Search Results (27)

Dairy-borne Pseudomonas spp., known for causing spoilage, may also exhibit antibiotic resistance and form biofilms, enhancing their persistence in dairy environments and contaminating final products. This study examined biofilm formation and antibiotic resistance in 106 Pseudomonas spp. strains isolated from milk, whey, and spoiled dairy products. Phylogenetic analysis (based on partial ileS sequences) grouped most strains within the P. fluorescens group, clustering into the P. fluorescens, P. gessardii, P. koorensis, and P. fragi subgroups. Biofilm formation in polystyrene microplates was assessed at 6 °C and 25 °C by crystal violet staining. After 48 h, 72% and 65% of Pseudomonas strains formed biofilms at 6 °C and 25 °C, respectively, with higher biomass production at 6 °C. High biofilm producers included most P. fluorescens, P. shahriarae, P. salmasensis, P. atacamensis, P. gessardii, P. koreensis, and P. lundensis strains. The adnA gene, associated with biofilm formation, was detected in 60% of the biofilm producers, but was absent in P. fragi, P. lundensis, P. weihenstephanensis, and P. putida. Antibiotic susceptibility was tested using the disk diffusion method. All strains were susceptible to amikacin and tobramycin; however, 73% of the strains were resistant to aztreonam, 28% to imipenem and doripenem, 19% to ceftazidime, 13% to meropenem, and 7% to cefepime. A multiple antibiotic resistance index (MARI) > 0.2 was found in 30% of the strains, including multidrug-resistant (n = 15) and extensively drug-resistant (n = 3) strains. These findings highlight Pseudomonas spp. as persistent contaminants and antibiotic resistance reservoirs in dairy environments and products, posing public health risks and economic implications for the dairy industry. Full article

Levansucrases are key enzymes responsible for the synthesis of β-2,6-linked fructans, found in plants and microbes, especially in bacteria. Levansucrases have been applied in the production of levan biopolymer and fructooligosaccharides (FOSs) using sucrose as a substrate as well as in reducing sugar levels in fruit juice. As a result, levansucrases that are active at low temperatures are required for industrial applications to maintain product stability. Therefore, this work firstly reports the novel cold-active levansucrase (SacBPk) isolated from a sucrolytic bacterial strain, P. koreensis HL12. The SacBPk was classified into glycoside hydrolase family 68 subfamily 1 (GH68_1) and comprised a single catalytic domain with the Asp104/Asp267/Glu362 catalytic triad. Interestingly, the recombinant SacBPk demonstrated cold-active levansucrase activity at low temperatures (on ice and 4–40 °C) with the highest specific activity (167.46 U/mg protein) observed at 35 and 40 °C in 50 mM sodium phosphate buffer pH 6.0. SacBPk mainly synthesized levan polymer as the major product (129 g/L, corresponding to 25.8% of total sugar) with a low number of short-chain FOSs (GF2–4) (12.8 g/L, equivalent to 2.5% of total sugar) from 500 g/L sucrose after incubating at 35 °C for 48 h. These results demonstrate the industrial application potential of SacBPk levansucrase for levan and FOSs production. Full article

