Search Results (6,954)

This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora: P. kaengkrachanensis, P. mira, P. phitsanulokensis, P. silvatica, and P. thailandica, with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora. However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research. Full article

The species Lactococcus lactis is a bacterium extensively used in the dairy industry. This bacterium is Generally Recognized as Safe and was added to the European Food Safety Authority’s Qualified Presumption of Safety list. The major functions of this species in dairy fermentation are the production of lactic acid from lactose, citric acid fermentation, and the hydrolysis of casein. But, the representatives of this species that produce bacteriocin substances can also exert an inhibitory effect against spoilage bacteria. The aims of this study were to test three lactococcal strains isolated from raw goat milk for their postbiotic activity and to test their stability in goat milk yogurts after their application in encapsulated form for their further application. To achieve these aims, validated methods were used. Three Lactococcus lactis strains (identified by Blastn 16S rRNA analysis) produced bacteriocin substances/postbiotics. These concentrated postbiotics inhibited the growth of enterococci and staphylococci (by up to 97.8%), reaching an inhibitory activity of up to 800 AU/mL. The encapsulated (freeze-dried) lactococci survived in the goat milk yogurts with sufficient stability. Strain MK2/8 fortified the yogurts in the highest amount (8.1 ± 0.0 cfu/g log 10). It did not influence the pH of the yogurt. Full article

During the present study, DNA sequence and morphological data were used to delineate species boundaries in the velvet worm, Peripatopsis sedgwicki species complex. The combined mitochondrial cytochrome c oxidase subunit one (COI) and the nuclear 18S rRNA loci were phylogenetically analyzed using Bayesian inference and maximum likelihood platforms that both demonstrated the presence of four, statistically well-supported clades (A–D). In addition, five species delimitation methods (ASAP, bPTP, bGMYC, STACEY and iBPP) were used on the combined DNA sequence data to identify possible novel lineages. All five species delimitation methods supported the distinction of the Fort Fordyce Nature Reserve specimens in the Eastern Cape province, however, in the main P. sedgwicki s.l. species complex, the species delimitation methods revealed a variable number of novel operational taxonomic units. Gross morphological characters were of limited utility, with only the leg pair number in the Fort Fordyce Nature Reserve specimens and the white head-collar of the Van Stadens Wildflower Nature Reserve specimens being diagnostic. The RADseq results from the earlier study of P. sedgwicki s.l. provided highly congruent results with the four clades observed in the present study. The distribution of P. sedgwicki s.s. (clade B) is restricted to the western portions of its distribution in the Afrotemperate forested regions of the Western Cape Province, South Africa. Three novel species, P. collarium sp. nov., (clade C) P. margaritarius sp. nov., (clade A) and P. orientalis sp. nov., (clade D) are described, of which the first two species are narrow range endemics. The present study, along with several recent systematic studies of velvet worms affirms the importance of fine-scale sampling to detect and document the alpha taxonomic diversity of Onychophora. Full article

Infection with Campylobacter jejuni is the major cause of human gastroenteritis in the United States and Europe, leading to debilitating autoimmune sequelae in many cases. While considerable progress has been made in detailing the infectious cycle of C. jejuni, a full understanding of the molecular mechanisms responsible for virulence remains to be elucidated. Here, we apply a novel approach by modulating protein expression on the pathogen’s ribosomes by inactivating a highly conserved rRNA methyltransferase. Loss of the RsmA methyltransferase results in a more motile strain with greater adhesive and cell-invasive properties. These phenotypical effects correlate with enhanced expression of specific proteins related to flagellar formation and function, together with enzymes involved in cell wall/membrane and amino acid synthesis. Despite the enhancement of certain virulent traits, the null strain grows poorly on minimal media and is rapidly out-competed by the wild-type strain. Complementation with an active copy of the rsmA gene rescues most of the traits changed in the mutant. However, the complemented strain overexpresses rsmA and displays new flaws, including loss of the spiral cell shape, which is distinctive for C. jejuni. Proteins linked with altered virulence and morphology are identified here by mass spectrometry proteomic analyses of the strains. Full article

