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BMC Microbiology Nov 2023Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's...
BACKGROUND
Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity.
RESULTS
Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set).
CONCLUSIONS
Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.
Topics: Humans; Colitis, Ulcerative; Crohn Disease; Inflammatory Bowel Diseases; Gastrointestinal Microbiome; Bacteria; Biomarkers
PubMed: 37951857
DOI: 10.1186/s12866-023-03084-5 -
The New Phytologist Apr 2024
Topics: Herbicides; Plant Weeds; Herbicide Resistance; Weed Control
PubMed: 38320978
DOI: 10.1111/nph.19574 -
Frontiers in Plant Science 2023Walnut blight is a serious bacterial disease that affects the yield and quality of walnuts. is one of the main causative agents of walnut blight. However, there have...
INTRODUCTION
Walnut blight is a serious bacterial disease that affects the yield and quality of walnuts. is one of the main causative agents of walnut blight. However, there have been few studies on the response of walnuts to infection.
METHODS
In this study, the soluble sugar, photosynthesis, antioxidant enzyme activities, and secondary metabolites were measured, and the transcriptomic analysis was performed to determine the response of walnut tissue cultures to infection.
RESULTS
After pathogen inoculation, the soluble sugar content decreased, and photosynthesis was inhibited. Antioxidant enzyme (superoxide dismutase and peroxidase) activities and secondary metabolites (phenol and flavonoid) contents increased, especially in the early stages of inoculation. Transcriptomic analysis revealed that the phenylpropanoid biosynthesis pathway is induced after infection, and pathogen infection promotes ABA and ethylene signal transduction and inhibits auxin signaling. In addition, SA and JA-related gene expression was altered after inoculation with , and the FLS- and calcium-mediated disease resistance signaling pathways were activated. Furthermore, our results suggested an involvement of the R-protein RPM-mediated disease resistance pathway in the response of walnuts to bacterial infections.
DISCUSSION
Our findings indicated that phenylpropanoid biosynthesis, hormone signal transduction, and plant-pathogen interaction have key roles in pathogenic inoculation, which provide insights into the molecular mechanisms in the response of walnuts to infection.
PubMed: 38116156
DOI: 10.3389/fpls.2023.1294643 -
Molecules (Basel, Switzerland) Jan 2024L-cysteine is a proteogenic amino acid with many applications in the pharmaceutical, food, animal feed, and cosmetic industries. Due to safety and environmental issues... (Review)
Review
L-cysteine is a proteogenic amino acid with many applications in the pharmaceutical, food, animal feed, and cosmetic industries. Due to safety and environmental issues in extracting L-cysteine from animal hair and feathers, the fermentative production of L-cysteine offers an attractive alternative using renewable feedstocks. Strategies to improve microbial production hosts like , , sp., and are summarized. Concerning the metabolic engineering strategies, the overexpression of feedback inhibition-insensitive L-serine O-acetyltransferase and weakening the degradation of L-cysteine through the removal of L-cysteine desulfhydrases are crucial adjustments. The overexpression of L-cysteine exporters is vital to overcome the toxicity caused by intracellular accumulating L-cysteine. In addition, we compiled the process engineering aspects for the bioproduction of L-cysteine. Utilizing the energy-efficient sulfur assimilation pathway via thiosulfate, fermenting cheap carbon sources, designing scalable, fed-batch processes with individual feedings of carbon and sulfur sources, and implementing efficient purification techniques are essential for the fermentative production of L-cysteine on an industrial scale.
Topics: Animals; Cysteine; Amino Acids; Animal Feed; Carbon; Escherichia coli; Sulfur
PubMed: 38257399
DOI: 10.3390/molecules29020486 -
International Journal of Systematic and... Aug 2023A facultative anaerobic, Gram-stain-negative rod-shaped bacterium, designated R, was isolated from the faecal material of a rabbit (). The strain could not be identified...