Although current diet and nutrition trends in developed countries led the poultry industry to shift to alternative breeding/production methods, such as organic and free-range, limited data on the microbiology of alternative compared to conventional poultry meat products exist. Therefore, this study assessed the evolution and composition of the spoilage microbiota and the growth potential of inoculated (3 log cfu/g) Listeria monocytogenes in freshly minced free-range chicken meat stored at 4 °C in vacuum packages (VP; four batches) for 0, 3, 5, 7, and 10 days. Additionally, two VP batches were compared with their resultant retail products stored in modified atmosphere packages (MAP 30:70 CO₂/N₂) at 4 °C to detect potential differences with the MAP spoilage community described previously. The initial pH of the VP minces was 6.0–6.1, except for one mince, designated VP + AA, which had initial pH 5.8 and was found to contain ‘external’ 1.26% L-lactate and 0.24% acetate associated with a vinegar smell during storage. The rest of the VP batches contained on average 0.75% L-lactate and 0.02% acetate on day 0. After 7 days at 4 °C, L-lactate decreased by at least 3-fold in VP and over 5-fold in VP + AA vs. minor decreases in MAP. Acetate increased 2-fold in all batches. D-lactate (ca. 0.02% on day 0) increased by 4-fold in VP batches only. Lactic acid bacteria (LAB) became the dominant spoilers in all samples. Only VP allowed a delayed 10-fold growth (>5.0 to 6.2 log cfu/g) of pseudomonads from day 7 to day 10 at 4 °C. Compared to VP, VP + AA and MAP retarded growth of LAB, pseudomonads, and enterobacteria by 1–2 log units, at final levels below 6.5, 4.5, and 3.0 log cfu/g, respectively. Enterococci, staphylococci, yeasts, and L. monocytogenes did not grow. Latilactobacillus sakei predominated in all spoiled VP batches (65.8% of 80 meat isolates) followed by Latilactobacillus fuchuensis (9.2%), Leuconostoc carnosum (6.6%), Carnobacterium divergens (6.6%), Latilactobacillus curvatus (5.3%), and Weissella koreensis (2.6%). VP + AA favored Latilactobacillus. Brochothrix thermosphacta was frequent in one VP batch. In conclusion, cold-stored (4 °C), minced, free-range chicken meat spoils more rapidly and offensively under VP than MAP or VP combined with acetate-containing (VP + AA) antimicrobial blends. Full article

Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative. The aim of this study was to characterise milk microbiota from SCM and apparently healthy dairy cows (non-SCM) by 16S rRNA sequencing. Alpha-diversity metrics showed significant differences between SCM cows and non-SCM counterparts. The beta-diversity metrics in the principal coordinate analysis significantly clustered samples by type (PERMANOVA test, p < 0.05), while non-metric dimensional scaling did not (PERMANOVA test, p = 0.07). The overall analysis indicated a total of 95 phyla, 33 classes, 82 orders, 124 families, 202 genera, and 119 bacterial species. Four phyla, namely Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria collectively accounted for more than 97% of all sequencing reads from SCM and non-SCM cow samples. The most abundant bacterial classes were Actinobacteria, Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria in non-SCM cow samples, whilst SCM cow samples were mainly composed of Actinobacteria, Alphaproteobacteria, Bacilli, Clostridia, and Gammaproteobacteria. Dominant bacterial species in non-SCM cow samples were Anthropi spp., Pseudomonas azotoformans, P. fragi, Acinetobacter guillouiae, Enterococcus italicus, Lactococcus lactis, whilst P. azotoformans, Mycobacterium bovis, P. fragi, Acinetobacter guillouiae, and P. koreensis were dominant in the SCM cow samples. The current study found differences in bacterial species between SCM and non-SCM cow milk; hence, the need for detailed epidemiological studies. Full article

T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population. Full article

One of the worst environmental conditions limiting crop plant productivity is salinity. As a result, ecologically friendly methods are urgently needed to boost the development and yield of wheat growing on saltine soils. Two-year field studies to examine the effects of applying compost tea (CT) and effective microorganisms (EMs; Azospirillum brasilense, Pseudomonas koreensis, and Bacillus circulans) on the growth and yield of two wheat cultivars, namely Sids 12 as a salinity susceptible cultivar and Misr 1 as a salinity resistant cultivar, under salt-affected soils. The findings corroborated our hypothesis that, in comparison to the control and the individual applications of EM or CT, the combined application (EM + CT) significantly improved growth, yield, uptake of nutrients, and photosynthetic characteristics. Furthermore, the combined application markedly (p ≤ 0.05) boosted the antioxidant enzymes. Our research showed that the combination treatment could increase soil microbial activity and activate critical soil enzymes, primarily dehydrogenase and urease. In general, the combination treatment has demonstrated a good effect in terms of stimulating plant development and raising element concentrations in wheat under salt stress. Full article

The root microbiota contributes to the plant’s defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08–61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota. Full article

