. Serum FITC-D using a fluorescent spectrophotometer and corticosterone using a commercial competitive ELISA kit were analyzed. Following DNA isolation from the ileum contents, the V4 region of the 16S rRNA gene was sequenced. Sequence data were filtered in Mothur v1.43.0, followed by de novo operational taxonomic unit (OTU) clustering and classifying with the SILVA SSU v138 reference database. Serum FITC-D was altered by housing type, age of hens, and the interaction between housing type and age of hens (p < 0.001), with 76-week-old hens housed in EC having the highest FITC-D. Corticosterone increased with age (p = 0.023). Microbial community diversity measurements favored hens housed in the CF housing system as ileal contents tended to have increased species evenness (p = 0.008) and greater alpha diversity (p = 0.006). The majority of the over-representation of OTUs were associated with peak lay. Full article

In this study, the expression profiles of miR-148a were constructed in eight different ovine tissues, including mammary gland tissue, during six different developmental periods. The effect of miR-148a on the viability, proliferation, and milk fat synthesis of ovine mammary epithelial cells (OMECs) was investigated, and the target relationship of miR-148a with two predicted target genes was verified. The expression of miR-148a exhibited obvious tissue-specific and temporal-specific patterns. miR-148a was expressed in all eight ovine tissues investigated, with the highest expression level in mammary gland tissue (p < 0.05). Additionally, miR-148a was expressed in ovine mammary gland tissue during each of the six developmental periods studied, with its highest level at peak lactation (p < 0.05). The overexpression of miR-148a increased the viability of OMECs, the number and percentage of Edu-labeled positive OMECs, and the expression levels of two cell-proliferation marker genes. miR-148a also increased the percentage of OMECs in the S phase. In contrast, transfection with an miR-148a inhibitor produced the opposite effect compared to the miR-148a mimic. These results indicate that miR-148a promotes the viability and proliferation of OMECs in Small-tailed Han sheep. The miR-148a mimic increased the triglyceride content by 37.78% (p < 0.01) and the expression levels of three milk fat synthesis marker genes in OMECs. However, the miR-148a inhibitor reduced the triglyceride level by 87.11% (p < 0.01). These results suggest that miR-148a promotes milk fat synthesis in OMECs. The dual-luciferase reporter assay showed that miR-148a reduced the luciferase activities of DNA methyltransferase 1 (DNMT1) and peroxisome proliferator-activated receptor gamma coactivator 1-A (PPARGC1A) in wild-type vectors, suggesting that they are target genes of miR-148a. The expression of miR-148a was highly negatively correlated with PPARGC1A (r = −0.789, p < 0.001) in ovine mammary gland tissue, while it had a moderate negative correlation with DNMT1 (r = −0.515, p = 0.029). This is the first study to reveal the molecular mechanisms of miR-148a underlying the viability, proliferation, and milk fat synthesis of OMECs in sheep. Full article

Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress. Full article

In this study, we assessed the therapeutic effects of Macleaya cordata (Willd). R. Br.-derived protopine-type alkaloids (MPTAs) in a mouse model of lipopolysaccharide (LPS)-induced intestinal inflammation. The experimental design involved the allocation of mice into distinct groups, including a control group, a model group treated with 6 mg/kg LPS, a berberine group treated with 50 mg/kg berberine hydrochloride and low-, medium- and high-dose MPTA groups treated with 6, 12 and 24 mg/kg MPTAs, respectively. Histological analysis of the ileum, jejunum and duodenum was performed using Hematoxylin and Eosin (H&E) staining. Moreover, the quantification of intestinal goblet cells (GCs) was performed based on PAS staining. The serum levels of IL-1β, IL-6, IL-8 and TNF-α were quantified using an enzyme-linked immunosorbent assay (ELISA), while the mRNA levels of TLR4, NF-κB p65, NLRP3, IL-6 and IL-1β were assessed using quantitative PCR (qPCR). The protein levels of TLR4, Md-2, MyD88, NF-κB p65 and NLRP3 were determined using Western blotting. Furthermore, the 16S rDNA sequences of bacterial taxa were amplified and analysed to determine alterations in the gut microbiota of the mice following MPTA treatment. Different doses of MPTAs were found to elicit distinct therapeutic effects, leading to enhanced intestinal morphology and an increased abundance of intestinal GCs. A significant decrease was noted in the levels of pro-inflammatory cytokines (IL-1β, IL-6, IL-8 and TNF-α). Additionally, the protein levels of TLR4, MyD88, NLRP3 and p-p65/p65 were markedly reduced by MPTA treatment. Furthermore, 16S rDNA sequencing analysis revealed that the administration of 24 mg/kg MPTAs facilitated the restoration of microbial composition. Full article

Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them. Full article

A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166^T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166^T was observed at 10–45 °C (optimum 34–37 °C), at pH 5–10 (optimum 6–8), and in the presence of 0–5% NaCl (optimum 1–3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166^T shared the highest similarity (98.58%) with Aquibium oceanicum B7^T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73–76.79%), average amino identity (AAI, 88.50–79.03%), and digital DNA–DNA hybridization (dDDH, 36.1–22.2%) values between LZ166^T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166^T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin–Benson–Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166^T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166^T (=MCCC M28807^T = KACC 23148^T = KCTC 82889^T). Full article