The manure–compost–soil process is the main avenue for using agricultural livestock waste. Biochar not only impacts the composting process but also enhances the soil’s organic matter and nitrogen content when applied with compost. This paper explores the profound impact of biochar as an additive on the manure–compost–soil process, uncovering novel mechanisms driving enhanced soil health and bacterial succession. The basic physicochemical properties (organic matter, total nitrogen, etc.) and microbial structure of the composting and soil samples were analyzed. Biochar additive increased the C/N ratio and the total carbon content of the compost. Biochar, compost, and biochar-based compost improved the total carbon and organic matter of the soil. After high-temperature composting, Saccharomonospora (from 2.68% to 0.80%), Atopostipes (from 5.71% to 0.13%), and Lactobacillus (from 5.27% to 0.04%) were almost eliminated. Lysobacter, Glutamicibacter, and Streptomyces were the dominant genera in the soil samples, promoting plant growth. Nocardiopsis, Saccharomonospora, Bacillus, and Oceanobacillus dominated the genera in the whole manure–compost–soil process. Thus, composting could eliminate the toxic or negative bacteria directly deposited into soil by manure. Those genera arising from compost or biochar-based compost in the soil could contribute to organic matter’s cycle. Full article

Helicobacter pylori is a human pathogen bacterium associated with gastritis, peptic ulcer, and gastric cancer. It can be identified through the 16S rRNA gene and characterized through cagA and vacA virulence genes. Clinical cultures of H. pylori were isolated and identified from human stomach biopsies. The isolates were characterized according to their colonial and microscopic morphology, and molecular genotyping was conducted to determine the bacterial virulence. A phylogenetic analysis of the 16S rRNA gene sequencing was performed. In addition, multilocus sequence typing analysis was performed to determine the phylogeographic nature of the isolated strains. Three bacterial isolates were selected from 22 gastric biopsies, identified as H. pylori through colonial morphology, Gram staining, urease, catalase, and oxidase tests and identification of the ureC gene through end-point PCR. Amplification of 16S rRNA, urea, and tonB genes was performed, as well. Differences between the cagA and vacA genotypes were determined among the isolates. The phylogenetic analysis confirmed the identity of the three isolates as the specie Helicobacter pylori. Different genotypes were obtained for each H. pylori strain, and all the clinical isolates showed the vacA s2/m2 genotype, indicating an absence of the VacA cytotoxin. Only HCGDL-MR01 is a cagA gene carrier with a greater risk to develop a serious disease, such as stomach cancer and peptic ulcer. The multilocus sequence typing placed all the strains within the hpEurope population structure. Full article

Alginate lyase is an attractive biocatalyst that can specifically degrade alginate to produce oligosaccharides, showing great potential for industrial and medicinal applications. Herein, an alginate-degrading strain HB236076 was isolated from Sargassum sp. in Qionghai, Hainan, China. The low 16S rRNA gene sequence identity (<98.4%), ANI value (<71.9%), and dDDH value (<23.9%) clearly indicated that the isolate represented a potential novel species of the genus Vibrio. The genome contained two chromosomes with lengths of 3,007,948 bp and 874,895 bp, respectively, totaling 3,882,843 bp with a G+C content of 46.5%. Among 3482 genes, 3332 protein-coding genes, 116 tRNA, and 34 rRNA sequences were predicted. Analysis of the amino acid sequences showed that the strain encoded 73 carbohydrate-active enzymes (CAZymes), predicting seven PL7 (Alg1–7) and two PL17 family (Alg8, 9) alginate lyases. The extracellular alginate lyase from strain HB236076 showed the maximum activity at 50 °C and pH 7.0, with over 90% activity measured in the range of 30–60 °C and pH 6.0–10.0, exhibiting a wide range of temperature and pH activities. The enzyme also remained at more than 90% of the original activity at a wide pH range (3.0–9.0) and temperature below 50 °C for more than 2 h, demonstrating significant thermal and pH stabilities. Fe²⁺ had a good promoting effect on the alginate lyase activity at 10 mM, increasing by 3.5 times. Thin layer chromatography (TLC) and electrospray ionization mass spectrometry (ESI-MS) analyses suggested that alginate lyase in fermentation broth could catalyze sodium alginate to produce disaccharides and trisaccharides, which showed antimicrobial activity against Shigella dysenteriae, Aeromonas hydrophila, Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. This research provided extended insights into the production mechanism of alginate lyase from Vibrio sp. HB236076, which was beneficial for further application in the preparation of pH-stable and thermo-stable alginate lyase and alginate oligosaccharides. Full article

