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Ryu H, Kim S, Kim Y, Han JA, Kim EY, Lee HS. Complete genome sequence of Pseudomonas fluorescens IMGN2 isolated from undisturbed soil. Microbiol Resour Announc 2024; 13:e0045424. [PMID: 39206952 PMCID: PMC11465816 DOI: 10.1128/mra.00454-24] [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: 05/06/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Here, we report the complete genome sequence of Pseudomonas fluorescens IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotechnology, including genes related to secondary metabolite synthesis and plant-microbe interactions.
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Affiliation(s)
- Hyeonmin Ryu
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, South Korea
| | - Soomin Kim
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, South Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Yeongjun Kim
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, South Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Jeong A. Han
- Gyeonggido Agricultural Research & Extension Services, Hwaseong, South Korea
| | - Eun Yu Kim
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, South Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
- Environment Research Center Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ho-Seok Lee
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, South Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
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Gallegos MT, Garavaglia M, Valverde C. Small Regulatory RNAs of the Rsm Clan in Pseudomonas. Mol Microbiol 2024; 122:563-582. [PMID: 39282792 DOI: 10.1111/mmi.15313] [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: 06/13/2024] [Revised: 08/21/2024] [Accepted: 08/24/2024] [Indexed: 10/17/2024]
Abstract
Bacteria of the genus Pseudomonas are ubiquitous on Earth due to their great metabolic versatility and adaptation to fluctuating environments and different hosts. Some groups are important animal/human and plant pathogens, whereas others are studied for their biotechnological applications, including bioremediation, biological control of phytopathogens and plant growth promotion. Notably, their adaptability is mediated by various signal transduction systems, with the post-transcriptional Gac-Rsm cascade playing a key role. This pervasive Pseudomonas pathway controls major transitions at the population level, such as motile/sessile lifestyle, primary/secondary metabolism or replicative/infective behaviour. A hallmark of the Gac-Rsm cascade is the participation of small, regulatory, non-coding RNAs of the Rsm clan. These RNAs are synthetised in response to cell-density-dependent autoinducer signals channelled through the GacS/GacA two-component system, and they counteract, by molecular mimicry, the translational control that RNA-binding proteins of the RsmA family exert over hundreds of mRNAs. Rsm RNAs have been investigated in a few Pseudomonas model species, evidencing the presence of a variable number and families of genes depending on the taxonomic clade. However, the global picture of the distribution of these riboregulators at the genus level was unknown until now. We have undertaken a comprehensive survey and annotation of the vast array of gene sequences encoding members of the Rsm RNA clan in 245 complete genomes that cover 28 phylogenomic clades across the entire genus. The properties of the different families of rsm genes, their phylogenetic radiation, as well as the features of their promoters and adjacent regions, are discussed. The novel insights presented in our manuscript will significantly boost research on the biology of these prevalent RNAs in understudied species of the genus Pseudomonas and closely related genera.
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Affiliation(s)
- María Trinidad Gallegos
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Bioinsumos, Instituto de Biotecnología, Universidad Nacional de Hurlingham, Hurlingham, Buenos Aires, Argentina
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Burillo A, Bouza E. The evolution of knowledge for treating Gram-negative bacterial infections. Curr Opin Infect Dis 2024:00001432-990000000-00181. [PMID: 39259682 DOI: 10.1097/qco.0000000000001055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
PURPOSE OF REVIEW Infections caused by nonprimarily pathogenic Gram-negative bacilli (GNB) have been increasingly reported from the second half of the 20th century to the present. This phenomenon has expanded during the antibiotic era and in the presence of immunodeficiency.Before the discovery of sulphonamides and penicillin G, infections caused by GNB were rare compared to Gram-positive infections. The advent of anticancer therapy, the expansion of surgical procedures, the use of corticosteroids, and the implantation of prosthetic materials, along with better control of Gram-positive infections, have promoted the current increase in GNB infections.GNB have similar antimicrobial targets to Gram-positive bacteria. However, only antibiotics that can penetrate the double membrane of GNB and remain in them for a sufficient duration have antibacterial activity against them. RECENT FINDINGS Sulphonamides and early penicillins had limited activity against GNB. Ampicillin and subsequent beta-lactams expanded their spectrum to treat GNB. Aminoglycosides may re-surge with less toxic drugs, as highly resistant to beta-lactams GNB rise. Polymyxins, tetracyclines, and fluoroquinolones are also used for GNB. Combinations with other agents may be needed in specific cases, such as in the central nervous system and prostate, where beta-lactams may have difficulty reaching the infection site.Alternatives to current treatments must be sought in the discovery of new drug families and therapies such as phage therapy combined with antibiotics. SUMMARY Narrower-spectrum immunosuppressive therapies and antibiotics, antimicrobials that minimally intervene with the human microbiota, and instant diagnostic methods are necessary to imagine a future where currently dominant bacteria in infectious pathology lose their preeminence.
