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PloS One 2021As part of a screening programme for antibiotic-producing bacteria, a novel Actinomadura species was discovered from a soil sample collected in Santorini, Greece....
As part of a screening programme for antibiotic-producing bacteria, a novel Actinomadura species was discovered from a soil sample collected in Santorini, Greece. Preliminary 16S rRNA gene sequence comparisons highlighted Actinomadura macra as the most similar characterised species. However, whole-genome sequencing revealed an average nucleotide identity (ANI) value of 89% with A. macra, the highest among related species. Further phenotypic and chemotaxonomic analyses confirmed that the isolate represents a previously uncharacterised species in the genus Actinomadura, for which the name Actinomadura graeca sp. nov. is proposed (type strain 32-07T). The G+C content of A. graeca 32-07 is 72.36%. The cell wall contains DL-diaminopimelic acid, intracellular sugars are glucose, ribose and galactose, the predominant menaquinone is MK-9(H6), the major cellular lipid is phosphatidylinositol and fatty acids consist mainly of hexadecanoic acid. No mycolic acid was detected. Furthermore, A. graeca 32-07 has been confirmed as a novel producer of the non-ribosomal peptide antibiotic zelkovamycin and we report herein a provisional description of the unique biosynthetic gene cluster.
Topics: Actinomadura; Antimicrobial Cationic Peptides; Base Composition; Macrocyclic Compounds
PubMed: 34847153
DOI: 10.1371/journal.pone.0260413 -
Ecotoxicology and Environmental Safety Sep 2021Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different...
Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW, ermB, ermC, sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas, and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost.
Topics: Animals; Bacteria; Carbon; Chickens; Composting; Drug Resistance, Microbial; Genes, Bacterial; Lignin; Manure; Microbiota; Nitrogen
PubMed: 34139628
DOI: 10.1016/j.ecoenv.2021.112413 -
The Science of the Total Environment Jul 2023The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and...
Synergistic mechanisms of bioorganic fertilizer and AMF driving rhizosphere bacterial community to improve phytoremediation efficiency of multiple HMs-contaminated saline soil.
The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and promote plant growth, while their synergistic effects on plant growth and rhizosphere microorganism are largely unknown. This study explored the effects of AMF (Rhizophagus intraradices), BOF and BOF + RI assisted phytoremediation on heavy metals contaminated saline soil improvement and revealed the microbial mechanism. For this purpose, a pot trial consisting of four treatments (CK, RI, BOF and BOF + RI) was carried out. The results showed that the biomass, nutrient element contents, the accumulation of heavy metals and Na of Astragalus adsurgens and soil properties were most significantly improved by BOF + RI. BOF + RI significantly impacted rhizosphere microbial diversity, abundance and community composition. Chloroflexi and Patescibacteria at the phylum level and Actinomadura, Iamia, and Desulfosporosinus at the genus level were significantly enriched in BOF + RI. Network analysis revealed that BOF + RI significantly changed the keystone and enhanced complexity and interaction. Most of the keystones had roles in promoting plant growth and stress resistance. This study suggested that phytoremediation assisted by BOF and AMF is an attractive approach to ameliorate heavy metals contaminated saline soil.
Topics: Mycorrhizae; Fertilizers; Biodegradation, Environmental; Rhizosphere; Metals, Heavy; Bacteria; Soil; Soil Pollutants; Soil Microbiology; Plant Roots
PubMed: 37105481
DOI: 10.1016/j.scitotenv.2023.163708 -
Bioresource Technology May 2022This study investigated effects of composite microbes (CMs) (Phanerochaete chrysosporium and Trichoderma longibrachiatum) on humification during co-composting of biogas...
This study investigated effects of composite microbes (CMs) (Phanerochaete chrysosporium and Trichoderma longibrachiatum) on humification during co-composting of biogas residue, spent mushroom substrate and rice straw. Results showed that CMs inoculation elevated degradation ratios of cellulose, hemicellulose and lignin by 7.86%, 8.87% and 6.45%, and contents of humus and humic acid were correspondingly promoted by 15.5% and 23.6%, respectively. Relative abundances of bacteria associated with refractory macromolecules degradation (Flavobacterium, Anseongella and Actinomadura) and cellulolytic fungi (Hypocreales_Incertae_sedis, Hypocreaceae and Psathyrellaceae) were raised by CMs addition. Redundancy analysis demonstrated a positive correlation between microbial communities and temperature, fulvic acid and lignocellulose contents. Moreover, CMs inoculation promoted pathways of xenobiotics biodegradation and metabolism, and biosynthesis of other secondary metabolites, which was closely associated with lignocellulose degradation and humus formation. These results suggested that biological inoculation could enhance composting efficiency and improve compost quality, benefiting biogas residues composting.