Stress, unhealthy lifestyle, and sleep disturbance worsen cognitive function in mood disorders, prompting a rise in the development of integrative health approaches. The recent investigations in the gut–brain axis field highlight the strong interplay among microbiota, inflammation, and mental health. Thus, this study aimed to investigate a new nutraceutical formulation comprising prebiotics, minerals, and silymarin’s impact on microbiota, inflammation, mood, and sleep quality. The study evaluated the LL1 + silymarin capsule supplementation over 180 days in overweight adults. We analyzed the fecal gut microbiota using partial 16S rRNA sequences, measured cytokine expression via CBA, collected anthropometric data, quality of life, and sleep questionnaire responses, and obtained plasma samples for metabolic and hormonal analysis at baseline (T0) and 180 days (T180) post-supplementation. Our findings revealed significant reshaping in gut microbiota composition at the phylum, genus, and species levels, especially in the butyrate-producer bacteria post-supplementation. These changes in gut microbiota were linked to enhancements in sleep quality, mood perception, cytokine expression, and anthropometric measures which microbiota-derived short-chain fatty acids might enhance. The supplementation tested in this study seems to be able to improve microbiota composition, reflecting anthropometrics and inflammation, as well as sleep quality and mood improvement. Full article

Spartina alterniflora is recognized as one of the most detrimental invasive species along China’s coastlines, highlighting the need for effective and environmentally safe management strategies to preserve intertidal zones. This study assessed the effectiveness of combining plant growth regulators (PRGs) with physical cutting to manage S. alterniflora, using 16S rRNA and 18S rRNA gene sequencing to evaluate the impacts on the plant and associated soil micro-organisms. The results showed that compared to the control (CK), the regeneration numbers for treatments with abscisic acid (ABA), gibberellin (GA), paclobutrazol (PP₃₃₃), garcinol (GC), and glyphosate (GP) decreased by 29.75%, 23.25%, 15.75%, 94.50%, and 40.50%, respectively. Comparative analysis revealed no statistically significant variation in the inhibitory effects of ABA and GP on the germination of S. alterniflora (p > 0.05). Additionally, applying PRGs and herbicides increased the diversity indices of soil bacteria and fungi. Principal Coordinates Analysis (PCoA) showed that the impact of PRGs on the fungal community was less pronounced than that of herbicides. Significant differences were also noted in the abundance of microbial functional genes related to methanotrophy, hydrocarbon degradation, and denitrification compared to the control (p < 0.05). This study aimed to assess the potential of PRGs in controlling the invasion of S. alterniflora and to elucidate their impacts on soil microbial communities and functional gene expression. Full article

Acanthamoeba keratitis (AK) is a rare but serious infection of the cornea, typically associated with contact lens wear. Here, we present a case of AK caused by the Acanthamoeba genotype T4D/T4e in a patient without identifiable risk factors: a 34-year-old woman who initially presented with signs and symptoms suggestive of herpetic keratitis, and who did not respond to conventional treatment. Corneal culture and targeted metagenomic analysis (18S rRNA, 16S-like rRNA) revealed the presence of an Acanthamoeba species closely related to the ‘Nagington’ strain. Despite intensive anti-Acanthamoeba therapy, complications arose necessitating penetrating keratoplasty. In conclusion, this case underscores the importance of considering Acanthamoeba as a causal agent of keratitis in non-contact-lens wearers. The identification of Acanthamoeba genotype T4D/T4e challenges the previous understanding of its pathogenic potential. Furthermore, it emphasizes the need for ongoing research into the pathogenicity of different Acanthamoeba subtypes. Early diagnosis and treatment are essential for preventing vision-threatening complications associated with AK. Full article

