Isolation and characterization of endophytic bacteria from soybean (Glycine max L.)

Endofitske bakterije koloniziraju unutrašnjost biljnih tkiva, a pritom ne uzrokuju negativne posljedice. Glavni cilj ovih istraživanja je genotipska i fenotipska karakterizacija endofitskih bakterija izoliranih iz različitih sorti soje. Izolirano je ukupno 29 endofita iz tri različita tkiva – korijena, kvržica i stabljike. Genotipska karakterizacija uključila je primjenu sekvenciranja 16S rRNA (rrs) gena. Pomoću navedene molekularne metode identificirane su bakterijske vrste i utvrđena je genetska raznolikost unutar populacija endofitskih bakterija na soji. Identificirano je pet skupina bakterija različitih rodova: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp. i Agrobacterium spp. Od 29 izolata, najveća pripadnost jednoj vrsti pripada skupini roda Pseudomonas spp. Svi izolati koji su identificirani kao B. japonicum, izolirani su iz korijena i kvržice biljke. Dokazana je uska povezanost rodova Rhizobium i Agrobacterium. Fenotipska karakterizacija sojeva prikazala je raznolikost i otpornost endofitskih bakterija. Većina izolata je Gram negativna, štapićastog oblika, bez mogućnosti stvaranja kapsule. Dokazana je varijabilnost fenotipskih karakteristika izolata, ali i otpornost prema nepovoljnim uvjetima poput povišene temperature, povećanog sadržaja soli te niske i visoke pH vrijednosti. Prilikom ispitivanja izolata za detekciju fluorescentnog pigmenta dokazano je kako samo bakterije vrste Pseudomonas produciraju pigment pod UV svjetlom. Većina sojeva pokazala je tolerantnost na istraživane antibiotike. Većina katalaza pozitivnih izolata pripadaju unutar rodova Bradyrhizobium ili Rhizobium, dok su katalaza negativni izolati identificirani kao Pseudomonas, Sphingomonas i Agrobacterium spp.. Dokazano je kako 85% ispitanih izolata ne reagira na enzim oksidazu, dok oni koji reagiraju pripadaju vrsti Pseudomonas spp. Potrebna je daljnja karakterizacija endofita kako bi se utvrdio njihov utjecaj na razvoj biljke.Endophytic bacteria colonize the inside of the tissue without causing any negative effects. The main aim of this study is the genotypic and phenotypic characterization of endophyitic bacteria isolated from different soybean cultivar. A total of 29 endophytes were isolated from three different tissues – root, nodule and stem. Genotypic characterization includes using of sequencing 16S rRNA (rrs) genes. Bacterial species were identified by using this molecular method and genetic diversity was determined within the population of endophztic bacteria of the soybean. Five different genera of bacteria were identified: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp., and Agrobacterium spp. From a total of 29 endophytes, most strains were identified as Pseudomonas spp. All isolates identified as B. japonicum were isolated from the roots and nodules of the plant. The close assocation beetwen Rhizobium and Agrobacterium species is proven. The phenotypic characterization of strains shows diversity and resistance of endophytes. Most of the isolates are Gram negative, rod-shaped, without capability of capsule production. The variability of the phenotypic characteristics of isolates was demonstrated, as well as the resistance to adverse conditions such as elevated temperature, increased salt content, and low and high pH values. During the detection of fluorescent pigment, it has been shown that only Pseudomonas species produce pigment under UV light. Most strains showed tolerance to the specific antibiotics. Most of the catalase positive isolates belong to Bradyrhizobium or Rhizobium spp., while the catalase negative isolates belong to the Pseudomonas, Sphingomonas and Agrobacterium spp. It was shown that 85% of the tested isolates do not respond to the enzyme oxidase while those that react to the enzyme belongs to the Pseudomonas spp. Further characterization of endophytes is needed to determine their influence on plant development

Isolation and characterization of endophytic bacteria from soybean (Glycine max L.)