Most conventional methods to remove heavy metals from water are efficient for high concentrations, but they are expensive, produce secondary pollution, and cannot remove low concentrations. This paper proposes a biological system to remove Cr(VI) from aqueous solutions; the biofilter is composed of a native Pseudomonas koreensis immobilized in calcium alginate beads. Lab experiments were conducted in batch reactors, considering different operating conditions: Cr(VI) concentration, temperature, pH, and time. At 30 °C and a pH of 6.6, the immobilized bacteria achieved their optimal adsorption capacity. In the chromium adsorption system, saturation was reached at 30 h with a q_max = 625 mg g⁻¹. By adjusting the experimental data to the Langmuir and Freundlich models, it is suggested that P. koreensis forms a biofilm with a homogeneous surface where Cr(VI) is adsorbed and that the bacteria also incorporates the metal in its metabolism, leading to a multilayer adsorption. On the other hand, using Fourier transform infrared spectroscopy, it was inferred that the functional groups involved in the adsorption process were O-H and C=O, which are a part of the P. koreensis cell wall. Full article

Salix species, including willow trees, are distributed in the temperate regions of Asian countries, including South Korea. Willow trees are used to treat pain and inflammatory diseases. Due to the medicinal properties of willow trees, pharmacological studies of other Salix spp. have gained attention; however, only a few studies have investigated the phytochemicals of these species. As part of our ongoing natural product research to identify bioactive phytochemicals and elucidate their chemical structures from natural resources, we investigated the marker compounds from indigenous Korean Salix species, namely, Salix triandra, S. chaenomeloides, S. gracilistyla, S. koriyanagi, S. koreensis, S. pseudolasiogyne, S. caprea, and S. rorida. The ethanolic extract of each Salix sp. was investigated using high-performance liquid chromatography combined with thin-layer chromatography and liquid chromatography–mass spectrometry-based analysis, and marker compounds of each Salix sp. were isolated. The chemical structures of the marker compounds (1–8), 3-(4-hydroxyphenyl)propyl β-D-glucopyranoside (1), 2-O-acetylsalicin (2), 1-O-p-coumaroyl glucoside (3), picein (4), isograndidentatin B (5), 2′-O-acetylsalicortin (6), dihydromyricetin (7), and salicin (8) were elucidated via nuclear magnetic resonance spectroscopy and high-resolution liquid chromatography–mass spectrometry using ultrahigh-performance liquid chromatography coupled with a G6545B Q-TOF MS system with a dual electrospray ionization source. The identified marker compounds 1–8 were examined for their antimicrobial effects against plant pathogenic fungi and bacteria. Dihydromyricetin (7) exhibited antibacterial activity against Staphylococcus aureus, inducing 32.4% inhibition at a final concentration of 125 μg/mL with an MIC₅₀ value of 250 μg/mL. Overall, this study isolated the marker compounds of S. triandra, S. chaenomeloides, S. gracilistyla, S. koriyanagi, S. koreensis, S. pseudolasiogyne, S. caprea, and S. rorida and identified the anti-Staphylococcus aureus bacterial compound dihydromyricetin. Full article

The modern approach to the creation of biological products to stimulate plant growth is based on the study of specific inter-bacterial interactions. This study describes the impact that the introduction of strains of the genus Pseudomonas has on annual and perennial leguminous plants and the ecosystem of the leguminous plant—the indigenous microbial community. The objects of research under the conditions of vegetation experiments were plants of field peas (Pisum sativum L.), white lupine (Lupinus albus L.), chickpea (Cicer arietinum L.), alfalfa (Medicago sativa subsp. varia (Martyn) Arcang.), and white sweet clover (Melilotus albus Medik.). For the treatment of plant seeds, a liquid culture of strains of growth-stimulating bacteria Pseudomonas koreensis IB-4, and P. laurentiana ANT 17 was used. The positive effect of the studied strains on the germination, growth and development of plants was established. There was no inhibitory effect of inoculants on rhizobia; on the contrary, an increase in nodule formation was observed. The possibility of recultivation of oil-contaminated soil using chickpea and alfalfa as phytomeliorants and growth-stimulating strains P. koreensis IB-4, P. laurentiana ANT 17 as inoculants was evaluated. It is proved that seed treatment improved the morphological parameters of plants, as well as the efficiency of oil destruction. Full article