A facultative anaerobic, Gram-stain-negative rod-shaped bacterium, designated R, was isolated from the faecal material of a rabbit (). The strain could not be identified using an MALDI Biotyper sirius CA System. The closest matches based on the Bruker library were members of the genera and . However, the score value was in the range of no organism identification possible. Based on pairwise of 16S rRNA gene sequence analysis, the isolate was found to be a member of the family . The highest sequence similarities were found to the sequences of LMG 26273 (98.7 %), NBRC 102595 (98.5 %) and 090008 (98.4 %). Phylogenetic and whole genome analysis demonstrated that strain R represents a novel species within the genus . The predominant cellular fatty acids of strain R were C and products present in summed feature 2 (C) aldehyde, summed feature 3 (C ω6 and/or Cω7) and summed feature 8 (C ω7 and/or C ω6). genome analysis showed the presence of enzymes required for production of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The G+C content determined from the genome was 54.94 mol %. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is strain R (=CCUG 76269=ATCC TSD-291).
Topics: Animals; Rabbits; Fatty Acids; Phospholipids; Pantoea; Ubiquinone; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Base Composition; DNA, Bacterial; Bacterial Typing Techniques
PubMed: 37535055
DOI: 10.1099/ijsem.0.005968 -
Applied and Environmental Microbiology Dec 2023Phage-derived bacteriocins (tailocins) are ribosomally synthesized structures produced by bacteria in order to provide advantages against competing strains under natural...
Phage-derived bacteriocins (tailocins) are ribosomally synthesized structures produced by bacteria in order to provide advantages against competing strains under natural conditions. Tailocins are highly specific in their target range and have proven to be effective for the prevention and/or treatment of bacterial diseases under clinical and agricultural settings. We describe the discovery and characterization of a new tailocin locus encoded within genomes of and subsp. , which may enable the development of tailocins as preventative treatments against phytopathogenic infection by these species.
Topics: Bacteriocins; Pantoea; Plant Diseases
PubMed: 37982620
DOI: 10.1128/aem.00929-23 -
Advanced Science (Weinheim,... Sep 2023Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance...
Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance against shear forces. From a physical perspective, biofilms can be described as colloidal gels, where bacterial cells are analogous to colloidal particles distributed in the polymeric ECM. However, the influence of the ECM in altering the cellular packing fraction (ϕ) and the resulting viscoelastic behavior of biofilm remains unexplored. Using biofilms of Pantoea sp. (WT) and its mutant (ΔUDP), the correlation between biofilm structure and its viscoelastic response is investigated. Experiments show that the reduction of exopolysaccharide production in ΔUDP biofilms corresponds with a seven-fold increase in ϕ, resulting in a colloidal glass-like structure. Consequently, the rheological signatures become altered, with the WT behaving like a weak gel, whilst the ΔUDP displayed a glass-like rheological signature. By co-culturing the two strains, biofilm ϕ is modulated which allows us to explore the structural changes and capture a change in viscoelastic response from a weak to a strong gel, and to a colloidal glass-like state. The results reveal the role of exopolysaccharide in mediating a structural transition in biofilms and demonstrate a correlation between biofilm structure and viscoelastic response.
Topics: Biofilms; Extracellular Matrix; Glass
PubMed: 37522628
DOI: 10.1002/advs.202207373 -
Antibiotics (Basel, Switzerland) Dec 2023(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales,...
(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales, species have been seen to be implicated in several human infections, but their clinical and microbiological framework is currently based on a few anecdotal reports. (2) Methods: We conducted this five-year (2018-2023) single-center study aimed at investigating the prevalence and clinical and microbiological findings of species bloodstream infections. (3) Results: Among the 4996 bloodstream infection Gram-negative isolates collected during the study period, species accounted for 0.4% (n = 19) of isolates from 19 different patients, 5 of them being pediatric cases. Among species isolates, was the most frequently detected (45%; n = 9) followed by (30%; n = 6) and (15%; n = 3). Malignancy (35.7%) in adults and malignancy (40%) and cerebrovascular disease following meconium aspiration (40%) in pediatric patients as comorbidities and shivering and/or fever following parenteral infusion (36.8%) as a symptom/sign of species bloodstream infection onset were the most frequently observed clinical features. Among adults, primary bloodstream infection was the most frequent (50%), whereas among pediatric patients, the most commonly identified sources of infection were catheter-related (40%) and the respiratory tract (40%). Overall, species bloodstream infection isolates displayed high susceptibility to all the antibiotics except for ampicillin (63.2%), fosfomycin (73.7%), and piperacillin/tazobactam (84.2%). Targeted antibiotic treatment was prescribed as monotherapy for adults (71.4%) and combination therapy for pediatric patients (60%). The most prescribed antibiotic regimens were piperacillin/tazobactam (21.4%) in adults and meropenem- (40%) and aminoglycoside-containing (40%) antibiotics in pediatric patients. The overall 28-day all-cause mortality rate was 5.3% (n = 1). (4) Conclusions: The prevalence and 28-day mortality rate of species bloodstream infections were low. The prescription of targeted therapy including broad-spectrum antibiotics could indicate an underestimation of the specific involvement of the species in the onset of the disease, warranting further studies defining their pathogenic potential.
