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Frontiers in Plant Science 2023The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. is an aquatic...
INTRODUCTION
The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).
METHODS
In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the plant beneficial potential of isolated bacterial endophytes of .
RESULTS AND DISCUSSION
Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as were mainly associated with leaf tissue, whereas the genera and from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from showed plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of to various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.
PubMed: 37404529
DOI: 10.3389/fpls.2023.1176648 -
International Journal of Medical... 2021The prevalence of drug-resistant (Mtb) strains makes disease control more complicated, which is the main cause of death in tuberculosis (TB) patients. Early detection... (Observational Study)
Observational Study
The prevalence of drug-resistant (Mtb) strains makes disease control more complicated, which is the main cause of death in tuberculosis (TB) patients. Early detection and timely standard treatment are the key to current prevention and control of drug-resistant TB. In recent years, despite the continuous advancement in drug-resistant TB diagnostic technology, the needs for clinical rapid and accurate diagnosis are still not fully met. With the development of sequencing technology, the research of human microecology has been intensified. This study aims to use 16 rRNA sequencing technology to detect and analyze upper respiratory flora of TB patients with anti-TB drug sensitivity (DS, n = 55), monoresistance isoniazide (MR-INH, n = 33), monoresistance rifampin (MR-RFP, n = 12), multidrug resistance (MDR, n = 26) and polyresistance (PR, n = 39) in southern China. Potential microbial diagnostic markers for different types of TB drug resistance are searched by screening differential flora, which provides certain guiding significance for drug resistance diagnosis and clinical drug use of TB. The results showed that the pulmonary microenvironment of TB patients was more susceptible to infection by external pathogens, and the infection of different drug-resistant Mtb leads to changes in different flora. Importantly, seven novel microorganisms (Leptotrichia, Granulicatella, Campylobacter, Delfitia, Kingella, Chlamydophila, Bordetella) were identified by 16S rRNA sequencing as diagnostic markers for different drug resistance types of TB. Leptotrichia, Granulicatella, Campylobacter were potential diagnostic marker for TB patients with INH single-resistance. Delftia was a potential diagnostic marker for TB patients with RFP single drug-resistance. Kingella and Chlamydophila can be used as diagnostic markers for TB patients with PR. Bordetella can be used as a potential diagnostic marker for identification of TB patients with MDR.
Topics: Adolescent; Adult; Aged; Antitubercular Agents; DNA, Bacterial; Female; Humans; Isoniazid; Male; Microbial Sensitivity Tests; Microbiota; Middle Aged; Mycobacterium tuberculosis; RNA, Ribosomal, 16S; Rifampin; Sensitivity and Specificity; Sputum; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary; Young Adult
PubMed: 33850462
DOI: 10.7150/ijms.53492 -
Frontiers in Microbiology 2022Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism....
Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism. In this work, the changes of BA content were analyzed during mustard fermentation, and microbes and gene abundance responsible for producing BAs were revealed by metagenomic analyses. The results showed that cadaverine, putrescine, tyramine, and histamine were generated during mustard fermentation, which mainly accumulate in the first 6 days of fermentation. According to the metagenome sequencing, the predominant genus was (64.78%), followed by (11.67%), (8.88%), and (1.71%) in the initial fermentation stage (second day), while (76.03%) became the most dominant genus in the late stage. In addition, the gene abundance of BA production enzymes was the highest in the second day and decreased continuously as fermentation progressed. By tracking the source of the enzyme in the KEGG database, both and closely correlated to the generation of putrescine. Besides, also correlated to the generation of tyramine and spermidine, and also correlated to the generation of cadaverine and spermine. In the processes of fermentation, the pH of fermented mustard showed slower decrease compared with other similar fermented vegetables, which may allow to grow at high levels before the pH <4. This study reveals the change of BA content and microbes involved in BA formation during mustard fermentation.
PubMed: 35572710
DOI: 10.3389/fmicb.2022.824644 -
Frontiers in Microbiology 2021The increasing number of multi-drug-resistant bacteria and cancer cases, that are a real threat to humankind, forces research world to develop new weapons to deal with...
