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International Journal of Molecular... Jun 2024and , bacterial degraders of the herbicide glyphosate, were found to induce phosphonatase (phosphonoacetaldehyde hydrolase, EC 3.11.1.1) when grown on minimal media...
and , bacterial degraders of the herbicide glyphosate, were found to induce phosphonatase (phosphonoacetaldehyde hydrolase, EC 3.11.1.1) when grown on minimal media with glyphosate as the sole source of phosphorus. The phosphonatases of the strains were purified to an electrophoretically homogeneous state and characterized. The enzymes differed in their kinetic characteristics and some other parameters from the previously described phosphonatases. The phosphonatase of was first revealed to separate into two stable forms, which had similar kinetic characteristics but interacted differently with affinity and ion-exchange resins. The genomes of the investigated bacteria were sequenced. The phosphonatase genes were identified, and their context was determined: the bacteria were shown to have gene clusters, which, besides the phosphonatase operon, included genes for LysR-type transcription activator (substrate sensor) and putative iron-containing oxygenase PhnHD homologous to monooxygenases PhnY and TmpB of marine organophosphonate degraders. Genes of 2-aminoethylphosphonate aminotransferase (PhnW, EC 2.6.1.37) were absent in the achromobacterial phosphonatase operons; instead, we revealed the presence of genes encoding the putative flavin oxidase HpnW. In silico simulation showed 1-hydroxy-2-aminoethylphosphonate to be the most likely substrate of the new monooxygenase, and a number of glycine derivatives structurally similar to glyphosate to be substrates of flavin oxidase.
Topics: Glyphosate; Glycine; Achromobacter; Operon; Soil Microbiology; Bacterial Proteins; Herbicides; Multigene Family; Kinetics; Gene Expression Regulation, Bacterial
PubMed: 38928116
DOI: 10.3390/ijms25126409 -
Science Advances Jun 2024Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and...
Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and infection. We previously showed that aspects of the diabetic foot ulcer microbiota were correlated with poor healing outcomes, but many microbial species recovered remain uninvestigated with respect to wound healing. Here, we focused on , a Gram-negative bacterium that is frequently recovered from chronic wounds but rarely causes infection. Treatment of diabetic wounds with accelerated healing during early stages. We investigated the underlying mechanisms and found that treatment promotes reepithelialization of diabetic keratinocytes, a process that is necessary for healing but deficient in chronic wounds. Overexpression of matrix metalloproteinases in diabetes contributes to failed epithelialization, and we found that treatment balances this overexpression to allow proper healing. This work uncovers a mechanism of bacterial-driven wound repair and provides a foundation for the development of microbiota-based wound interventions.
Topics: Alcaligenes faecalis; Wound Healing; Animals; Keratinocytes; Humans; Matrix Metalloproteinases; Diabetic Foot; Mice; Re-Epithelialization; Male
PubMed: 38924411
DOI: 10.1126/sciadv.adj2020 -
Journal of Hazardous Materials Jun 2024Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still...
Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still limitedly understood. Here we collected soil samples from typical reclaimed wetlands (RW) and ditch wetlands (DW) in coastal reclamation areas and examined the effects of Cd contamination on the bacterial network complexity and stability. The results showed that the bacterial networks were destabilized by the Cd contamination, while bacteria in DW soils showed robust invulnerability characterized by higher node constancy and compositional stability compared with RW soils. Soil bacteria resisted Cd stress by forming a network with intensive connections in the module but sparser connections among the modules. Especially, network modularity was higher in DW soils than in RW soils, but made it more vulnerable to nodes removal. In addition, Cd contamination promoted bacterial positive cohesion but decreased negative cohesion in RW soils. Flavobacteriaceae, Xanthomonadaceae, and Alcaligenaceae were identified as core phylotypes, which played pivotal roles in regulating interspecies interactions due to higher contributions to cohesion and significant correlations with soil nutrients. The findings of this work indicate the changes of bacterial network structure and the indispensable role of core phylotypes in regulating interactions and maintaining network sustainability under Cd contamination.
