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Chen Y, Xiao L, Zhou M, Zhang H. The microbiota: a crucial mediator in gut homeostasis and colonization resistance. Front Microbiol 2024; 15:1417864. [PMID: 39165572 PMCID: PMC11333231 DOI: 10.3389/fmicb.2024.1417864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/23/2024] [Indexed: 08/22/2024] Open
Abstract
The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of manipulating the microbiota to treat infectious diseases in the gut.
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Affiliation(s)
- Yiding Chen
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Ling Xiao
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Min Zhou
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
| | - Hu Zhang
- Department of Gastroenterology, West China Tianfu Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
- Center for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China
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Calland JK, Pesonen ME, Mehat J, Pascoe B, Haydon DJ, Lourenco J, Lukasiewicz B, Mourkas E, Hitchings MD, La Ragione RM, Hammond P, Wallis TS, Corander J, Sheppard SK. Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork. NPJ Vaccines 2024; 9:105. [PMID: 38866805 PMCID: PMC11169640 DOI: 10.1038/s41541-024-00879-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/19/2024] [Indexed: 06/14/2024] Open
Abstract
Campylobacter is a leading cause of food-borne gastroenteritis worldwide, linked to the consumption of contaminated poultry meat. Targeting this pathogen at source, vaccines for poultry can provide short-term caecal reductions in Campylobacter numbers in the chicken intestine. However, this approach is unlikely to reduce Campylobacter in the food chain or human incidence. This is likely as vaccines typically target only a subset of the high genomic strain diversity circulating among chicken flocks, and rapid evolution diminishes vaccine efficacy over time. To address this, we used a genomic approach to develop a whole-cell autogenous vaccine targeting isolates harbouring genes linked to survival outside of the host. We hyper-immunised a whole major UK breeder farm to passively target offspring colonisation using maternally-derived antibody. Monitoring progeny, broiler flocks revealed a near-complete shift in the post-vaccination Campylobacter population with an ~50% reduction in isolates harbouring extra-intestinal survival genes and a significant reduction of Campylobacter cells surviving on the surface of meat. Based on these findings, we developed a logistic regression model that predicted that vaccine efficacy could be extended to target 65% of a population of clinically relevant strains. Immuno-manipulation of poultry microbiomes towards less harmful commensal isolates by competitive exclusion, has major potential for reducing pathogens in the food production chain.
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Affiliation(s)
- Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway.
| | - Maiju E Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Jai Mehat
- School of Biosciences, University of Surrey, Surrey, UK
| | - Ben Pascoe
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - David J Haydon
- Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Berkshire, UK
| | - Jose Lourenco
- Faculty of Medicine, Biomedical Research Centre, Universidade Católica Portuguesa, Lisbon, Portugal
| | | | - Evangelos Mourkas
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
| | | | - Roberto M La Ragione
- School of Biosciences, University of Surrey, Surrey, UK
- School of Veterinary Medicine, University of Surrey, Surrey, UK
| | | | - Timothy S Wallis
- Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Berkshire, UK
| | - Jukka Corander
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK.
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Chen X, He L, Zhang C, Zheng G, Lin S, Zou Y, Lu Y, Feng Y, Zheng D. Exploring new avenues of health protection: plant-derived nanovesicles reshape microbial communities. J Nanobiotechnology 2024; 22:269. [PMID: 38764018 PMCID: PMC11103870 DOI: 10.1186/s12951-024-02500-w] [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: 03/10/2024] [Accepted: 04/27/2024] [Indexed: 05/21/2024] Open
Abstract
Symbiotic microbial communities are crucial for human health, and dysbiosis is associated with various diseases. Plant-derived nanovesicles (PDNVs) have a lipid bilayer structure and contain lipids, metabolites, proteins, and RNA. They offer unique advantages in regulating microbial community homeostasis and treating diseases related to dysbiosis compared to traditional drugs. On the one hand, lipids on PDNVs serve as the primary substances that mediate specific recognition and uptake by bacteria. On the other hand, due to the multifactorial nature of PDNVs, they have the potential to enhance growth and survival of beneficial bacterial while simultaneously reducing the pathogenicity of harmful bacteria. In addition, PDNVs have the capacity to modulate bacterial metabolism, thus facilitating the establishment of a harmonious microbial equilibrium and promoting stability within the microbiota. These remarkable attributes make PDNVs a promising therapeutic approach for various conditions, including periodontitis, inflammatory bowel disease, and skin infection diseases. However, challenges such as consistency, isolation methods, and storage need to be addressed before clinical application. This review aims to explore the value of PDNVs in regulating microbial community homeostasis and provide recommendations for their use as novel therapeutic agents for health protection.