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Affiliation(s)
- Almudena Burillo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón
- Medicine Department, School of Medicine, Universidad Complutense de Madrid
- CIBER of Respiratory Diseases (CIBERES CB06/06/0058)
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón
- Medicine Department, School of Medicine, Universidad Complutense de Madrid
- CIBER of Respiratory Diseases (CIBERES CB06/06/0058)
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
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Abreu R, Mouro S, Guerreiro JF, Sousa SA, Leitão JH, Pissarra H, Cunha E, Tavares L, Oliveira M. Pseudomonas aestus Isolation from the Nasal Cavity of a Cat with Chronic Rhinitis. Vet Sci 2024; 11:382. [PMID: 39195836 PMCID: PMC11359275 DOI: 10.3390/vetsci11080382] [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: 06/21/2024] [Revised: 07/25/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024] Open
Abstract
The Pseudomonas genus includes ubiquitous bacteria frequently described as animal and human opportunistic pathogens. A 9-year-old cat was referred for rhinoscopy at the Veterinary Hospital of the Faculty of Veterinary Medicine, University of Lisbon, Portugal, for an investigation of the chronic respiratory signs. Upon rhinoscopy, nasal and nasopharyngeal discharge were observed, and the nasal turbinates showed signs of inflammation. The nasal biopsies were evaluated by histopathology and mycological and bacterial cultures. The histopathology revealed chronic lymphoplasmacytic inflammation. The mycological culture was negative, but the bacterial culture revealed the growth of a bacterial isolate in the pure culture, identified as P. aestus by the sequencing of a 1750 bp PCR amplicon obtained with BCR1 and BCR2 primers, followed by homologous sequences analysis using the NCBI database. The isolate's susceptibility profile towards 14 antimicrobials was evaluated through the disk diffusion method, being observed that it presented a multidrug resistance profile. The studies available on this environmental Pseudomonas strain focused on its potential use for biocide production and application in agricultural settings, and, to the authors' best knowledge, there are no reports describing its association with infectious diseases in humans or animals, highlighting the importance of establishing protocols aiming at the identification and characterization of non-traditional, multidrug-resistant Pseudomonas in the clinical setting.
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Affiliation(s)
- Raquel Abreu
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
| | - Sofia Mouro
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Joana F. Guerreiro
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
| | - Sílvia A. Sousa
- Department of Bioengineering, IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Associate Laboratory, i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Jorge H. Leitão
- Department of Bioengineering, IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Associate Laboratory, i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Hugo Pissarra
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
| | - Eva Cunha
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
| | - Luís Tavares
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
| | - Manuela Oliveira
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal (M.O.)
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisbon, Portugal
- cE3c—Centre for Ecology, Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
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Tao M, Cao K, Pu X, Hou Y, He L, Liu W, Ren Y, Yang X. Cadmium exposure induces changes in gut microbial composition and metabolic function in long-tailed dwarf hamsters, Cricetulus longicaudatus. Ecol Evol 2024; 14:e11682. [PMID: 38966245 PMCID: PMC11222731 DOI: 10.1002/ece3.11682] [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: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
Numerous studies have demonstrated that exposure to cadmium disrupts the diversity and composition of the gut microbiota, resulting in damage to organ tissue. However, there remains a lack of comprehensive understanding regarding the broader ecological reality associated with this phenomenon. In this study, we conducted a thorough evaluation of the effects of different concentrations of Cd (6, 12, 24, and 48 mg/L) over a period of 35 consecutive days on the organ viscera and the gut microbiota of long-tailed dwarf hamsters, Cricetulus longicaudatus (Rodentia: Cricetidae), using histopathological analysis, 16S rDNA, and metagenome sequencing. Our findings revealed that the results suggest that Cd exposure induced liver, spleen, and kidney damage, potentially leading to increased intestinal permeability and inflammation. These alterations were accompanied by significant perturbations in the gut microbiota composition, particularly affecting potentially pathogenic bacteria such as Prevotella and Treponema within the gut ecosystem. Consequently, host susceptibility to underlying diseases was heightened due to these changes. Notably though, Cd exposure did not significantly impact the overall structure of the gut microbiota itself. Additionally, Cd exposure induced significant changes in the metabolic functions, with the pathways related to disease and environmental information processing notably enhanced, possibly indicating stronger innate defense mechanisms against external injuries among wild mammals exposed to Cd. This study offers a novel approach to comprehensively evaluate the significant impact of Cd pollution on ecosystems by investigating both structural and functional alterations in the digestive system, as well as disruptions in intestinal flora among wild mammals.