The role of gut microbes has been suggested in type 2 diabetes (T2DM) risk. However, their results remain controversial. We hypothesized that Asians with T2DM had different fecal bacterial compositions, co-abundance networks, and metagenome functions compared to healthy individuals, according to enterotypes. This hypothesis was examined using the combined gut microbiota data from human fecal samples from previous studies. The human fecal bacterial FASTA/Q files from 36 different T2DM studies in Asians were combined (healthy, n = 3378; T2DM, n = 551), and operational taxonomic units (OTUs) and their counts were obtained using qiime2 tools. In the machine learning approaches, fecal bacteria rich in T2DM were found. They were separated into two enterotypes, Lachnospiraceae (ET-L) and Prevotellaceae (ET-P). The Shannon and Chao1 indices, representing α-diversity, were significantly lower in the T2DM group compared to the healthy group in ET-L (p < 0.05) but not in ET-P. In the Shapley additive explanations analysis of ET-L, Escherichia fergusonii, Collinsella aerofaciens, Streptococcus vestibularis, and Bifidobacterium longum were higher (p < 0.001), while Phocaeicola vulgatus, Bacteroides uniformis, and Faecalibacterium prausnitzii were lower in the T2DM group than in the healthy group (p < 0.00005). In ET-P, Escherichia fergusonii, Megasphaera elsdenii, and Oscillibacter valericigenes were higher, and Bacteroides koreensis and Faecalibacterium prausnitzii were lower in the T2DM group than in the healthy group. In ET-L and ET-P, bacteria in the healthy and T2DM groups positively interacted with each other within each group (p < 0.0001) but negatively interacted between the T2DM and healthy groups in the network analysis (p < 0.0001). In the metagenome functions of the fecal bacteria, the gluconeogenesis, glycolysis, and amino acid metabolism pathways were higher, whereas insulin signaling and adenosine 5′ monophosphate-activated protein kinase (AMPK) signaling pathways were lower in the T2DM group than in the healthy group for both enterotypes (p < 0.00005). In conclusion, Asians with T2DM exhibited gut dysbiosis, potentially linked to intestinal permeability and the enteric vagus nervous system. Full article

Pullulanase is an effective starch debranching enzyme widely used in starch saccharification and modification. In this work, the biochemical characteristics and potential application of a new type I pullulanase from Priestia koreensis HL12 (HL12Pul) were evaluated and reported for the first time. Through in-depth evolutionary analysis, HL12Pul was classified as type I pullulanase belonging to glycoside hydrolase family 13, subfamily 14 (GH13_14). HL12Pul comprises multi-domains architecture, including two carbohydrate-binding domains, CBM68 and CBM48, at the N-terminus, the TIM barrel structure of glycoside hydrolase family 13 (GH13) and C-domain. Based on sequence analysis and experimental cleavage profile, HL12Pul specifically hydrolyzes only α-1,6 glycosidic linkage-rich substrates. The enzyme optimally works at 40 °C, pH 6.0, with the maximum specific activity of 181.14 ± 3.55 U/mg protein and catalytic efficiency (k_cat/K_m) of 49.39 mL/mg·s toward pullulan. In addition, HL12Pul worked in synergy with raw starch-degrading α-amylase, promoting raw cassava starch hydrolysis and increasing the sugar yield by 2.9-fold in comparison to the α-amylase alone in a short reaction time. Furthermore, HL12Pul effectively produces type III-resistant starch (RSIII) from cassava starch with a production yield of 70%. These indicate that HL12Pul has the potential as a biocatalyst for starch saccharification and modification. Full article