Endofitske bakterije koloniziraju unutrašnjost biljnih tkiva, a pritom ne uzrokuju negativne posljedice. Glavni cilj ovih istraživanja je genotipska i fenotipska karakterizacija endofitskih bakterija izoliranih iz različitih sorti soje. Izolirano je ukupno 29 endofita iz tri različita tkiva – korijena, kvržica i stabljike. Genotipska karakterizacija uključila je primjenu sekvenciranja 16S rRNA (rrs) gena. Pomoću navedene molekularne metode identificirane su bakterijske vrste i utvrđena je genetska raznolikost unutar populacija endofitskih bakterija na soji. Identificirano je pet skupina bakterija različitih rodova: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp. i Agrobacterium spp. Od 29 izolata, najveća pripadnost jednoj vrsti pripada skupini roda Pseudomonas spp. Svi izolati koji su identificirani kao B. japonicum, izolirani su iz korijena i kvržice biljke. Dokazana je uska povezanost rodova Rhizobium i Agrobacterium. Fenotipska karakterizacija sojeva prikazala je raznolikost i otpornost endofitskih bakterija. Većina izolata je Gram negativna, štapićastog oblika, bez mogućnosti stvaranja kapsule. Dokazana je varijabilnost fenotipskih karakteristika izolata, ali i otpornost prema nepovoljnim uvjetima poput povišene temperature, povećanog sadržaja soli te niske i visoke pH vrijednosti. Prilikom ispitivanja izolata za detekciju fluorescentnog pigmenta dokazano je kako samo bakterije vrste Pseudomonas produciraju pigment pod UV svjetlom. Većina sojeva pokazala je tolerantnost na istraživane antibiotike. Većina katalaza pozitivnih izolata pripadaju unutar rodova Bradyrhizobium ili Rhizobium, dok su katalaza negativni izolati identificirani kao Pseudomonas, Sphingomonas i Agrobacterium spp.. Dokazano je kako 85% ispitanih izolata ne reagira na enzim oksidazu, dok oni koji reagiraju pripadaju vrsti Pseudomonas spp. Potrebna je daljnja karakterizacija endofita kako bi se utvrdio njihov utjecaj na razvoj biljke.Endophytic bacteria colonize the inside of the tissue without causing any negative effects. The main aim of this study is the genotypic and phenotypic characterization of endophyitic bacteria isolated from different soybean cultivar. A total of 29 endophytes were isolated from three different tissues – root, nodule and stem. Genotypic characterization includes using of sequencing 16S rRNA (rrs) genes. Bacterial species were identified by using this molecular method and genetic diversity was determined within the population of endophztic bacteria of the soybean. Five different genera of bacteria were identified: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp., and Agrobacterium spp. From a total of 29 endophytes, most strains were identified as Pseudomonas spp. All isolates identified as B. japonicum were isolated from the roots and nodules of the plant. The close assocation beetwen Rhizobium and Agrobacterium species is proven. The phenotypic characterization of strains shows diversity and resistance of endophytes. Most of the isolates are Gram negative, rod-shaped, without capability of capsule production. The variability of the phenotypic characteristics of isolates was demonstrated, as well as the resistance to adverse conditions such as elevated temperature, increased salt content, and low and high pH values. During the detection of fluorescent pigment, it has been shown that only Pseudomonas species produce pigment under UV light. Most strains showed tolerance to the specific antibiotics. Most of the catalase positive isolates belong to Bradyrhizobium or Rhizobium spp., while the catalase negative isolates belong to the Pseudomonas, Sphingomonas and Agrobacterium spp. It was shown that 85% of the tested isolates do not respond to the enzyme oxidase while those that react to the enzyme belongs to the Pseudomonas spp. Further characterization of endophytes is needed to determine their influence on plant development

Izolacija i karakterizacija endofitskih bakterija iz soje (Glycine max L.)

