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Microorganisms Jun 2024Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist...
Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria.
Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of and , notably the genera , , , , and . The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of and There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes , , , (macrolides); , , , and (tetracyclines); and (sulphonamides); and , (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems OXA-58 and IMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.
PubMed: 38930632
DOI: 10.3390/microorganisms12061250 -
Microorganisms Jun 2024The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends...
The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: , , , and . At the species level, bacteria such as relative abundance decreased between raw and treated wastewater, but , , and increased, as did the persistence of in both raw and treated wastewater. A total of 172 different ARGs were detected; , , , , , , , , , , , , , , , , and were found at the highest abundance and persistence. This study demonstrates the ability of bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment.
PubMed: 38930614
DOI: 10.3390/microorganisms12061231 -
Microorganisms Jun 2024Removable denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. This...
Removable denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. This study aimed to characterize and compare the metagenomic composition of saliva in denture wearers with different periodontal statuses. Twenty-four community-dwelling elders were recruited and grouped into denture wearers with active periodontitis (APD), non-denture wearers with active periodontitis (APXD), denture wearers with stable periodontal health conditions (SPCD), and non-denture wearers with stable periodontal health conditions (SPCXD). Saliva samples were collected and underwent Type IIB restriction-site-associated DNA for microbiome (2bRAD-M) metagenomic sequencing to characterize the species-resolved microbial composition. Alpha diversity analysis based on the Shannon index revealed no significant difference between groups. Beta diversity analysis using the Jaccard distance matrix was nearly significantly different between denture-wearing and non-denture-wearing groups ( = 0.075). Some respiratory pathogens, including and , were detected as the top 30 species in saliva samples. Additionally, LEfSe analysis revealed a substantial presence of pathogenic bacteria in denture groups. In the cohort of saliva samples collected from community-dwelling elders, a remarkable abundance of certain opportunistic pathogens was detected in the microbial community.
PubMed: 38930579
DOI: 10.3390/microorganisms12061197 -
Microorganisms Jun 2024Salt-tolerant aerobic granular sludge(AGS) was successfully cultivated under the dual stress of tetracycline and 2.5% salinity, resulting in an average particle size of...
Salt-tolerant aerobic granular sludge(AGS) was successfully cultivated under the dual stress of tetracycline and 2.5% salinity, resulting in an average particle size of 435.0 ± 0.5 and exhibiting a chemical oxygen demand(COD) removal rate exceeding 80%, as well as excellent sedimentation performance. The analysis of metagenomics technology revealed a significant pattern of succession in the development of AGS. The proportion of , a type of salt-tolerant bacteria, exhibited a gradual increase and reached 38.07% after 42 days, which indicated that an AGS system based on moderate halophilic bacteria was successfully constructed. The expression levels of targeted genes were found to be reduced across the entire AGS process and formation, as evidenced by qPCR analysis. The presence of (7.67 log10 gene copies g in 0 d sludge sample) enabled microbes to horizontally transfer ARGs genes along the AGS formation under the double pressure of TC and 2.5% salinity. These findings will enhance our understanding of ARG profiles and the development in AGS under tetracycline pressure, providing a foundation for guiding the use of AGS to treat hypersaline pharmaceutical wastewater.
PubMed: 38930555
DOI: 10.3390/microorganisms12061173 -
Microorganisms Jun 2024Numerous studies have reported a correlation between gut microbiota and influenza A virus (IAV) infection and disease severity. However, the causal relationship between...
Numerous studies have reported a correlation between gut microbiota and influenza A virus (IAV) infection and disease severity. However, the causal relationship between these factors remains inadequately explored. This investigation aimed to assess the influence of gut microbiota on susceptibility to human infection with H7N9 avian IAV and the severity of influenza A (H1N1)pdm09 infection. A two-sample Mendelian randomization analysis was conducted, integrating our in-house genome-wide association study (GWAS) on H7N9 susceptibility and H1N1pdm09 severity with a metagenomics GWAS dataset from a Chinese population. Twelve and fifteen gut microbiotas were causally associated with H7N9 susceptibility or H1N1pdm09 severity, separately. Notably, and were negative associated with H7N9 susceptibility and H1N1pdm09 severity, respectively. Moreover, and were associated with H7N9 susceptibility, while and were correlated with H1N1pdm09 severity. These results provide novel insights into the interplay between gut microbiota and IAV pathogenesis as well as new clues for mechanism research regarding therapeutic interventions or IAV infections. Future studies should concentrate on clarifying the regulatory mechanisms of gut microbiota and developing efficacious approaches to reduce the incidence of IAV infections, which could improve strategy for preventing and treating IAV infection worldwide.
PubMed: 38930552
DOI: 10.3390/microorganisms12061170 -
Microorganisms Jun 2024Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way,...
Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.
PubMed: 38930544
DOI: 10.3390/microorganisms12061162 -
Microorganisms May 2024In medicine, parasitic cysts (e.g., brain cysticerci) are believed to be sterile, and are primarily treated with antiparasitic medications, not antibiotics, which could...