PubMed: 38136757
DOI: 10.3390/antibiotics12121723 -
Biotechnology For Biofuels and... Aug 2023β-Carotene is one of the economically important carotenoids, having functions as the antioxidant to remove harmful free radicals and as the precursor for vitamin A and...
β-Carotene is one of the economically important carotenoids, having functions as the antioxidant to remove harmful free radicals and as the precursor for vitamin A and other high-valued xanthophyll such as zeaxanthin and astaxanthin. Lycopene cyclase plays an important role in the branching of β-carotene and α-carotene. Aiming to develop the microalgae with enhanced β-carotene productivity, the CrtY gene from bacterium Pantoea agglomerans was integrated into Chlamydomonas reinhardtii. The lycopene-producing E. coli harboring CrtY gene produced 1.59 times of β-carotene than that harboring DsLcyb1 from Dunaliella salina (a microalga with abundant β-carotene), confirming the superior activity of CrtY on β-carotene biosynthesis. According to the pigment analysis by HPLC, in microalgal transformants that were confirmed by molecular analysis, the expression of CrtY significantly increased β-carotene content from 12.48 mg/g to 30.65 mg/g (dry weight), which is about 2.45-fold changes. It is noted that three out of five transformants have statistically significant higher amount of lutein, even though the increment was 20% in maximum. Besides, no growth defect was observed in the transformants. This is the first report of functional expression of prokaryotic gene in eukaryotic microalgae, which will widen the gene pool targeting carotenoids biosynthesis using microalgae as the factory and thereby provide more opportunity for high-valued products engineering in microalgae.
PubMed: 37573357
DOI: 10.1186/s13068-023-02377-1 -
Ecotoxicology (London, England) Aug 2023The application of synthetic pesticides is one of the fastest acting tools at farmers' disposal to prevent and mitigate the threats posed by plant pests in agriculture....
The application of synthetic pesticides is one of the fastest acting tools at farmers' disposal to prevent and mitigate the threats posed by plant pests in agriculture. However, the effects of these above-ground applications of pesticides are known to be detrimental to some belowground, non-target soil biota. At present, the effects many pesticides have on key functional microbial groups associated with phosphate (P) solubilization in the soil are still largely unknown. The purpose of this study was to compare the effects of two herbicides, glyphosate, and paraquat, on phosphate solubilizing bacteria (PSB) with and without pH adjustment (after herbicide addition) since pH is a major indicator of P solubilization. In our assay, two PSB strains (Pantoea agglomerans and Serratia rubidaea) were chosen to assess their ability to solubilize tricalcium phosphate (TCP) by using the vanadate-molybdate method (to measure the amount of P solubilized) in the presence of glyphosate (5.4 g/L and 10.8 g/L) or paraquat (2 g/L and 4 g/L) separately. To assess the effect of PSB treated by the herbicides, a growth experiment using PSB inoculated wheat seedlings was performed under greenhouse conditions (25 °C, light 16 h/8 h dark). After four weeks, wheat above-ground growth parameters were measured. Our results showed that even under recommended doses of glyphosate (5.4 g/L) and paraquat (2 g/L), a decrease in P solubilization activity was observed in P. agglomerans and S. rubidaea. Whilst paraquat affected TCP solubilization more than glyphosate with and without pH adjustment, there was a significant decrease (p < 0.05) in TCP solubilization, up to 39% and 93% in the presence of glyphosate and paraquat, respectively, for S. rubidaea, and up to 45% and 95% in the presence of glyphosate and paraquat, respectively, for P. agglomerans. The effect of the herbicides on the PSB had the same results as in the greenhouse test on wheat seedling growth, confirming that these herbicides have both above and belowground negative effects, despite being used at recommended doses.
Topics: Phosphates; Herbicides; Soil; Pantoea; Paraquat
PubMed: 37407783
DOI: 10.1007/s10646-023-02681-4