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Affiliation(s)
- Mengfan Tao
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Kanglin Cao
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Xinsheng Pu
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Yu Hou
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Lei He
- Shanxi Forestry and Grassland General Engineering StationTaiyuanChina
| | - Wei Liu
- Shanxi Forestry and Grassland General Engineering StationTaiyuanChina
| | - Yue Ren
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Xin'gen Yang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
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Martin LC, O'Hare MA, Ghielmetti G, Twesigomwe D, Kerr TJ, Gumbo R, Buss PE, Kitchin N, Hemmings SMJ, Miller MA, Goosen WJ. Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana). Sci Rep 2024; 14:14768. [PMID: 38926469 PMCID: PMC11208578 DOI: 10.1038/s41598-024-65841-4] [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: 11/30/2023] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.
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Affiliation(s)
- Lauren C Martin
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Michaela A O'Hare
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Giovanni Ghielmetti
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 270, 8057, Zurich, Switzerland
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya J Kerr
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Rachiel Gumbo
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Peter E Buss
- South African National Parks, Veterinary Wildlife Services, Kruger National Park, Skukuza, South Africa
| | - Natasha Kitchin
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Unit, Cape Town, South Africa
| | - Michele A Miller
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Wynand J Goosen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
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Jones KR, Belden LK, Hughey MC. Priority effects alter microbiome composition and increase abundance of probiotic taxa in treefrog tadpoles. Appl Environ Microbiol 2024; 90:e0061924. [PMID: 38757977 PMCID: PMC11218634 DOI: 10.1128/aem.00619-24] [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: 03/29/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024] Open
Abstract
Host-associated microbial communities, like other ecological communities, may be impacted by the colonization order of taxa through priority effects. Developing embryos and their associated microbiomes are subject to stochasticity during colonization by bacteria. For amphibian embryos, often developing externally in bacteria-rich environments, this stochasticity may be particularly impactful. For example, the amphibian microbiome can mitigate lethal outcomes from disease for their hosts; however, this may depend on microbiome composition. Here, we examined the assembly of the bacterial community in spring peeper (Pseudacris crucifer) embryos and tadpoles. First, we reared embryos from identified mating pairs in either lab or field environments to examine the relative impact of environment and parentage on embryo and tadpole bacterial communities. Second, we experimentally inoculated embryos to determine if priority effects (i) could be used to increase the relative abundance of Janthinobacterium lividum, an amphibian-associated bacteria capable of preventing fungal infection, and (ii) would lead to observed differences in the relative abundances of two closely related bacteria from the genus Pseudomonas. Using 16S rRNA gene amplicon sequencing, we observed differences in community composition based on rearing location and parentage in embryos and tadpoles. In the inoculation experiment, we found that priority inoculation could increase the relative abundance of J. lividum, but did not find that either Pseudomonas isolate was able to prevent colonization by the other when given priority. These results highlight the importance of environmental source pools and parentage in determining microbiome composition, while also providing novel methods for the administration of a known amphibian probiotic. IMPORTANCE Harnessing the functions of host-associated bacteria is a promising mechanism for managing disease outcomes across different host species. In the case of amphibians, certain frog-associated bacteria can mitigate lethal outcomes of infection by the fungal pathogen Batrachochytrium dendrobatidis. Successful probiotic applications require knowledge of community assembly and an understanding of the ecological mechanisms that structure these symbiotic bacterial communities. In our study, we show the importance of environment and parentage in determining bacterial community composition and that community composition can be influenced by priority effects. Further, we provide support for the use of bacterial priority effects as a mechanism to increase the relative abundance of target probiotic taxa in a developing host. While our results show that priority effects are not universally effective across all host-associated bacteria, our ability to increase the relative abundance of specific probiotic taxa may enhance conservation strategies that rely on captive rearing of endangered vertebrates.