The increasing number of multi-drug-resistant bacteria and cancer cases, that are a real threat to humankind, forces research world to develop new weapons to deal with it. Biogenic silver nanoparticles (AgNPs) are considered as a solution to this problem. Biosynthesis of AgNPs is regarded as a green, eco-friendly, low-priced process that provides small and biocompatible nanostructures with antimicrobial and anticancer activities and potential application in medicine. The biocompatibility of these nanoparticles is related to the coating with biomolecules of natural origin. The synthesis of AgNPs from actinobacterial strain was confirmed using UV-Vis spectroscopy while their morphology, crystalline structure, stability, and coating were characterized using, transmission electron microscopy (TEM), X-ray diffraction (XRD), Zeta potential and Fourier transform infrared spectroscopy (FTIR). Antibacterial activity of biogenic AgNPs was evaluated by determination of minimum inhibitory and minimum biocidal concentrations (MIC and MBC) against , , , and . The potential mechanism of antibacterial action of AgNPs was determined by measurement of ATP level. Since the use of AgNPs in biomedical applications depend on their safety, the cytotoxicity of biosynthesized AgNPs on MCF-7 human breast cancer cell line and murine macrophage cell line RAW 264.7 using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, cell lactate dehydrogenase (LDH) release and measurement of reactive oxygen species (ROS) level were assessed. The nanoparticle protein capping agent that can be involved in reduction of silver ions to AgNPs and their stabilization was identified using LC-MS/MS. Nanoparticles were spherical in shape, small in size (mean 13.2 nm), showed crystalline nature, good stability (-18.7 mV) and presence of capping agents. They exhibited antibacterial activity (MIC of 8-128 μg ml, MBC of 64-256 μg ml) and significantly decreased ATP levels in bacterial cells after treatment with different concentrations of AgNPs. The analysis showed that the AgNPs demonstrated dose-dependent cytotoxicity against RAW 264.7 macrophages and MCF-7 breast cancer cells but higher against the latter than the former. Cell viability decrease was found to be 42.2-14.2 and 38.0-15.5% while LDH leakage 14.6-42.7% and 19.0-45.0%, respectively. IC values calculated for MTT assay was found to be 16.3 and 12.0 μg ml and for LDH assay 102.3 and 76.2 μg ml, respectively. Moreover, MCF-7 cells released a greater amount of ROS than RAW 264.7 macrophages during stimulation with all tested concentrations of AgNPs (1.47-3.13 and 1.02-2.58 fold increase, respectively). The SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) analysis revealed the presence of five protein bands at a molecular weight between 31.7 and 280.9 kDa. These proteins showed the highest homology to hypothetical proteins and porins from , sp. and . Based on obtained results it can be concluded that biogenic AgNPs were capped with proteins and demonstrated potential as antimicrobial and anticancer agent.
PubMed: 33967977
DOI: 10.3389/fmicb.2021.632505 -
Microorganisms Apr 2023Strains of the genus are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading strain ULwDis3 isolated from seawater of the...
Strains of the genus are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading strain ULwDis3 isolated from seawater of the Gulf of Finland of the Baltic Sea was assembled. For the first time, genes encoding naphthalene cleavage pathways via salicylate and gentisate were identified in a strain of the genus . The genes are part of one operon ( genes). Three open reading frames (ORFs) were found in the genome of strain ULwDis3 that encode gentisate 1.2-dioxygenase. One of the ORFs is part of the operon. The physiological and biochemical characteristics of the strain ULwDis3 when cultured in mineral medium with naphthalene as the sole source of carbon and energy were also studied. It was found that after 22 h of growth, the strain stopped consuming naphthalene, and at the same time, naphthalene 1.2-dioxygenase and salicylate 5-hydroxylase activities were not detected. Later, a decrease in the number of living cells and the death of the culture were observed. Gentisate 1.2-dioxygenase activity was detected from the time of gentisate formation until culture death.
PubMed: 37110515
DOI: 10.3390/microorganisms11041092 -
Experimental Biology and Medicine... May 2023Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial...
Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild ( = 15) and severe ( = 13) SARS-CoV-2-infected patients as well as healthy controls ( = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to , , and , while bacterial genera belonging to , , and were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that , , , and were enriched in the mild condition, while , , , , , and were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.
Topics: Humans; COVID-19; SARS-CoV-2; RNA, Ribosomal, 16S; Bacteria; DNA, Ribosomal
PubMed: 36946423
DOI: 10.1177/15353702231157931 -
Scientific Reports Jan 2022Faecal (FM) and colon mucosal associated microbiota (MAM) were studied in a model of colorectal cancer (CRC), the Apc-mutated Pirc rats, and in age-paired wt F344 rats....
Faecal (FM) and colon mucosal associated microbiota (MAM) were studied in a model of colorectal cancer (CRC), the Apc-mutated Pirc rats, and in age-paired wt F344 rats. Principal Coordinates Analysis indicated that samples' distribution was driven by age, with samples of young rats (1 month old; without tumours) separated from older ones (11-month-old; bearing tumours). Diversity analysis showed significant differences between FM and MAM in older Pirc rats, and between MAM of both Pirc and wt rats and the tumour microbiota, enriched in Enterococcus, Escherichia/Shigella, Proteus and Bifidobacteriaceae. In young animals, Pirc FM was enriched in the genus Delftia, while wt FM was enriched in Lactobacillus and Streptococcus. Some CRC biomarkers and faecal short chain fatty acids (SCFAs) were also measured. Colon proliferation and DClK1 expression, a pro-survival mucosal marker, were higher in Pirc than in wt rats, while the mucin MUC2, was lower in Pirc rats. Branched SCFAs were higher in Pirc than in wt animals. By Spearman analysis CRC biomarkers correlated with FM (in both young and old rats) and with MAM (in young rats), suggesting a specific relationship between the gut microbiota profile and these functional mucosal parameters deserving further investigation.
Topics: Age Factors; Animals; Bifidobacterium; Biomarkers, Tumor; Carcinogenesis; Colon; Colonic Neoplasms; Disease Models, Animal; Doublecortin-Like Kinases; Enterococcus; Escherichia; Fatty Acids, Volatile; Feces; Gene Expression Regulation; Lactobacillus; Male; Mucin-2; Principal Component Analysis; Proteus; Rats; Rats, Inbred F344; Shigella; Streptococcus
PubMed: 35082322
DOI: 10.1038/s41598-022-05249-0 -
The Science of the Total Environment Jun 2024Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed...
Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.
PubMed: 38871316
DOI: 10.1016/j.scitotenv.2024.173846 -
New Microbes and New Infections Jan 2021The aim of the study was to describe the contamination in heater-cooler devices after the application of a protocol of cleaning and disinfection in a tertiary hospital....
The aim of the study was to describe the contamination in heater-cooler devices after the application of a protocol of cleaning and disinfection in a tertiary hospital. It was an observational study at the La Paz-Cantoblanco-Carlos III University Hospital, Madrid, Spain. Seven heater-cooler devices are used in our hospital: five 3T Sorin (LivaNova) and two Maquet. We followed the manufacturers' instructions for cleaning and disinfection of the different heater-cooler devices. Environmental testing was developed monthly from January 2017 to July 2019. Samples were obtained from both cardioplegia and patient circuits and before and after the disinfection process and were cultured in appropriate media for non-tuberculous mycobacteria and heterotrophic bacteria (coliforms and ). A total of 320 samples were taken. grew in four water samples (1.25%) from three different heater-cooler devices, with two positive results occurring after disinfection. The heterotrophic bacteria and were also found. There has not been a case of infection in patients after cardiac surgery in our hospital. In March 2019, we decided to move the heater-cooler device outside the operating room. contamination is not always eradicated by disinfection processes. We believe that placing 3T heater-cooler devices outside the operating room is the best option in preventing infection during cardiac surgery.
PubMed: 33437492
DOI: 10.1016/j.nmni.2020.100757 -
Microorganisms Sep 2023Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH,...
Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as sp., sp., sp., sp., sp., sp., and sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.
PubMed: 37894041
DOI: 10.3390/microorganisms11102383