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Affiliation(s)
- Xiaohang Chen
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Lianghang He
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Chaochao Zhang
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Genggeng Zheng
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Shuoqi Lin
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Yuchun Zou
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Youguang Lu
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Yan Feng
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China.
- Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China.
| | - Dali Zheng
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China.
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Kowalski CH, Lawhorn S, Smith TJ, Corrigan RM, Barber MF. Adaptation to skin mycobiota promotes antibiotic tolerance in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592489. [PMID: 38952794 PMCID: PMC11216364 DOI: 10.1101/2024.05.03.592489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The microbiota can promote host health by inhibiting pathogen colonization, yet how host-resident fungi, or the mycobiota, contribute to this process remains unclear. The human skin mycobiota is uniquely stable compared to other body sites and dominated by yeasts of the genus Malassezia . We observe that colonization of human skin by Malassezia sympodialis significantly reduces subsequent colonization by the prominent bacterial pathogen Staphylococcus aureus . M. sympodialis secreted products possess potent bactericidal activity against S. aureus and are sufficient to impair S. aureus skin colonization. This bactericidal activity requires an acidic environment and is exacerbated by free fatty acids, demonstrating a unique synergy with host-derived epidermal defenses. Leveraging experimental evolution to pinpoint mechanisms of S. aureus adaptation in response to the skin mycobiota, we identified multiple mutations in the stringent response regulator Rel that promote survival against M. sympodialis . Similar Rel alleles have been reported in S. aureus clinical isolates, and natural Rel variants are sufficient for tolerance to M. sympodialis antagonism. Partial stringent response activation underlies tolerance to clinical antibiotics, with both laboratory-evolved and natural Rel variants conferring multidrug tolerance. These findings demonstrate the ability of the mycobiota to mediate pathogen colonization resistance, identify new mechanisms of bacterial adaptation in response to fungal antagonism, and reveal the potential for microbiota-driven evolution to shape pathogen antibiotic susceptibility. Highlights - M. sympodialis reduces colonization of human skin by S. aureus - Bactericidal activity of M. sympodialis is exacerbated by features of the skin niche - S. aureus Rel variants are sufficient for tolerance to Malassezia antagonism - Evolved tolerance to yeast antagonism coincides with S. aureus multidrug tolerance.
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Hudson J, Egan S. Marine diseases and the Anthropocene: Understanding microbial pathogenesis in a rapidly changing world. Microb Biotechnol 2024; 17:e14397. [PMID: 38217393 PMCID: PMC10832532 DOI: 10.1111/1751-7915.14397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
Healthy marine ecosystems are paramount for Earth's biodiversity and are key to sustaining the global economy and human health. The effects of anthropogenic activity represent a pervasive threat to the productivity of marine ecosystems, with intensifying environmental stressors such as climate change and pollution driving the occurrence and severity of microbial diseases that can devastate marine ecosystems and jeopardise food security. Despite the potentially catastrophic outcomes of marine diseases, our understanding of host-pathogen interactions remains an understudied aspect of both microbiology and environmental research, especially when compared to the depth of information available for human and agricultural systems. Here, we identify three avenues of research in which we can advance our understanding of marine disease in the context of global change, and make positive steps towards safeguarding marine communities for future generations.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
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de Nies L, Kobras CM, Stracy M. Antibiotic-induced collateral damage to the microbiota and associated infections. Nat Rev Microbiol 2023; 21:789-804. [PMID: 37542123 DOI: 10.1038/s41579-023-00936-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 08/06/2023]
Abstract
Antibiotics have transformed medicine, saving millions of lives since they were first used to treat a bacterial infection. However, antibiotics administered to target a specific pathogen can also cause collateral damage to the patient's resident microbial population. These drugs can suppress the growth of commensal species which provide protection against colonization by foreign pathogens, leading to an increased risk of subsequent infection. At the same time, a patient's microbiota can harbour potential pathogens and, hence, be a source of infection. Antibiotic-induced selection pressure can cause overgrowth of resistant pathogens pre-existing in the patient's microbiota, leading to hard-to-treat superinfections. In this Review, we explore our current understanding of how antibiotic therapy can facilitate subsequent infections due to both loss of colonization resistance and overgrowth of resistant microorganisms, and how these processes are often interlinked. We discuss both well-known and currently overlooked examples of antibiotic-associated infections at various body sites from various pathogens. Finally, we describe ongoing and new strategies to overcome the collateral damage caused by antibiotics and to limit the risk of antibiotic-associated infections.