The aim of this study was to evaluate the effect of conjugated linoleic acid (CLA) on milk fat globule (MFG) size and the ruminal microbiome of goats. Twenty-four mid-lactation Saanen dairy goats weighing 49 ± 4.5 kg (168 ± 27 d in milk, 1.2 ± 0.1 kg milk/d, 2–3 years old) were randomly divided into four groups—a control (CON) group, which was fed a basal diet, and three CLA supplementation groups, in which 30 g CLA (low-dose group, L-CLA), 60 g CLA (medium-dose group, M-CLA), or 90 g CLA (high-dose group, H-CLA) was added to the basal diet daily. The experiment lasted for 21 days, during which time goat milk was collected for composition and MFG size analysis. On day 21 of feeding, ruminal fluid was collected from the CON and H-CLA groups for analysis of the changes in microorganismal abundance. The results showed that CLA supplementation did not affect milk production, milk protein, or lactose content in the dairy goats (p > 0.05), but significantly reduced the milk fat content (p < 0.01) compared with the CON group. The CLA supplementation significantly decreased the D_[3,2] and D_[4,3] of the MFGs in a dose-dependent manner (p < 0.01). Moreover, dietary CLA inclusion increased the proportion of small-sized MFGs and decreased that of large-sized ones. The results of 16S rRNA gene sequencing showed that CLA-induced milk fat depression in dairy goats was accompanied by significant changes in the relative abundance of ruminal bacterial populations, most of which belonged to the Firmicutes and Bacteroidetes phyla. The relative abundance of Rikenellaceae_RC9_gut_group and Prevolellaceae_UCG-003 in Bacteroidetes and UCG-002, Succiniclasticum, and norank_f__norank_o__Clostridia_vadinBB60_group in Firmicutes was significantly higher in the CON group than in the H-CLA group. In contrast, the relative abundance of norank_f__UCG-011, norank_f_Eubacterium_coprostanoligenes_group, unclassified_f__Lachnospiraceae, and UCG-001 in Firmicutes and norank_f__Muribaculaceae in Bacteroidetes was significantly higher in the H-CLA group than in the CON group. Correlation analysis showed that the milk fat content was negatively correlated with the relative abundance of some bacteria, including members of Firmicutes and Bacteroidetes. Similarly, MFG size (D_[3,2] and D_[4,3]) was negatively correlated with several members of Firmicutes and Bacteroidetes, including Lachnospiraceae, norank_f__UCG-011, UCG-001, norank_f__Eubacterium_coprostanoligenes_group (Firmicutes), and norank_f__Muribaculaceae (Bacteroidetes), while positively correlated with the relative abundance of some members of Firmicutes and Bacteroidetes, including Mycoplasma, Succiniclasticum, norank_f__norank_o__Clostridia_vadinBB60_group, UCG-002 (Firmicutes), and Rikenellaceae_RC9_gut_group (Bacteroidetes). Overall, our data indicated that CLA treatment affected milk fat content and MFG size in dairy goats, and these effects were correlated with the relative abundance of ruminal bacterial populations. These results provide the first evidence to explain the mechanism underlying diet-induced MFG from the perspective of the ruminal microbiome in dairy goats. Full article

Oysters are sessile, filter-feeding bivalve molluscs widely distributed in estuarine and coastal habitats worldwide. They constitute a valuable resource for fisheries and extensive aquaculture and provide essential ecological services. Yet, their genetic diversity and distribution remain understudied. The variability in shell morphology complicates species classification, which is influenced by environmental and genetic factors. Although molecular phylogenetics research has refined oyster taxonomy and identified approximately 100 extant species, numerous taxonomic uncertainties persist. In the present study, we aimed to document the occurrence of small flat oysters of the genus Ostrea along the Mediterranean coastal areas of Liguria and Sardinia (Italy). Specifically, 16S rRNA sequence data were used to identify Ostrea species. Our findings offer novel insights into the O. stentina species complex and O. neostentina, a new species in the Mediterranean coastal areas of Italy. The study data further our understanding of Ostrea species diversity, distribution, and evolutionary patterns. Full article

