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Zhang M, Zhao B, Yan Y, Cheng Z, Li Z, Han L, Sun Y, Zheng Y, Xia Y. Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169203. [PMID: 38086476 DOI: 10.1016/j.scitotenv.2023.169203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.
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Affiliation(s)
- Miao Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zengyi Li
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Long Han
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuqin Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Sajjad B, Rasool K, Siddique A, Jabbar KA, El-Malaha SS, Sohail MU, Almomani F, Alfarra MR. Size-resolved ambient bioaerosols concentration, antibiotic resistance, and community composition during autumn and winter seasons in Qatar. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122401. [PMID: 37598930 DOI: 10.1016/j.envpol.2023.122401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
This study investigates the size distribution, microbial composition, and antibiotic resistance (ABR) of airborne bioaerosols at a suburban location in Doha, Qatar between October 2021 and January 2022. Samples were collected using an Andersen six-stage viable cascade impactor and a liquid impinger. Findings showed that the mean bacteria concentration (464 CFU/m3) was significantly higher than that of fungi (242 CFU/m3) during the study period. Both bacteria and fungi were most abundant in the aerodynamic size fractions of 1.10-2.21 μm, with peak concentrations observed in the mornings and lowest concentrations in the afternoons across all size fractions. A total of 24 different culturable species were identified, with the most abundant ones being Pasteurella pneumotropica (9.71%), Pantoea spp. 1 (8.73%), and Proteus penneri (7.77%) spp. At the phylum level, the bacterial community configurations during the autumn and winter seasons were nearly identical as revealed by molecular genomics, with Proteobacteria being the most predominant, followed by Firmicutes, Bacteroidetes, Acidobacteriota, and Planctomycetota. However, there was a significant variation in dominant genera between autumn and winter. The most abundant genera included Sphingomonas, Paraburkholderia, Comamonas, Bacillus, and Lysinibacillus. Several bacterial genera identified in this study have important public health and ecological implications, including the risk of respiratory tract infections. Furthermore, the study found that ABR was highest in December, with bioaerosols exhibiting resistance to at least 5 out of 10 antibiotics, and 100% resistance to Metronidazole in all samples. Metagenomics analysis revealed the presence of various airborne bacteria that were not detected through culture-dependent methods. This study provides valuable insights into the airborne microbial composition, temporal variability and ABR in the Arabian Gulf region.
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Affiliation(s)
- Bilal Sajjad
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar; Department of Chemical Engineering, Qatar University, Qatar
| | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar.
| | - Azhar Siddique
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar
| | - Khadeeja Abdul Jabbar
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar
| | - Shimaa S El-Malaha
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar
| | | | - Fares Almomani
- Department of Chemical Engineering, Qatar University, Qatar
| | - M Rami Alfarra
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P. O. Box 34110, Doha, Qatar
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Cotton S, Clayton CA, Tropini C. Microbial endocrinology: the mechanisms by which the microbiota influences host sex steroids. Trends Microbiol 2023; 31:1131-1142. [PMID: 37100633 DOI: 10.1016/j.tim.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
Recent progress in microbial endocrinology has propelled this field from initially providing correlational links to defining the mechanisms by which microbes influence systemic sex hormones. Importantly, the interaction between the gut-resident bacteria and host-secreted hormones has been shown to be critical for host development as well as hormone-mediated disease progression. This review investigates how microbes affect active sex hormone levels, with a focus on gut-associated bacteria hormonal modifications and the resulting host physiological status. Specifically, we focus on the ability of the microbiota to reactivate estrogens and deactivate androgens and thereby influence systemic levels of host hormones in a clinically significant manner.
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Affiliation(s)
- Sophie Cotton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Charlotte A Clayton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Canada.
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Li Y, Fang C, Wang X, Liu Q, Qiu Y, Dai X, Zhang L. A new class A beta-lactamase gene bla CAE-1 coexists with bla AFM-1 in a novel untypable plasmid in Comamonas aquatica. Sci Rep 2023; 13:3634. [PMID: 36869066 PMCID: PMC9984417 DOI: 10.1038/s41598-023-28312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/17/2023] [Indexed: 03/05/2023] Open
Abstract
Antimicrobial resistance, especially carbapenem resistance, poses a serious threat to global public health. Here, a carbapenem-resistant Comamonas aquatica isolate SCLZS63 was recovered from hospital sewage. Whole-genome sequencing showed that SCLZS63 has a 4,048,791-bp circular chromosome and three plasmids. The carbapenemase gene blaAFM-1 is located on the 143,067-bp untypable plasmid p1_SCLZS63, which is a novel type of plasmid with two multidrug-resistant (MDR) regions. Notably, a novel class A serine β-lactamase gene, blaCAE-1, coexists with blaAFM-1 in the mosaic MDR2 region. Cloning assay showed that CAE-1 confers resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone, and elevates the MIC of ampicillin-sulbactam two-fold in Escherichia coli DH5α, suggesting that CAE-1 functions as a broad-spectrum β-lactamase. Amino acid sequences analysis suggested that blaCAE-1 may originate from Comamonadaceae. The blaAFM-1 in p1_SCLZS63 is located in a conserved structure of ISCR29-ΔgroL-blaAFM-1-ble-ΔtrpF-ΔISCR27-msrB-msrA-yfcG-corA. Comprehensive analysis of the blaAFM-bearing sequences revealed important roles of ISCR29 and ΔISCR27 in the mobilization and truncation of the core module of blaAFM alleles, respectively. The diverse passenger contents of class 1 integrons flanking the blaAFM core module make the complexity of genetic contexts for blaAFM. In conclusion, this study reveals that Comamonas may act as an important reservoir for antibiotics-resistance genes and plasmids in the environment. Continuous monitoring for the environmental emergence of antimicrobial-resistant bacteria is needed to control the spread of antimicrobial resistance.
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Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Science, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xu Wang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Qian Liu
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Yichuan Qiu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
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Ryan MP, Sevjahova L, Gorman R, White S. The Emergence of the Genus Comamonas as Important Opportunistic Pathogens. Pathogens 2022; 11:pathogens11091032. [PMID: 36145464 PMCID: PMC9504711 DOI: 10.3390/pathogens11091032] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.
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