Topics: Agaricales; Biofuels; Composting; Hypocreales; Manure; Phanerochaete; Soil
PubMed: 35292388
DOI: 10.1016/j.biortech.2022.126973 -
Microbiological Research Oct 2022Gut microbiota is involved in maintaining homeostasis, and intestinal dysbiosis may lead to opportunistic infections and diseases. Pathogens can disrupt the gut...
Gut microbiota is involved in maintaining homeostasis, and intestinal dysbiosis may lead to opportunistic infections and diseases. Pathogens can disrupt the gut homeostasis and establish colonization, but how they modulate the microbiome and metabolome along the gut-lung axis warrants further investigation. In the present study, we used a classical low virulence Klebsiella pneumoniae (cKp) strain to address this question. We assessed the gut microbiome and lung metabolome in cKp-infected mice by 16S rRNA sequencing and untargeted liquid chromatography-mass spectrometry, respectively. Our data revealed that cKp infection reduced gut microbiota diversity and altered microbiome composition. Specifically, cKp infection increased the abundance of MWH-CFBk5 and Actinomadura and reduced the abundance of Lachnospiraceae_NK4A136_group, Clostridium sensu_stricto 1, Bifidobacterium, and Intestinimonas at the genus level. Notably, caffeine and caffeine metabolism were significantly affected in the lung by cKp infection. Moreover, Spearman correlation analysis revealed remarkable correlations of specific lung metabolites and bacteria species at the genus level. These findings suggest that cKp infection is linked to gut dysbiosis and alterations in the lung metabolome. This study is of significance for developing innovative gut microbiota-directed therapy for respiratory diseases.
Topics: Animals; Caffeine; Dysbiosis; Gastrointestinal Microbiome; Klebsiella pneumoniae; Lung; Metabolome; Mice; RNA, Ribosomal, 16S
PubMed: 35905579
DOI: 10.1016/j.micres.2022.127139 -
Environmental Pollution (Barking, Essex... Aug 2023The potential of sulphur (S), MgSO (Mg), and KHPO (P) in nitrogen retention, ammonia emission decrease, and microbial community succession during composting needs to be...
The potential of sulphur (S), MgSO (Mg), and KHPO (P) in nitrogen retention, ammonia emission decrease, and microbial community succession during composting needs to be investigated. To achieve this, different levels of S (0, 0.2, 0.4, 0.6, and 0.8% in dry weight) plus Mg and P (S + Mg + P) were progressively added in 70 days pig manure aerobic composting. The results revealed that the amendment increased salinity and lowered pH and dephytotoxication of the product with the increase of S amount. However, no significant inhibition effects were observed on the evolution of the thermophilic phase and product maturity. In addition, the amendment significantly reduced the total NH and NO emissions by 29.66%-58.81% and 20.6%-56.7%, increased NH level by 17.22%-73.21% in thermophilic phase and NO content by 26.17%-57.48% in a mature phase, and elevated the total Kjeldahl nitrogen content by 34.28%-46.6% during the composting. In addition, compared to the control, the supplement markedly encouraged the formation of guanite in the compost product. The S addition stimulated the growth of Anseongella, Actinomadura, Chelativorans, Castellaniella, Luteimonas, and Steroidobacter microbial communities which functioned well in the degradation of nitrogen-containing compounds and organic matter. Evidence from Redundancy Analysis, Firmicutes, Myxococcus, Chloroflexi, Gemmatimonadota, and Deinococcota showed positive correlations with pH. These results imply that adding S-Mg-P amendment encourages the population and activity of specific functional microorganisms, and facilitated the ammonia emission reduction by lowering pH and thus reserved nitrogen through the formation of guanite during composting. The investigation of bacterial community abundance and environmental variables at the phylum and genus levels over time revealed that adding of 0.6% S in conjunction with P and Mg minerals was suitable for nitrogen loss mitigation in composting. The findings suggest using S + Mg + P supplement to conserve nitrogen in pig dung aerobic composting.