Endophytic bacteria colonize the internal tissue of the plant usually forming beneficial association with their host. The main aim of this study was to genotypically and phenotypically characterize endophytic bacteria isolated from roots, stems and nodules of two soybean cultivars (AFZG Ana and Gabriela). A total of 29 endophytes were isolated from three different tissues of soybean. Genotypic characterization included rrs genes sequencing. Among soybean endophytes five different genera of bacteria were identified: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp., and Agrobacterium spp. Most of the isolates were Gram negative, rod-shaped, without capability of capsule production. The variability of the phenotypic characteristics of isolates was demonstrated, as well as the resistance to adverse environmental conditions such as high temperature, increased salt content, and low and high pH values. Most strains showed tolerance to the specific antibiotics. Most of the catalase positive isolates belong to Bradyrhizobium or Rhizobium spp., while the catalase negative isolates belong to the Pseudomonas, Sphingomonas and Agrobacterium spp. It was also shown that 85% of the tested isolates were oxidase negative while those that were positive belong to the Pseudomonas spp. Further characterization of endophytes is needed to determine their influence on plant growth.Endofitske bakterije koloniziraju unutrašnjost biljnih tkiva stvarajući pozitivne interakcije sa svojim domaćinom. Glavni cilj ovog istraživanja bio je genotipska i fenotipska karakterizacija endofitskih bakterija izoliranih iz korijena, stabiljke i nodula dva različita kultivara soje (AFZG Ana and Gabriela). Izolirano je ukupno 29 endofita iz tri različita tkiva soje. Genotipska karakterizacija uključivala je sekvenciranje rrs gena. Identificirano je pet skupina bakterija različitih rodova: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp. i Agrobacterium spp. Većina izolata je Gram negativna, štapićastog oblika, bez mogućnosti stvaranja kapsule. Dokazana je varijabilnost fenotipskih karakteristika izolata, ali i otpornost prema nepovoljnim uvjetima poput povišene temperature, povećanog sadržaja soli te niske i visoke pH vrijednosti. Većina sojeva pokazala je tolerantnost na istraživane antibiotike. Većina katalaza pozitivnih izolata pripadaju rodovima Bradyrhizobium ili Rhizobium, dok su katalaza negativni izolati identificirani kao Pseudomonas, Sphingomonas i Agrobacterium spp. Dokazano je da 85% ispitanih izolata ne reagira na enzim oksidazu, dok oni koji reagiraju pripadaju vrsti Pseudomonas spp. Potrebna je daljnja karakterizacija endofita kako bi se utvrdio njihov utjecaj na razvoj biljke

Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at the onset of disease is still scarce. We compared gut microbiota in newly diagnosed, treatment-naïve adult IBD (Crohn’s disease (CD) and ulcerative colitis (UC)) to irritable bowel syndrome (IBS) patients and healthy group. Mucosal and fecal microbiota of 49 patients (13 UC, 10 CD, and 26 IBS) before treatment initiation, and fecal microbiota of 12 healthy subjects was characterized by 16S rRNA gene sequencing. Mucosa was sampled at six positions, from terminal ileum to rectum. We demonstrate that mucosal microbiota is spatially homogeneous, cannot be differentiated based on the local inflammation status and yet provides bacterial footprints superior to fecal in discriminating disease phenotypes. IBD groups showed decreased bacterial diversity in mucosa at all taxonomic levels compared to IBS. In CD and UC, Dialister was significantly increased, and expansion of Haemophilus and Propionibacterium characterized UC. Compared to healthy individuals, fecal microbiota of IBD and IBS patients had increased abundance of Proteobacteria, Enterobacteriaceae, in particular. Shift toward reduction of Adlercreutzia and butyrate-producing taxa was found in feces of IBD patients. Microbiota alterations detected in newly diagnosed treatment-naïve adult patients indicate that the microbiota changes are set and detectable at the disease onset and likely have a discerning role in IBD pathophysiology. Our results justify further investigation of the taxa discriminating between disease groups, such as H. parainfluenzae, R. gnavus, Turicibacteriaceae, Dialister, and Adlercreutzia as potential biomarkers of the disease

Isolation and characterization of endophytic bacteria from soybean (Glycine max L.)