Sclerotinia minor (S. minor) Jagger is a phytopathogenic fungus that causes lettuce drop, a serious problem in lettuce (Lactuca sativa L.) production. The control of this pathogen is challenging because of the resistance of sclerotia, which can survive in the soil under favorable conditions. In Bulgaria, the management of lettuce drop relies primarily on the strategic application of synthetic fungicides. To find alternative methods for disease management, four bacterial isolates were screened for antagonism against S. minor. This study reports the in vitro evaluation of the antifungal activity of Bacillus subtilis, Priestia megaterium, Bacillus safensis, and Bacillus mojavensis against S. minor. The molecular identification of the isolates involved in the activity was examined through 16s rRNA sequencing. Isolated bacterial strains produced indole-3-acetic acid (IAA) in a medium supplemented with 0.1% L-tryptophan. The ability of these strains to increase the mobility of phosphorus and zinc was elucidated. The production of siderophores was confirmed on CAS (Chrom azurol S) medium. The inhibitory action of the bacterial growth broth filtrates against S. minor was demonstrated, indicating the nature of the molecules involved. The evaluation of antifungal activity was carried out in vitro and in pot experiments. This study determined the effect of growth-promoting rhizobacteria on the development of lettuce. This research focuses mainly on the development of biocontrol strategies for the management of lettuce drop in greenhouses. Full article

Salvinia auriculata Aublet is a floating aquatic plant, capable of absorbing the excess of nutrients and water contaminants and can be used in effluent treatment plants. The ability to survive in degraded areas may be related to the association with beneficial bacteria capable of promoting plant growth. However, little is known about the microbiota associated with this aquatic plant and its potential application to the aquatic environment. In this sense, this work aims to identify bacteria associated with S. auriculata that could be able to promote plant growth. Eighteen bacterial strains were identified by sequencing of the 16S rRNA gene, belonging to the genera Agrobacterium, Bacillus, Curtobacterium, Enterobacter, Pseudomonas, Siccibacter, and Stenotrophomonas. All isolates produced indole compounds, 12 fixed N₂, and 16 solubilized phosphate. A new strain of Enterobacter (sp 3.1.3.0.X.18) was selected for inoculation into S. auriculata. For this purpose, 500 mL of nutrient solution and 1 g of the plant were used in the control and inoculated conditions. Enterobacter inoculation promoted a significant increase (p ≤ 0.05) in fresh plant biomass (17%) after 4 days of cultivation. In summary, the present study characterized 18 plant-growth-promoting bacteria isolated from S. auriculata with potential for biotechnological application, such as the production of bioinoculants or biomass resources, to protect or improve plant growth under conditions of stress. Full article

Anaerobic digestion (AD) produces useful biogas and waste streams with high levels of dissolved methane (CH₄) and ammonium (NH₄⁺), among other nutrients. Membrane biofilm reactors (MBfRs), which support dissolved methane oxidation in the same reactor as simultaneous nitrification and denitrification (ME-SND), are a potential bubble-less treatment method. Here, we demonstrate ME-SND taking place in single-stage, AD digestate liquid-fed MBfRs, where oxygen (O₂) and supplemental CH₄ were delivered via pressurized membranes. The effects of two O₂ pressures, leading to different O₂ fluxes, on CH₄ and N removal were examined. MBfRs achieved up to 98% and 67% CH₄ and N removal efficiencies, respectively. The maximum N removal rates ranged from 57 to 94 mg N L⁻¹ d⁻¹, with higher overall rates observed in reactors with lower O₂ pressures. The higher-O₂-flux condition showed NO₂⁻ as a partial nitrification endpoint, with a lower total N removal rate due to low N₂ gas production compared to lower-O₂-pressure reactors, which favored complete nitrification and denitrification. Membrane biofilm 16S rRNA amplicon sequencing showed an abundance of aerobic methanotrophs (especially Methylobacter, Methylomonas, and Methylotenera) and enrichment of nitrifiers (especially Nitrosomonas and Nitrospira) and anammox bacteria (especially Ca. Annamoxoglobus and Ca. Brocadia) in high-O₂ and low-O₂ reactors, respectively. Supplementation of the influent with nitrite supported evidence that anammox bacteria in the low-O₂ condition were nitrite-limited. This work highlights coupling of aerobic methanotrophy and nitrogen removal in AD digestate-fed reactors, demonstrating the potential application of ME-SND in MBfRs for the treatment of AD’s residual liquids and wastewater. Sensor-based tuning of membrane O₂ pressure holds promise for the optimization of bubble-less treatment of excess CH₄ and NH₄⁺ in wastewater. Full article