Topics: Swine; Animals; Ammonia; Manure; Composting; Soil; Nitrogen; Sulfur; Bacteria
PubMed: 37263560
DOI: 10.1016/j.envpol.2023.121934 -
The Journal of Dermatological Treatment Mar 2022Actinomycetoma due to is susceptible to numerous chemotherapeutic agents, however, the response to those treatments is variable and closely related to several factors.
BACKGROUND
Actinomycetoma due to is susceptible to numerous chemotherapeutic agents, however, the response to those treatments is variable and closely related to several factors.
OBJECTIVE
We aimed to evaluate the clinical-therapeutic characteristics of patients with actinomycetoma due to with two treatment modalities.
METHODS
This was a retrospective study of eighteen patients with a diagnosis of actinomycetoma. The most widely used therapeutic scheme was streptomycin 1 g every third day plus TMP/SMX 800 mg/160 mg/12h, followed by TMP/SMX with DDS 100 mg/day. In six patients (33%), ciprofloxacin 500 mg every 12 h was used instead of DDS.
RESULTS
Conventional scheme achieved clinical and mycological cure in 58% of the cases, improvement in 16%, and 25% of the patients failed to treatment; in the cases treated with ciprofloxacin, clinical and microbiological cure was achieved in 83% of patients and clinical improvement in 16%. The treatment time to achieve clinical and mycological did not have a statistically significant difference (median 10 ± 1.38 vs. 12 ± 4.6).
CONCLUSION
Treatment based on streptomycin + TMP/SMX with ciprofloxacin was found to be effective in treating patients with actinomycetoma, and comparable to the conventional treatment with DDS in actinomycetoma due to with minimal bone involvement.
Topics: Actinomadura; Humans; Mycetoma; Retrospective Studies; Trimethoprim, Sulfamethoxazole Drug Combination
PubMed: 32643472
DOI: 10.1080/09546634.2020.1793887 -
PLoS Neglected Tropical Diseases Feb 2020Mycetoma is a neglected tropical disease characterized by nodules, scars, abscesses, and fistulae that drain serous or purulent material containing the etiological...
BACKGROUND
Mycetoma is a neglected tropical disease characterized by nodules, scars, abscesses, and fistulae that drain serous or purulent material containing the etiological agent. Mycetoma may be caused by true fungi (eumycetoma) or filamentous aerobic bacteria (actinomycetoma). Mycetoma is more frequent in the so-called mycetoma belt (latitude 15° south and 30° north around the Tropic of Cancer), especially in Sudan, Nigeria, Somalia, India, Mexico, and Venezuela. The introduction of new antibiotics with fewer side effects, broader susceptibility profiles, and different administration routes has made information on actinomycetoma treatment and outcomes necessary. The objective of this report was to provide an update on clinical, therapeutic, and outcome data for patients with actinomycetoma attending a reference center in northeast Mexico.
METHODOLOGY/PRINCIPAL FINDINGS
This was a retrospective, cross-sectional, descriptive study of 31 patients (male to female ratio 3.4:1) diagnosed with actinomycetoma by direct grain examination, histopathology, culture, or serology from January 2009 to September 2018. Most lesions were caused by Nocardia brasiliensis (83.9%) followed by Actinomadura madurae (12.9%) and Actinomadura pelletieri (3.2%). About 50% of patients had bone involvement, and the right leg was the most commonly affected region in 38.7% of cases. Farmers/agriculture workers were most commonly affected, representing 41.9% of patients. The most commonly used treatment regimen was the Welsh regimen (35.5% of cases), a combination of trimethoprim/sulfamethoxazole (TMP/SMX) plus amikacin, which had a 90% cure rate, followed by TMP/SMX plus amoxicillin/clavulanic acid in 19.4% of cases with a cure rate of 100%. In our setting, 28 (90.3%) patients were completely cured and three (9.7%) were lost to follow-up. Four patients required multiple antibiotic regimens due to recurrences and adverse effects.
CONCLUSIONS/SIGNIFICANCE
In our sample, actinomycetoma was predominantly caused by N. brasiliensis. Most cases responded well to therapy with a combination of TMP/SMX with amikacin or TMP/SMX and amoxicillin/clavulanic acid. Four patients required multiple antibiotics and intrahospital care.