PubMed: 38909464
DOI: 10.1016/j.jhazmat.2024.134896 -
Applied Microbiology and Biotechnology Jun 2024Direct ammonia oxidation (Dirammox) might be of great significance to advance the innovation of biological nitrogen removal process in wastewater treatment systems....
Direct ammonia oxidation (Dirammox) might be of great significance to advance the innovation of biological nitrogen removal process in wastewater treatment systems. However, it remains unknown whether Dirammox bacteria can be selectively enriched in activated sludge. In this study, a lab-scale bioreactor was established and operated for 2 months to treat synthetic wastewater with hydroxylamine as a selection pressure. Three Dirammox strains (Alcaligenes aquatilis SDU_AA1, Alcaligenes aquatilis SDU_AA2, and Alcaligenes sp. SDU_A2) were isolated from the activated sludge, and their capability to perform Dirammox process was confirmed. Although these three Dirammox bacteria were undetectable in the seed sludge (0%), their relative abundances rapidly increased after a month of operation, reaching 12.65%, 0.69%, and 0.69% for SDU_A2, SDU_AA1, and SDU_AA2, respectively. Among them, the most dominant Dirammox (SDU_A2) exhibited higher nitrogen removal rate (32.35%) than the other two strains (13.57% of SDU_AA1 and 14.52% of SDU_AA2). Comparative genomic analysis demonstrated that the most dominant Dirammox bacterium (SDU_A2) possesses fewer complete metabolic modules compared to the other two less abundant Alcaligenes strains. Our findings expanded the understanding of the application of Dirammox bacteria as key functional microorganisms in a novel biological nitrogen and carbon removal process if they could be well stabilized. KEY POINTS: • Dirammox-dominated microbial community was enriched in activated sludge bioreactor. • The addition of hydroxylamine played a role in Dirammox enrichment. • Three Dirammox bacterial strains, including one novel species, were isolated.
Topics: Wastewater; Bioreactors; Nitrogen; Alcaligenes; Oxidation-Reduction; Sewage; Ammonia; Water Purification; Hydroxylamine; Phylogeny; RNA, Ribosomal, 16S; Bacteria; Microbiota
PubMed: 38904674
DOI: 10.1007/s00253-024-13214-2 -
International Journal of Systematic and... Jun 2024A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04, was isolated from chicken faeces. Its growth was optimal at 28 °C...
A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04, was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus and was most closely related to CCUG 53761A (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04 and CCUG 53761A were 76.3 and 18.2 %, respectively. Strain YLCF04 has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YLCF04 (=CCTCC AB 2022359= KCTC 92789).
Topics: Animals; Base Composition; Phylogeny; RNA, Ribosomal, 16S; Chickens; Feces; DNA, Bacterial; Nucleic Acid Hybridization; Bacterial Typing Techniques; Sequence Analysis, DNA; Alcaligenaceae; Fatty Acids; Genome, Bacterial
PubMed: 38896454
DOI: 10.1099/ijsem.0.006429 -
Annals of Clinical Microbiology and... Jun 2024Achromobacter spp. are opportunistic pathogens, mostly infecting immunocompromised patients and patients with cystic fibrosis (CF) and considered as difficult-to-treat...
BACKGROUND
Achromobacter spp. are opportunistic pathogens, mostly infecting immunocompromised patients and patients with cystic fibrosis (CF) and considered as difficult-to-treat pathogens due to both intrinsic resistance and the possibility of acquired antimicrobial resistance. Species identification remains challenging leading to imprecise descriptions of resistance in each taxon. Cefiderocol is a broad-spectrum siderophore cephalosporin increasingly used in the management of Achromobacter infections for which susceptibility data remain scarce. We aimed to describe the susceptibility to cefiderocol of a collection of Achromobacter strains encompassing different species and isolation sources from CF or non-CF (NCF) patients.
