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Microorganisms Mar 2024Peru is one of the leading countries that produce and export specialty coffees, favorably positioned in the international markets for its physical and organoleptic cup...
Peru is one of the leading countries that produce and export specialty coffees, favorably positioned in the international markets for its physical and organoleptic cup qualities. In recent years, yellow coffee rust caused by the phytopathogenic fungus stands out as one of the main phytosanitary diseases that affect coffee culture yields. Many studies have demonstrated bacteria antagonistic activity against a number of phytopathogen fungi. In this context, the aim of this work was to select and characterize phyllospheric bacteria isolated from with antagonistic features against coffee rust to obtain biocontrollers. For that purpose, a total of 82 phyllospheric bacteria were isolated from two coffee leaf rust-susceptible varieties, and , and one tolerant variety, . Of all the isolates, 15% were endophytic and 85% were epiphytes. Among all the isolates, 14 were capable of inhibiting the mycelial radial growth of , and sp. 16S rRNA gene sequence-based analysis showed that 9 isolates were related to , 2 were related to and 1 was related to , and . A total of 7 representative bacteria of each group were selected based on their antagonistic activity and tested in germination inhibition assays of coffee rust uredinospores. The CRRFLT7 and TRFLT8 isolates showed a high inhibition percentage of urediniospores germination (81% and 82%, respectively), similar to that obtained with the chemical control (91%). An experimental field assay showed a good performance of both strains against rust damage too, making them a promising alternative for coffee leaf rust biocontrol.
PubMed: 38543633
DOI: 10.3390/microorganisms12030582 -
Microorganisms Feb 2024The low-temperature environment significantly inhibits the growth and metabolism of denitrifying bacteria, leading to an excessive concentration of ammonia nitrogen and...
The low-temperature environment significantly inhibits the growth and metabolism of denitrifying bacteria, leading to an excessive concentration of ammonia nitrogen and total nitrogen in sewage treatment plants during the cold season. In this study, an efficient denitrifying strain of heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria named HS2 was isolated and screened from industrial sewage of a chemical factory in Inner Mongolia at 8 °C. The strain was confirmed to be , a colorless rod-shaped bacterium. When cultured with sodium succinate as the carbon source, a carbon-to-nitrogen ratio of 20-30, a shaking rate of 150-180 r/min, and an initial pH of 6-10, the strain HS2 exhibited excellent nitrogen removal at 8 °C. Through the results of whole-genome sequencing, gene amplification, and gas product detection, the strain HS2 was determined to possess key enzyme genes in both nitrification and denitrification pathways, suggesting a HN-AD pathway of NH-N → NHOH → NON → NO → NO → N. At 8 °C, the strain HS2 could completely remove ammonia nitrogen from industrial sewage with an initial concentration of 127.23 mg/L. Microbial species diversity analysis of the final sewage confirmed sp. as the dominant genus, which indicated that the low-temperature denitrifying strain HS2 plays an important role in nitrogen removal in actual low-temperature sewage.
PubMed: 38543502
DOI: 10.3390/microorganisms12030451 -
Heliyon Mar 2024In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a...
Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture.
In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, , , KB913035, , and , known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included , , , , , , , , , and Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.
PubMed: 38533070
DOI: 10.1016/j.heliyon.2024.e27985 -
Foods (Basel, Switzerland) Mar 2024This study assessed the physicochemical properties of air-fried hairtail fillets (190 °C, 24 min) under different storage temperatures (4, 25, and 35 °C). The findings...
This study assessed the physicochemical properties of air-fried hairtail fillets (190 °C, 24 min) under different storage temperatures (4, 25, and 35 °C). The findings revealed a gradual decline in sensory scores across all samples during storage, accompanied by a corresponding decrease in thiobarbituric acid reactive substances (TBARS) and total viable count over time. Lower storage temperatures exhibited an effective capacity to delay lipid oxidation and microbiological growth in air-fried hairtail fillets. Subsequently, alterations in the microbiota composition of air-fried hairtail fillets during cold storage were examined. Throughout the storage duration, , , and emerged as the three dominant genera in the air-fried hairtail samples. Additionally, Pearson correlation analysis demonstrated that among the most prevalent microbial genera in air-fried hairtail samples, and exhibited positive correlations with the * value, * value, and sensory scores. Conversely, they displayed negative correlations with pH, * value, and TBARS. Notably, air-fried samples stored at 4 °C exhibited prolonged freshness compared with those stored at 25 °C and 35 °C, suggesting that 4 °C is an optimal storage temperature. This study offers valuable insights into alterations in the physicochemical properties and microbial distribution in air-fried hairtail fillets during storage, facilitating the improvement of meat quality by adjusting microbial communities in air-fried hairtail fillets.