Endofitske bakterije koloniziraju unutrašnjost biljnih tkiva, a pritom ne uzrokuju negativne posljedice. Glavni cilj ovih istraživanja je genotipska i fenotipska karakterizacija endofitskih bakterija izoliranih iz različitih sorti soje. Izolirano je ukupno 29 endofita iz tri različita tkiva – korijena, kvržica i stabljike. Genotipska karakterizacija uključila je primjenu sekvenciranja 16S rRNA (rrs) gena. Pomoću navedene molekularne metode identificirane su bakterijske vrste i utvrđena je genetska raznolikost unutar populacija endofitskih bakterija na soji. Identificirano je pet skupina bakterija različitih rodova: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp. i Agrobacterium spp. Od 29 izolata, najveća pripadnost jednoj vrsti pripada skupini roda Pseudomonas spp. Svi izolati koji su identificirani kao B. japonicum, izolirani su iz korijena i kvržice biljke. Dokazana je uska povezanost rodova Rhizobium i Agrobacterium. Fenotipska karakterizacija sojeva prikazala je raznolikost i otpornost endofitskih bakterija. Većina izolata je Gram negativna, štapićastog oblika, bez mogućnosti stvaranja kapsule. Dokazana je varijabilnost fenotipskih karakteristika izolata, ali i otpornost prema nepovoljnim uvjetima poput povišene temperature, povećanog sadržaja soli te niske i visoke pH vrijednosti. Prilikom ispitivanja izolata za detekciju fluorescentnog pigmenta dokazano je kako samo bakterije vrste Pseudomonas produciraju pigment pod UV svjetlom. Većina sojeva pokazala je tolerantnost na istraživane antibiotike. Većina katalaza pozitivnih izolata pripadaju unutar rodova Bradyrhizobium ili Rhizobium, dok su katalaza negativni izolati identificirani kao Pseudomonas, Sphingomonas i Agrobacterium spp.. Dokazano je kako 85% ispitanih izolata ne reagira na enzim oksidazu, dok oni koji reagiraju pripadaju vrsti Pseudomonas spp. Potrebna je daljnja karakterizacija endofita kako bi se utvrdio njihov utjecaj na razvoj biljke.Endophytic bacteria colonize the inside of the tissue without causing any negative effects. The main aim of this study is the genotypic and phenotypic characterization of endophyitic bacteria isolated from different soybean cultivar. A total of 29 endophytes were isolated from three different tissues – root, nodule and stem. Genotypic characterization includes using of sequencing 16S rRNA (rrs) genes. Bacterial species were identified by using this molecular method and genetic diversity was determined within the population of endophztic bacteria of the soybean. Five different genera of bacteria were identified: Pseudomonas spp., Sphingomonas spp., Bradyrhizobium spp., Rhizobium spp., and Agrobacterium spp. From a total of 29 endophytes, most strains were identified as Pseudomonas spp. All isolates identified as B. japonicum were isolated from the roots and nodules of the plant. The close assocation beetwen Rhizobium and Agrobacterium species is proven. The phenotypic characterization of strains shows diversity and resistance of endophytes. Most of the isolates are Gram negative, rod-shaped, without capability of capsule production. The variability of the phenotypic characteristics of isolates was demonstrated, as well as the resistance to adverse conditions such as elevated temperature, increased salt content, and low and high pH values. During the detection of fluorescent pigment, it has been shown that only Pseudomonas species produce pigment under UV light. Most strains showed tolerance to the specific antibiotics. Most of the catalase positive isolates belong to Bradyrhizobium or Rhizobium spp., while the catalase negative isolates belong to the Pseudomonas, Sphingomonas and Agrobacterium spp. It was shown that 85% of the tested isolates do not respond to the enzyme oxidase while those that react to the enzyme belongs to the Pseudomonas spp. Further characterization of endophytes is needed to determine their influence on plant development

The Storage Efficiency of Immobilized Bradyrhizobium japonicum Strain Using Encapsulation Method

There is a growing need for new formulations of carriers with better protection for bacterial inoculum. One of the newer techniques in inoculum making is encapsulation method. With this method, the whole bacterial cells are immobilized in defined space – matrix, where the cells are protected from environmental activities before use. Encapsulation of the inoculum was performed with ionic gelation method. The alginate-based microparticles (500-600 µm) containing viable B. japonicum strain were solidified in CaCl2. The initial number of viable bacteria in every sample was 9.0 log CFU/ml. Chitosan coated particles had a higher mortality rate than non-coated particles, with 1.3 log CFU/ml in lyophilized and wet microparticles stored at room temperature. High viability of B. japonicum was registered in wet particles stored at constant −20°C for thirty days with a viability rate of 8.84 log CFU/ml