The vegetation changes in the abandoned rice fields with different abandonment histories were analyzed across the country of South Korea. The successional process was confirmed by changes in vegetation profiles and species composition. The vegetation profile showed the process of starting with grassland, passing through the shrub stage, and turning into a tree-dominated forest. DCA ordination based on vegetation data showed that the process began with grasslands consisting of Persicaria thunbergii, Juncus effusus var. decipiens, Phalaris arundinacea, etc., then partially went through shrubland stages consisting of Salix gracilistyla, S. integra, young Salix koreensis, etc., and ultimately changed to a Salix koreensis dominated forest. In order to study the relationship between the succession process of the abandoned rice paddies and riparian vegetation, information on riparian vegetation was collected in the same watershed as the abandoned rice paddies investigated. Riparian vegetation tended to be distributed in the order of grasslands consisting of Phragmites japonica, Miscanthus sacchariflorus, P. arundinacea, etc., shrubland dominated by Salix gracilistyla, S. integra, etc., and a S. koreensis community dominated forest by reflecting the flooding regime as far away from the waterway. The result of stand ordination based on the riparian vegetation data also reflected the trend. From this result, we confirmed that the temporal sequence of the vegetation change that occurred in the abandoned rice fields resembled the spatial distribution of the riparian vegetation. Consequently, succession of the abandoned rice fields restored the riparian forest, which has almost disappeared in Korea and other Asian countries that use rice as their staple food. Full article

Tomatoes are susceptible to bacterial diseases, mainly related to some Pseudomonas syringae pathovars. Many Pseudomonas species are considered innocuous, but some have shown the ability to opportunistically infect tomato plants. Antimicrobial compounds have been used to control pathogenic organisms, and this can lead to environmental selection of phenotypically resistant bacteria. We assessed the diversity of Pseudomonas species associated with tomato plants from Chilean orchards and analyzed antimicrobial resistance among the isolated strains. A total of 64 Pseudomonas isolates (P. syringae, P. viridiflava, P. fluorescens, P. koreensis, P. gessardii, and P. azotoformans) were evaluated for their phenotypic resistance to seven antimicrobial compounds, including copper, streptomycin, and five other antibiotics typically not used in agriculture. The results showed that 95%, 86%, 70%, 53%, 45%, and 1.6% of the isolates were resistant to rifampin, ampicillin, copper, chloramphenicol, streptomycin, and tetracycline, respectively, with no isolates being resistant to gentamicin. A total of 96.9% of Pseudomonas isolates exhibited a multiresistant phenotype to at least two of the antimicrobials tested. The most frequent multiresistance phenotype was Cu-Str-Amp-Cm-Rif (23.4%). The presence of Pseudomonas strains tolerant to conventional bactericides, metals, and other antimicrobials makes these bacteria an emerging threat to the agriculture industry and to human health. Full article

Exploitation of low-quality water or irrigation of field crops with saline water in salt-affected soil is a critical worldwide challenge that rigorously influences agricultural productivity and sustainability, especially in arid and semiarid zones with limited freshwater resources. Therefore, we investigated a synergistic amendment strategy for salt-affected soil using a singular and combined application of plant growth-promoting rhizobacteria (PGPR at 950 g ha⁻¹; Azotobacter chroococcum SARS 10 and Pseudomonas koreensis MG209738) and silica nanoparticles (SiNPs) at 500 mg L⁻¹ to mitigate the detrimental impacts of irrigation with saline water on the growth, physiology, and productivity of barley (Hordum vulgare L.), along with soil attributes and nutrient uptake during 2019/2020 and 2020/2021. Our field trials showed that the combined application of PGPR and SiNPs significantly improved the soil physicochemical properties, mainly by reducing the soil exchangeable sodium percentage. Additionally, it considerably enhanced the microbiological counts (i.e., bacteria, azotobacter, and bacillus) and soil enzyme activity (i.e., urease and dehydrogenase) in both growing seasons compared with the control. The combined application of PGPR and SiNPs alleviated the detrimental impacts of saline water on barley plants grown in salt-affected soil compared to the single application of PGPR or SiNPs. The marked improvement was due to the combined application of PGPR and SiNPs, which enhanced the physiological properties (e.g., relative chlorophyll content (SPAD), relative water content (RWC), stomatal conductance, and K/Na ratio), enzyme activity (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POX)), and yield and yield-related traits and nutrient uptake (N, P, and K) of barley plants. Moreover, the Na+ content, hydrogen peroxide (H₂O₂) content, lipid peroxidation (MDA), electrolyte leakage (EL), and proline content were reduced upon the application of PGPR + SiNPs. These results could be important information for cultivating barley and other cereal crops in salt-affected soil under irrigation with saline water. Full article