PubMed: 38472899
DOI: 10.3390/foods13050786 -
Environment International Mar 2024High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a...
High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.
Topics: Metagenome; Phenanthrenes; Isotopes; DNA; Biodegradation, Environmental; Soil Microbiology; Soil Pollutants
PubMed: 38458119
DOI: 10.1016/j.envint.2024.108555 -
Narra J Apr 2023An accurate and timely identification of causative microorganisms as well as determination of their antibiotic susceptibility patterns will help in the selection of...
An accurate and timely identification of causative microorganisms as well as determination of their antibiotic susceptibility patterns will help in the selection of proper antibiotics and prevention of their misuse in pneumonia patients. The aim of this study was to determine the distribution and antibiotic susceptibility pattern of bacteria isolated from endotracheal aspirates of ventilator-assisted pneumonia patients in Indonesia. A retrospective cross-sectional study was conducted at Dr. Zainoel Abidin Hospital, a provincial reference hospital in Banda Aceh, Indonesia, from January to December 2021. Ventilator-assisted pneumonia patients aged ≥17 years treated in the hospital were considered eligible. Antibiotic susceptibility was valuated using Kirby-Bauer disc-diffusion followed with VITEK 2 Compact. We included 57 patients of which 73.7% males and 26.3% aged 56-65 years (represent the majority group of the patients). Each patient reported at least one comorbidity and the average duration of receiving mechanical ventilation was 8.68 days, and more than half (59.7%) of the patients had a poor clinical outcome (died). A total 57 bacteria isolates (consisting nine species) were recovered; 68.5% Gram-negative and 31.5% Gram-positive bacteria. Among 57 patients, was the most frequent isolated Gram-negative bacteria (19.3%), followed by (17.5%), (15.8%), and (12.3%). exhibited <70% sensitivity to aminoglycoside and carbapenem antibiotics and 100% resistance to third-generation cephalosporins. The most abundant Gram-positive bacteria was (17.5%), followed by (10.5%) and (3.5%). All were sensitive to linezolid, tigecycline, vancomycin, and macrolide antibiotics (azithromycin, clarithromycin, clindamycin, and erythromycin), whereas 50% were sensitive to some beta-lactams. However, 50% of were methicillin resistant (MRSA). Given the magnitude of multi-drug resistance, an empiric antimicrobial therapy in particular to specific settings and implementation of antibiotic stewardship programs are crucial.
PubMed: 38450036
DOI: 10.52225/narra.v3i1.149 -
Heliyon Mar 2024Diarrhea is a severe issue in calves that causes fertility problems and economic issues worldwide. Sodium acetate/sodium butyrate (SA/SB) alleviates diarrhea in mice;...
Diarrhea is a severe issue in calves that causes fertility problems and economic issues worldwide. Sodium acetate/sodium butyrate (SA/SB) alleviates diarrhea in mice; however, little information is available about the preventive effect of SA/SB on diarrheic yak calves living on the Tibet plateau. Yak calves (n = 19) of age ≥4 months and weight 37 ± 2 Kg were randomly divided into control (C, n = 10) and supplement groups (S, n = 9). Yaks belonging to the supplement group were given sodium butyrate (10 g/kg) and sodium acetate (5 g/kg) for 28 days, along with normal feed, seasonal grasses, pasture, and water. The blood and fecal samples from yak calves were collected for assessment of antioxidant capacity, inflammatory cytokines, microbiome, and short-chain fatty acids (SCFAs) concentration analysis. Results of this study revealed that a lower diarrhea rate, higher weight, and net weight gain were recorded in yaks belonging to group S supplemented with SA/SB. Similarly, increased antioxidant capacity with higher levels of T-AOC, SOD, and GSH-px and decreased inflammatory reactions by decreasing both TNF-α and IL-1β concentrations were recorded in yaks of group S. The concentration of SCFAs was significantly higher ( < 0.05) in yaks from group S than group C. Microbiome analysis revealed that 8 phyla and 54 genera were significantly different ( < 0.05) in both yak groups, with increased probiotics (Akkermansia, Oscillospira), SCFAs producing genera (Oscillospira, ASF356, Anaerosporobacter and Phascolarctobacterium), and decreased inflammatory related genus (Flavonifractor, Fournierella) and harmful bacteria (Oscillibacter, Achromobacter) in group S. In conclusion, the results demonstrated that SA and SB could decrease diarrhea rates in yak calves on the plateau via increasing antioxidant ability and SCFAs, while decreasing inflammatory responses in yaks by moderating gut microbiota. The current results provide new insights for the prevention and treatment of diarrhea in yaks.