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Affiliation(s)
- Laura de Nies
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Carolin M Kobras
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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Zhao W, Han Q, Yang R, Wen W, Deng Z, Li H, Zheng Z, Ma Z, Yu G. Exposure to cadmium induced gut antibiotic resistance genes (ARGs) and microbiota alternations of Babylonia areolata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161243. [PMID: 36587667 DOI: 10.1016/j.scitotenv.2022.161243] [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: 09/02/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Cadmium (Cd) is widely distributed in aquatic environments and has multiple adverse effects on aquatic organisms such as the ivory shell (Babylonia areolata). However, its effects on antibiotic resistance genes (ARGs) and gut microbiota of B. areolata remain unclear. In this study, we explored the effects of different concentrations (0, 0.03, 0.18 and 1.08 mg/L) of Cd on intestinal microbial communities and ARGs in B. areolata through 16S rRNA gene sequencing and high-throughput quantitative PCR. The results showed that the structure and diversity of ARGs and microbiota in B. areolata gut were altered upon Cd exposure. Tetracycline, Vancomycin and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were identified as the major ARGs in B. areolata gut. The absolute abundance and alpha diversity of ARGs in B. areolata gut increased with the rise of cadmium concentration. The microbial communities at genus level were enriched in the low and medium Cd concentration groups, while decreased in the high Cd concentration group compared to the control groups. In addition, the influence of microbiota on the ARG profile was more significant than that of Cd concentration and MGEs in B. areolata gut. Null model analysis demonstrated that stochastic processes dominated ARG assembly in the Cd-exposed groups and were enhanced with the increasing Cd concentrations. Four opportunistic bacterial pathogens (Bacteroides, Legionella, Acinetobacter and Escherichia) detected in B. areolata gut maybe the potential hosts of ARGs. Our findings provide references for the hazards assessment of environmental Cd exposure of gut microbiome in aquatic animals.
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Affiliation(s)
- Wang Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China; School of Marine Sciences, Ningbo University, Ningbo 315823, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China
| | - Weigeng Wen
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China
| | - Zhenghua Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, Ningbo 315823, China
| | - Zhenhua Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China.
| | - Gang Yu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Lingshui 572426, China.
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Dávalos A, García-de los Santos A. Five copper homeostasis gene clusters encode the Cu-efflux resistome of the highly copper-tolerant Methylorubrum extorquens AM1. PeerJ 2023; 11:e14925. [PMID: 36846457 PMCID: PMC9948745 DOI: 10.7717/peerj.14925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Background In the last decade, the use of copper has reemerged as a potential strategy to limit healthcare-associated infections and to control the spread of multidrug-resistant pathogens. Numerous environmental studies have proposed that most opportunistic pathogens have acquired antimicrobial resistance in their nonclinical primary habitat. Thus, it can be presumed that copper-resistant bacteria inhabiting a primary commensal niche might potentially colonize clinical environments and negatively affect the bactericidal efficacy of Cu-based treatments. The use of copper in agricultural fields is one of the most important sources of Cu pollution that may exert selection pressure for the increase of copper resistance in soil and plant-associated bacteria. To assess the emergence of copper-resistant bacteria in natural habitats, we surveyed a laboratory collection of bacterial strains belonging to the order Rhizobiales. This study proposes that Methylorubrum extorquens AM1 is an environmental isolate well adapted to thrive in copper-rich environments that could act as a reservoir of copper resistance genes. Methods The minimal inhibitory concentrations (MICs) of CuCl2 were used to estimate the copper tolerance of eight plant-associated facultative diazotrophs (PAFD) and five pink-pigmented facultative methylotrophs (PPFM) belonging to the order Rhizobiales presumed to come from nonclinical and nonmetal-polluted natural habitats based on their reported source of isolation. Their sequenced genomes were used to infer the occurrence and diversity of Cu-ATPases and the copper efflux resistome of Mr. extorquens AM1. Results These bacteria exhibited minimal inhibitory concentrations (MICs) of CuCl2 ranging between 0.020 and 1.9 mM. The presence of multiple and quite divergent Cu-ATPases per genome was a prevalent characteristic. The highest copper tolerance exhibited by Mr. extorquens AM1 (highest MIC of 1.9 mM) was similar to that found in the multimetal-resistant model bacterium Cupriavidus metallidurans CH34 and in clinical isolates of Acinetobacter baumannii. The genome-predicted copper efflux resistome of Mr. extorquens AM1 consists of five large (6.7 to 25.7 kb) Cu homeostasis gene clusters, three clusters share genes encoding Cu-ATPases, CusAB transporters, numerous CopZ chaperones, and enzymes involved in DNA transfer and persistence. The high copper tolerance and the presence of a complex Cu efflux resistome suggest the presence of relatively high copper tolerance in environmental isolates of Mr. extorquens.
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