METHODS
We studied 230 Achromobacter strains (67 from CF, 163 from NCF patients) identified by nrdA gene-based analysis, with available susceptibility data for piperacillin-tazobactam, meropenem and trimethoprim-sulfamethoxazole. Minimal inhibitory concentrations (MICs) of cefiderocol were determined using the broth microdilution reference method according to EUCAST guidelines.
RESULTS
Strains belonged to 15 species. A. xylosoxidans represented the main species (71.3%). MICs ranged from ≤ 0.015 to 16 mg/L with MIC of ≤ 0.015/0.5 mg/L overall and 0.125/2 mg/L against 27 (11.7%) meropenem-non-susceptible strains. Cefiderocol MICs were not related to CF/NCF origin or species although A. xylosoxidans MICs were statistically lower than those of other species considered as a whole. Considering the EUCAST non-species related breakpoint (2 mg/L), 228 strains (99.1%) were susceptible to cefiderocol. The two cefiderocol-resistant strains (A. xylosoxidans from CF patients) represented 3.7% of meropenem-non-susceptible strains and 12.5% of MDR strains.
CONCLUSIONS
Cefiderocol exhibited excellent in vitro activity against a large collection of accurately identified Achromobacter strains, irrespective of species and origin.
Topics: Microbial Sensitivity Tests; Humans; Achromobacter; Anti-Bacterial Agents; Cephalosporins; Cefiderocol; Cystic Fibrosis; Gram-Negative Bacterial Infections
PubMed: 38886694
DOI: 10.1186/s12941-024-00709-z -
Frontiers in Oncology 2024This study employs a two-sample bidirectional Mendelian randomization (MR) approach to systematically evaluate the causal relationship between gut microbiota and oral...
UNLABELLED
This study employs a two-sample bidirectional Mendelian randomization (MR) approach to systematically evaluate the causal relationship between gut microbiota and oral cavity cancer (OCC).
OBJECTIVE
To address the challenge in establishing the causal relationship between gut microbiota and OCC, we applied a systematic MR analysis.
METHODS
Utilizing GWAS data from the MiBioGen consortium (18,340 individuals) and UK Biobank (n = 264,137), we selected instrumental variables and employed MR-Egger, weighted median, IVW, and weighted mode analyses. Heterogeneity and pleiotropy were assessed using Cochran's Q test and MR-Egger intercept test.
RESULTS
Our findings indicate, at the order level, (OR = 0.9990, 95% CI = 0.9980-1.0000, = ), (OR = 1.0009, 95% CI = 1.0001-1.0018, = ), and (OR = 0.9979, 95% CI = 0.9962-0.9995, = ) exhibit causality on OCC in the Weighted median, IVW, and MR-Egger analyses, respectively. At the family level, (OR = 1.0012, 95% CI = 1.0004-1.0019, = ) and (OR = 0.9970, 95% CI = 0.9948-0.9992, = ) show causality on OCC in IVW and MR-Egger analyses. At the genus level, (IVW, OR = 0.9987, 95% CI = 0.9980-0.9995, = ; MR-Egger, OR = 0.9978, 95% CI = 0.9962-0.9995, = ), (IVW, OR = 1.0008, 95% CI = 1.0001-1.0015, = ), (IVW, OR = 0.9995, 95% CI = 0.9990-1.0000, = ), group (IVW, OR = 1.0005, 95% CI = 1.0000-1.0009, = ), and (IVW, OR = 0.9994, 95% CI = 0.9989-0.9999, = ) are implicated in causing OCC in related analyses.
CONCLUSION
Our study identifies order, family, genus, and group as causally increasing OCC risk. In contrast, order, order, family, genus, genus, and genus are causally associated with a decreased OCC risk. However, further investigations are essential to delineate an optimal gut microbiota composition and unravel the underlying mechanisms of specific bacterial taxa in OCC pathophysiology.