PubMed: 38439875
DOI: 10.1016/j.heliyon.2024.e26564 -
Frontiers in Microbiology 2024Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4 T cells,...
Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4 T cells, causing a cascade of phenomena resulting in the instability of the gut mucosa. The effect of HIV infection on gut microbiome dysbiosis remains unresolved despite antiretroviral therapy. Here, we show the results of a longitudinal study of microbiome analysis of people living with HIV (PLWH). We contrasted the diversity and composition of the microbiome of patients with HIV at the first and second time points (baseline_case and six months later follow-up_case, respectively) with those of healthy individuals (baseline_control). We found that despite low diversity indices in the follow-up_case, the abundance of some genera was recovered but not completely, similar to baseline_control. Some genera were consistently in high abundance in PLWH. Furthermore, we found that the CD4 T-cell count and soluble CD14 level were significantly related to high and low diversity indices, respectively. We also found that the abundance of some genera was highly correlated with clinical features, especially with antiretroviral duration. This includes genera known to be correlated with worse HIV-1 progression ( and ) and a genus associated with gut protection (). The fact that a protector of the gut and genera linked to a worse progression of HIV-1 are both enriched may signify that despite the improvement of clinical features, the gut mucosa remains compromised.
PubMed: 38426062
DOI: 10.3389/fmicb.2024.1359402 -
Microbiology Spectrum Apr 2024A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA)...
UNLABELLED
A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA) transcriptome data. A recent study by Salzberg et al. argued that ITBs, being overstated as a methodology by Poore et al., were problematic. We previously reported that ITBs were prognostic in adrenocortical carcinoma (ACC), a highly aggressive rare disease using data by Poore et al., and here, we aimed to answer whether ITBs truly existed and were prognostic in ACC. ACC samples from our institutes underwent 16S rRNA sequencing [adrenocortical carcinoma blocks from Huashan Hospital and China Medical University (HS) cohort]. The ITB profile was compared to TCGA data processed by Poore et al. (TCGA-P) and TCGA data processed by Salzberg et al. (TCGA-S), respectively. The primary outcome was overall survival (OS). A total of 26 ACC cases (HS cohort) and 10 paraffin controls were sequenced. The TCGA cohort encompassed 77 cases. Two and four amid the top 10 abundant genera in HS cohort were not detected in TCGA-P and TCGA-S, respectively. Neither was alpha or beta diversity associated with survival nor could ACC be subtyped by ITB signature in the HS cohort. Notably, a five-genera ITB risk score (, , , , and ) for OS trained in the HS cohort was validated in both TCGA-P and TCGA-S cohorts and was independently prognostic. Whereas ITB signature on the whole may not be associated with ACC subtypes, certain ITB features are associated with prognosis, and a risk score could be generated and validated externally.
IMPORTANCE
In this report, we looked at the role of ITBs in ACC in patients with different race and sequencing platforms. We found a five-genera ITB risk score consistently predicted overall survival in all cohorts. We conclude that certain ITB features are universally pathogenic to ACC.
Topics: Humans; Adrenocortical Carcinoma; Prognosis; Adrenal Cortex Neoplasms; RNA, Ribosomal, 16S; Risk Factors; Bacteria
PubMed: 38421176
DOI: 10.1128/spectrum.03727-23 -
Antimicrobial Stewardship & Healthcare... 2024and are emerging nosocomial, non-glucose fermenting, Gram-negative pathogens. In this nested case-control trial, independent predictors for infections were...
and are emerging nosocomial, non-glucose fermenting, Gram-negative pathogens. In this nested case-control trial, independent predictors for infections were hemodialysis and recent antibiotic usage (overall), while recent usage of fluoroquinolones, was independently associated with infections. Infections were independently associated with multiple worse outcomes.
PubMed: 38415099
DOI: 10.1017/ash.2024.11