Uloga nealkoholne masne bolesti jetre u bakterijskim infekcijama i sepsi

Nealkoholna masna bolest jetre (engl. non-alcoholic fatty liver disease, NAFLD) najčešća je kronična bolest jetre, a povezana je sa sustavnim promjenama imunosnog odgovora koje potiču progresiju u nealkoholni steatohepatitis (NASH), cirozu jetre i razvoj hepatocelularnog karcinoma. Glavni rizični čimbenici za razvoj NAFLD-a jesu komponente metaboličkog sindroma, pretilost i šećerna bolest, koje su poznati rizični čimbenici za razvoj infekcija. Međutim, sve je više podataka o povezanosti NAFLD-a s bakterijskim infekcijama, neovisno o ostalim komponentama metaboličkog sindroma. Kod bolesnika s NAFLD-om opisane su češće rekurirajuće bakterijske infekcije, uroinfekcije, bakterijemije gastrointestinalnog ishodišta, enterokolitis Clostridoides difficile, kao i teža klinička slika i nepovoljni ishod pneumonije. Rastuća prevalencija NAFLD-a i NASH-a zahtjeva nove terapijske i profilaktičke pristupe bazirane na boljem razumijevanju imunopatogeneze bakterijskih infekcija u ovoj skupini bolesnika.Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease associated with systemic changes in immune response that drives the progression to non-alcoholic steatohepatitis (NASH), liver cirrhosis, and hepatocellular carcinoma (HCC). Major risk factors of NAFLD include obesity and type 2 diabetes mellitus which are associated with infections. However, there is growing evidence that NAFLD is linked with bacterial infections independently of other components of metabolic syndrome. Patients with NAFLD have been described to have more common recurrent bacterial infections, urinary tract infections, bacteriemia of gastrointestinal origin, Clostridoides difficile enterocolitis, and more severe pneumonia. The rapidly increasing prevalence of NAFLD and NASH require novel therapeutic and prophylactic approaches based on a better understanding of immunopathogenesis of bacterial infections in these patients

Case report: Sevelamer-associated colitis-a cause of pseudotumor formation with colon perforation and life-threatening bleeding

Chronic kidney disease (CKD) is a very common chronic non-communicable disease. Phosphate and calcium metabolism disorders are one of the most common features of CKD. Sevelamer carbonate is the most widely used non-calcium phosphate binder. Gastrointestinal (GI) injury associated with sevelamer use is a documented adverse effect but is underrecognized as a cause of gastrointestinal symptoms in patients with CKD. We report a case of a 74-year-old woman taking low-dose sevelamer with serious gastrointestinal adverse effects causing colon rupture and severe gastrointestinal bleeding

Accuracy of Controlled Attenuation Parameter and Liver Stiffness Measurement in Patients with Non-alcoholic Fatty Liver Disease

We evaluated the diagnostic accuracy of the controlled attenuation parameter (CAP) and liver stiffness measurements (LSM) measured with either an M or XL probe against liver biopsy (LB) in patients with non-alcoholic fatty liver disease (NAFLD). This study was a cross-sectional prospective study that included 179 NAFLD patients. With a cutoff value for CAP >= 345, we can exclude significant steatosis in 87% (79.4%-92.5%) of our population. With respect to the LSM, the highest accuracy was obtained for F >= F3 (area under the receiver operating characteristic curve [AUROC] = 0.98) and F = F4 (AUROC = 0.98). In a multivariable linear regression model, significant predictors influencing LSM were fibrosis stage (beta = 2.6, p < 0.001) as a positive predictor and lobular inflammation (beta = -0.68, p = 0.04) as a negative predictor, without significant influence after adjustment for CAP and probe type. We found that CAP is a satisfactory method for excluding advanced steatosis, while LSM is a good non-invasive marker for the exclusion of fibrosis

Prevalence and Prognostic Impact of Deranged Liver Blood Tests in COVID-19: Experience from the Regional COVID-19 Center over the Cohort of 3812 Hospitalized Patients

Background: Derangement of liver blood tests (LBT) is frequent in patients with Coronavirus disease 2019 (COVID-19). We aimed to evaluate (a) the prevalence of deranged LBT as well as their association with (b) clinical severity at admission and (c) 30-day outcomes among the hospitalized patients with COVID-19. ----- Methods: Consecutive patients with COVID-19 hospitalized in the regional referral center over the 12-month period were included. Clinical severity of COVID-19 at hospital admission and 30-day outcomes (need for intensive care, mechanical ventilation, or death) were analyzed. ----- Results: Derangement of LBT occurred in 2854/3812 (74.9%) of patients, most frequently due to elevation of AST (61.6%), GGT (46.1%) and ALT (33.4%). Elevated AST, ALT, GGT and low albumin were associated with more severe disease at admission. However, in multivariate Cox regression analysis, when adjusted for age, sex, obesity and presence of chronic liver disease, only AST remained associated with the risk of dying (HR 1.5081 and 2.1315, for elevations 1–3 × ULN and >3 × ULN, respectively) independently of comorbidity burden and COVID-19 severity at admission. Patients with more severe liver injury more frequently experienced defined adverse outcomes. ----- Conclusions: Deranged LBTs are common among patients hospitalized with COVID-19 and might be used as predictors of adverse clinical outcomes