PubMed: 38884080
DOI: 10.3389/fonc.2024.1389678 -
Euro Surveillance : Bulletin Europeen... Jun 2024We describe a pertussis outbreak in the Vallès region of Catalonia, from September 2023 to April 2024. Incidence was high in children aged 10-14 years compared with...
We describe a pertussis outbreak in the Vallès region of Catalonia, from September 2023 to April 2024. Incidence was high in children aged 10-14 years compared with previous outbreaks. Limited impact in newborns could be explained by the high vaccination coverage during pregnancy and at 11 months of age in 2022, at 85% and 94.1 %, respectively. A third booster vaccine dose during preadolescence should be considered and vaccination coverage in pregnant women be improved to control future outbreaks.
Topics: Humans; Whooping Cough; Spain; Female; Adolescent; Child; Incidence; Disease Outbreaks; Infant; Pertussis Vaccine; Pregnancy; Child, Preschool; Male; Infant, Newborn; Vaccination; Adult; Vaccination Coverage; Immunization, Secondary; Young Adult; Bordetella pertussis; Age Distribution; Population Surveillance
PubMed: 38873794
DOI: 10.2807/1560-7917.ES.2024.29.24.2400332 -
Fish Physiology and Biochemistry Jun 2024This study aims to evaluate the effects of substituting soybean meal with fermented rapeseed meal (FRM) on growth, antioxidant capacity, and liver and intestinal health...
Replacing soybean meal with fermented rapeseed meal in diets: potential effects on growth performance, antioxidant capacity, and liver and intestinal health of juvenile tilapia (Oreochromis niloticus).
This study aims to evaluate the effects of substituting soybean meal with fermented rapeseed meal (FRM) on growth, antioxidant capacity, and liver and intestinal health of the genetically improved farmed tilapia (GIFT, Oreochromis niloticus). A total of 450 tilapia (7.22 ± 0.15 g) were fed with five experimental diets, including a basal diet containing 40% soybean meal (CP0), which was subsequently replaced by 25% (CP25), 50% (CP50), 75% (CP75), and 100% (CP100) FRM in a recirculated aquiculture system for 9 weeks (30 fish per tank in triplicates). The results showed that the weight gain, specific growth rate, feed intake, feed efficiency, hepatosomatic index, and viscerosomatic index of fish in both CP75 and CP100 groups were significantly lower than those in CP0 group (P < 0.05). The fish in CP100 group had the lower content of muscle crude protein while the higher level of muscle crude lipid (P < 0.05). Activities of serum aspartate aminotransferase, alanine aminotransferase along with total triglyceride in CP100 group were significantly higher than those in CP0 group (P < 0.05). There were no significant differences in the contents of liver protease, amylase, and lipase among five groups (P > 0.05). The activities of liver total antioxidant capacity and superoxide dismutase exhibited the increased tendency with the increase of FRM replacement levels from 25 to 50% (P < 0.05), while then significantly decreased from 75 to 100% (P < 0.05). Histological morphology indicated that the fish in between CP75 and CP100 groups had poor liver and intestine health. Intestinal microbial diversity analysis showed that the relative abundance of Cetobacterium and Alcaligenaceae in both CP75 and CP100 groups were lower than that in other three groups. In conclusion, the maximum replacement level of soybean meal with FRM in the diet was determined to be 50% without compromising the growth performance, antioxidant status, and liver and intestinal health of tilapia under the current experimental conditions. The observed decrease in food intake and subsequent retarded growth performance in the CP75 and CP100 groups can be attributed directly to a reduction in feed palatability caused by FRM.
PubMed: 38869816
DOI: 10.1007/s10695-024-01363-0 -
Science Advances Jun 2024Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental...
Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in . We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.
Topics: Alcaligenes faecalis; Nitrification; Hydroxylamine; Heterotrophic Processes; Ammonium Compounds; Nitrites; Oxidation-Reduction
PubMed: 38848370
DOI: 10.1126/sciadv.adl3587