The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum. Full article

The early detection of spoilage microorganisms and food pathogens is of paramount importance in food production systems. We propose a novel strategy for the early detection of food production defects, harnessing the product microbiome. We hypothesize that by establishing microbiome datasets of proper and defective batches, indicator bacteria signaling production errors can be identified and targeted for rapid quantification as part of routine practice. Using the production process of pastrami as a model, we characterized its live microbiome profiles throughout the production stages and in the final product, using propidium monoazide treatment followed by 16S rDNA sequencing. Pastrami demonstrated product-specific and consistent microbiome profiles predominated by Serratia and Vibrionimonas, with distinct microbial signatures across the production stages. Based on the established microbiome dataset, we were able to detect shifts in the microbiome profile of a defective batch produced under lactate deficiency. The most substantial changes were observed as increased relative abundances of Vibrio and Lactobacillus, which were subsequently defined as potential lactate-deficiency indicators. PMA-qPCR efficiently detected increased levels of these species, thus proving useful in rapidly pinpointing the production defect. This approach offers the possibility of the in-house detection of defective production events with same-day results, promoting safer food production systems. Full article

To meet the demand of consumers for chicken products, poultry breeders have made improvements to chickens. However, this has led to a new problem in the modern poultry industry, namely excessive fat deposition. This study aims to understand the effects of dietary iron supplementation on fat deposition and gut microbiota in chickens. In this study, we investigated the effects of iron on the growth performance, fat deposition, and gut microbiota of silky fowl black-bone chickens. A total of 75 7-week-old silky fowl black-bone chickens were randomly divided into three groups (five replicates per group, five chickens per replicate) and fed them for 28 days using a growing diet (control group), a growing diet + 10% tallow (high-fat diet group, HFD group), and a growing diet + 10% tallow + 500 mg/kg iron (HFDFe500 group), respectively. We detected the effects of iron on the growth performance, fat deposition, and gut microbiota of silky fowl black-bone chickens using the growth performance index test, oil red O staining, and HE staining, and found that the high-fat diet significantly increased liver and serum fat deposition and liver injury, while the addition of iron to the diet could reduce the fat deposition caused by the high-fat diet and alleviate liver injury. In addition, 16S rDNA sequencing was used to compare the relative abundance of gut microbiota in the cecal contents in different feeding groups. The results showed that the high-fat diet could induce gut microbiota imbalance in chickens, while the high-iron diet reversed the gut microbiota imbalance. PICRUSt functional prediction analysis showed that dietary iron supplementation affected amino acid metabolism, energy metabolism, cofactors, and vitamin metabolism pathways. In addition, correlation analysis showed that TG was significantly associated with Firmicutes and Actinobacteriota (p < 0.05). Overall, these results revealed high dietary iron (500 mg/kg) could reduce fat deposition and affect the gut microbiota of silky fowl black-bone chickens, suggesting that iron may regulate fat deposition by influencing the gut microbiota of chickens and provides a potential avenue that prevents excessive fat deposition in chickens by adding iron to the diet. Full article

We studied the occurrence of endophytic fungi and bacteria in the roots of F. gigantea, a woodland perennial grass common throughout Europe and temperate Asia. The taxonomic assignment was carried out according to the isolate’s colony and cytological species morphotype characteristics and confirmed by the assessment of the standard DNA sequences, ITS, RPB2, SSU, and TEF1-a for fungi and 16S rDNA for bacteria. Our study has shown that F. gigantea roots are the habitat to a wide range of fungi and bacteria. The occurrence of fungal structures was determined in ~40% of the roots examined by Trypan Blue staining. In a surface-sterile root-cutting culture on PDA medium, we obtained isolates of six endophytic fungi species: four members of Ascomycota—Alternaria alternata, Cadophora fastigiata, Chaetomium funicola, and Microdochium bolleyi—and two of Basidiomycota—Coprinellus sp. and Sistotrema brinkmannii. In addition, we report bacteria co-occurring endophytically in the roots of this grass. The Firmicutes group was the most prevalent, consisting of four Gram-positive, endospore-forming bacteria taxa. The isolates were identified as Bacillus pumilus, Bacillus sp., Lysinibacillus sp., and Priestia aryabhattai. Moreover, two Gram-negative bacteria were detected—Kosakonia sp. (Proteobacteria) and Pedobacter sp. (Bacteroidetes). Thus, applying the isolate-culture approach, we identified a set of microorganisms in the roots of a typical grass native to the deciduous forest floor. The functional roles of these endophytes are diverse, and many of them, saprotrophs and decomposers of wood and plant debris, are linked to the decomposition of organic matter. This is the first detailed report on fungal and bacterial endophytes inhabiting the roots of F. gigantea. This study fills in a research gap on endophytes associated with the below-ground parts of Festuca spp., hitherto extensively studied for Epichloë/Neotyphodium associations in their foliar parts. Full article

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC’s vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome. Full article

Sheath rot and dirty panicle are some of the major diseases of rice in Thailand. The diseases are traditionally considered to be caused by the pathogen Sarocladium oryzae and damage and lower both the quantity and quality of rice grain. In this study, 32 fungal isolates collected from the central and northeastern regions of Thailand were analysed phylogenetically using three molecular markers (ITS, D1/D2 of 28S rDNA and ACT) and physiological races were determined on 10 differential rice cultivars. We found that S. oryzae is not the only causal agent of sheath rot in Thailand, but S. attenuatum was also found. Despite having similar morphological features, the phylogenetic analysis recognised 11 of 32 isolates as S. attenuatum and the remaining isolates as S. oryzae. This is the first report of S. attenuatum causing sheath rot of rice in Thailand in addition to S. oryzae. Evaluation of physiological races revealed high pathogenic diversity of the two species. Thus, 16 and 11 physiological races were recorded from 21 isolates of S. oryzae and 11 isolates of S. attenuatum, respectively. These results indicate that both S. oryzae and S. attenuatum are the causal agents of rice sheath rot and dirty panicle in Thailand and that they are pathologically diverse. Full article