In medicine, parasitic cysts (e.g., brain cysticerci) are believed to be sterile, and are primarily treated with antiparasitic medications, not antibiotics, which could prevent abscess formation and localized inflammation. This study quantified the microbial composition of parasitic cysts in a wild rodent, using multi-kingdom metagenomics to comprehensively assess if parasitic cysts are sterile, and further understand gut microbial translocation and adaptation in wildlife confined environments, outside the gut. Analysis was conducted on DNA from two hepatic parasitic cysts from a feline tapeworm, , affecting a wild vole mouse (), and from feces, liver and peritoneal fluid of this and two other concurrent individual wild voles trapped during pest control in one of our university research vegetable gardens. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, ; and inhabiting the cysts, and peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, and unexpectedly, a virus from the insect armyworm moth (), known as A (MyunGV-A), in both cysts, and in one fecal and one peritoneal sample from the other non-cyst voles, indicating the survival and adaption potential of the insect virus in voles. Metagenomics also revealed a significantly lower probability of fungal detection in cysts compared to that in peritoneal fluid/feces ( < 0.05), with single taxon detection in each cyst ( and ). The peritoneal fluid had the highest probability for fungi. In conclusion, metagenomics revealed that bacteria/viruses/fungi coexist within parasitic cysts supporting the potential therapeutic benefits of antibiotics in cystic diseases, and in inflammatory microniches of chronic diseases, such as Crohn's disease gut wall cavitating micropathologies, from which we recently isolated similar synergistic pathogenic and , and .
PubMed: 38930512
DOI: 10.3390/microorganisms12061130 -
Microorganisms May 2024University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of...
University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of antibiotic resistance gene (ARG) variation in washing machines within university dormitories and their potential health risks are largely unknown. To disclose the occurrence of ARGs and antibiotic-resistant bacteria from university dormitories, we collected samples from washing machines in 10 dormitories and used metagenomic sequencing technology to determine microbial and ARG abundance. Our results showed abundant microbial diversity, with Proteobacteria being the dominant microorganism that harbors many ARGs. The majority of the existing ARGs were associated with antibiotic target alteration and efflux, conferring multidrug resistance. We identified tnpA and IS91 as the most abundant mobile genetic elements (MGEs) in washing machines and found that , , and had high levels of ARGs. Our study highlights the potential transmission of pathogens from washing machines to humans and the surrounding environment. Pollution in washing machines poses a severe threat to public health and demands attention. Therefore, it is crucial to explore effective methods for reducing the reproduction of multidrug resistance.
PubMed: 38930496
DOI: 10.3390/microorganisms12061112 -
Microorganisms May 2024Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the...
Halo-alkali soil threatens agriculture, reducing growth and crop yield worldwide. In this study, physicochemical and molecular techniques were employed to explore the potential of halo-alkali-tolerant endophytic bacteria strains sp. pp01, sp. pp02, sp. pp04, and sp. pp06 to enhance the growth of hybrid under varying saline conditions. The strains exhibited tolerance to high salt concentrations, alkaline pH, and high temperatures. Under controlled conditions, all four strains showed significant growth-promoting effects on hybrid inoculated individually or in combination. However, the effects were significantly reduced in coastal saline soil. The best growth-promoting effect was achieved under greenhouse conditions, increasing shoot fresh and dry weights of hybrid by up to 457.7% and 374.7%, respectively, using irrigating trials. Metagenomic sequencing analysis revealed that the diversity and composition of rhizosphere microbiota underwent significant changes after inoculation with endophytic bacteria. Specifically, pp02 and co-inoculation significantly increased the and population. Firmicutes, Mycobacteria, and Proteobacteria phyla were enriched in PP02 samples. These may explain the best growth-promoting effects of pp02 and co-inoculation on hybrid under greenhouse conditions. Our findings reveal the performance of endophytic bacterial inoculants in enhancing beneficial microbiota, salt stress tolerance, and hybrid growth.
PubMed: 38930444
DOI: 10.3390/microorganisms12061062 -
Microorganisms May 2024COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this...
COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this disease but also its impact on the physiology of different organs and microbiomes. Multiple studies have reported the effects of COVID-19 on the gastrointestinal microbiota, such as promoting dysbiosis (imbalances in the microbiome) following the disease's progression. Deconstructing the dynamic changes in microbiome composition that are specifically correlated with COVID-19 patients remains a challenge. Motivated by this problem, we implemented a biomarker discovery pipeline to identify candidate microbes specific to COVID-19. This involved a meta-analysis of large-scale COVID-19 metagenomic data to decipher the impact of COVID-19 on the human gut and respiratory microbiomes. Metagenomic studies of the gut and respiratory microbiomes of COVID-19 patients and of microbiomes from other respiratory diseases with symptoms similar to or overlapping with COVID-19 revealed 1169 and 131 differentially abundant microbes in the human gut and respiratory microbiomes, respectively, that uniquely associate with COVID-19. Furthermore, by utilizing machine learning models (LASSO and XGBoost), we demonstrated the power of microbial features in separating COVID-19 samples from metagenomic samples representing other respiratory diseases and controls (healthy individuals), achieving an overall accuracy of over 80%. Overall, our study provides insights into the microbiome shifts occurring in COVID-19 patients, shining a new light on the compositional changes.
PubMed: 38930440
DOI: 10.3390/microorganisms12061058