Topics: Adolescent; Adult; Aged; Anti-Bacterial Agents; Female; Humans; Longitudinal Studies; Male; Mexico; Middle Aged; Mycetoma; Retrospective Studies; Young Adult
PubMed: 32097417
DOI: 10.1371/journal.pntd.0008123 -
Infection and Drug Resistance 2023was first isolated in 2012 in Gelibolu, Canakkale, Turkey, and has not been reported to be isolated from humans until now. We have isolated it from the bronchoalveolar...
BACKGROUND
was first isolated in 2012 in Gelibolu, Canakkale, Turkey, and has not been reported to be isolated from humans until now. We have isolated it from the bronchoalveolar lavage fluid (BLF) of a patient with pneumonia and found its drug resistance. It is the first time that has been isolated from humans since its discovery and naming. This case may provide new ideas and methods for the clinical diagnosis and treatment of pulmonary actinomycosis.
CASE DESCRIPTION
The patient was a 75-year-old male who was hospitalized in a township hospital and failed to improve after penicillin treatment. After admission to our hospital, the patient was treated with piperacillin/tazobactam according to clinical guidelines for 14 days. was isolated from the patient's BLF and was identified by 16S rRNA sequencing. This report shows the biological characteristics and in vitro drug susceptibility testing, as well as the genomics analysis based on next-generation sequencing (NGS). The results demonstrated that was easy to be mistakenly identified as dental caries by using the Merieux ANC identification card. Based on the MIC test, was susceptible to tetracyclines, quinolones and sulfonamides, but resistant to carbapenems, penicillins and cephalosporins. The K-B test results showed was highly sensitive to piperacillin/tazobactam. Genomic analysis based on NGS showed that the belongs to EF-Tu mutants conferring resistance to inhibitor , and .
CONCLUSION
is generally sensitive to Penicillin but is not. In vitro drug susceptibility test is needed to support individualized drug use to avoid delay in the disease.
PubMed: 37228659
DOI: 10.2147/IDR.S409701 -
Journal of Chromatography. A Feb 2023Lantipeptides from bacterial sources are increasingly important as biopharmaceuticals because of their broad range of applications. However, the availability of most...
Lantipeptides from bacterial sources are increasingly important as biopharmaceuticals because of their broad range of applications. However, the availability of most lantipeptides is low, and systematic approaches for downstream processing of this group of peptides is still lacking. Model-based development for chromatographic separations has proven to be a useful tool for developing reliable purification processes. One important compound of such a model is the adsorption behavior of the components of interest. In ion-exchange chromatography, the adsorption equilibrium between salt and proteins can be described using the steric mass action (SMA) formalism. Beyond, the model parameters may be related to the lanthipeptides physico-chemical properties. In this study, the antiviral lantipeptides labyrinthopeptin A1 and A2, purified from Actinomadura namibiensis culture broth, were characterized for their adsorption behavior in anion-exchange chromatography in the range from pH 5.0-7.4. The experiments necessary to determine the three SMA parameters were chosen in a way to limit the amount of peptides needed. Linear gradient elution was applied successfully to separate A1 and A2 and to determine the characteristic charge ν and the equilibrium constant [Formula: see text] . Batch adsorption experiments using a robotic workstation for high throughput and accuracy provided non-linear adsorption isotherms and the steric factor σ. Labyrinthopeptin A1 and A2 show a very different adsorption behavior even though the fundamental structure of the two peptides is similar. k of A1 ranging from 0.18 to 0.88 are approximately one order of magnitude smaller than that of A2 ranging from 3.44 to 9.73 indicating the higher affinity of A2 to the stationary phase. At pH 7.0 σ was 1.12 and 0.60 for A1 and A2, respectively which was expected based on the molecular weight of the peptides. The characteristic charge for both peptides was also theoretically estimated from the amino acids involved in electrostatic interactions which was in good agreement with experimental data. Thereby, this work provides an useful approach to estimate SMA parameters based on simple structural information that can be applied early in chromatographic ion-exchange process development for peptides and may help adapting the processes for future designed lanthipeptides.
Topics: Adsorption; Peptides; Proteins; Chromatography, Ion Exchange; Anions
PubMed: 36681006
DOI: 10.1016/j.chroma.2023.463792