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Affiliation(s)
- Korin Rex Jones
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
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Iqbal O, Syed RN, Rajput NA, Wang Y, Lodhi AM, Khan R, Jibril SM, Atiq M, Li C. Antagonistic activity of two Bacillus strains against Fusarium oxysporum f. sp. capsici ( FOC-1) causing Fusarium wilt and growth promotion activity of chili plant. Front Microbiol 2024; 15:1388439. [PMID: 38860216 PMCID: PMC11163047 DOI: 10.3389/fmicb.2024.1388439] [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: 02/19/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
Fusarium oxysporum f. sp. capsici (Foc) poses a significant position in agriculture that has a negative impact on chili plant in terms of growth, fruit quality, and yield. Biological control is one of the promising strategies to control this pathogen in crops. Chili is considered as one of the most important crops in the Hyderabad region that is affected by Fusarium wilt disease. The pathogen was isolated from the infected samples in the region and was confirmed by morphological characteristics and PCR with a band of 488 bp. The bacterial strains were isolated from the rhizosphere soil of healthy plant and also confirmed by PCR with a band of 1,542 bp.The molecular characterization of the fungal and bacterial strain has shown 99.9% homology with the retrieved sequences of Fusarium oxysporum f. sp. capsici and Bacillus subtilis from NCBI. The 1-month-old Ghotki chili plants were inoculated with 1×105 cfu spore/ml-1 suspension and confirmed that the FOC-1 is responsible for chili Fusarium wilt disease. Subsequently, among the 33 screened Bacillus strains, only 11 showed antagonistic activity against F. oxysporum. Out of these, only two strains (AM13 and AM21) have shown maximum antagonistic activity against the pathogen by reducing the infection and promoting growth parameters of chili plants under both in vitro and greenhouse conditions. The study suggested that biological control is the most promising control strategy for the management of Fusarium wilt of chili in the field.
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Affiliation(s)
- Owais Iqbal
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rehana Naz Syed
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Nasir Ahmed Rajput
- Department of Plant Pathology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Abdul Mubeen Lodhi
- Department of Plant Protection, Faculty of Crop Protection, Sindh Agriculture University, Tando Jam, Pakistan
| | - Rizwan Khan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sauban Musa Jibril
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, Yunnan, China
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Mock MB, Summers RM. Microbial metabolism of caffeine and potential applications in bioremediation. J Appl Microbiol 2024; 135:lxae080. [PMID: 38549434 DOI: 10.1093/jambio/lxae080] [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: 09/08/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.
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Affiliation(s)
- Meredith B Mock
- Department of Chemical and Biological Engineering, The University of Alabama, Box 870203, Tuscaloosa, AL 35487, United States
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Box 870203, Tuscaloosa, AL 35487, United States
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Perelomov L, Rajput VD, Gertsen M, Sizova O, Perelomova I, Kozmenko S, Minkina T, Atroshchenko Y. Ecological features of trace elements tolerant microbes isolated from sewage sludge of urban wastewater treatment plant. STRESS BIOLOGY 2024; 4:8. [PMID: 38273092 PMCID: PMC10810767 DOI: 10.1007/s44154-023-00144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024]
Abstract
Worldwide wastewater treatment plants generate enormous amounts of sewage sludge, and their further disposal depends on the treatment technologies applied and spontaneously occurring microbiological processes. From different ages urban sewage sludge, 12 strains of bacteria with simultaneous tolerance to two or more trace elements: Co, Ni, Cu, Zn, Cd and Pb at concentration of 3-5 mmol were isolated and identified by PCR of target genes and Sanger sequencing methods. The isloated metal(loids) tolerant strains belong to the species, i.e., Serratia fonticola, Rhodococcus qingshengii, Pseudomonas fragi, Pseudomonas extremaustralis, Pseudomonas cedrina, Stenotrophomonas maltophilia, Serratia liquefaciens and Citrobacter freundii. The ecological features of the isolated strains were studied. The optimal growth temperatures for most strains was 15-30°C at pH range of 5-9, although some strains grew at 7°C (Pseudomonas fragi SS0-4, Serratia fonticola SS0-9 and Serratia fonticola SS12-11). Satisfactory growth of two strains (Serratia fonticola SS0-1and Citrobacter freundii SS60-12) was noted in an acidic medium at pH 4. Most of the strains grew in the NaCl concentration range of 1-5%. The isolated bacteria resistant to high concentrations of trace elements can be used for the effective mineralization of sewage sludge and for the decontamination of wastewater.
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Affiliation(s)
- L Perelomov
- Tula State Lev Tolstoy Pedagogical University (Lev Tolstoy University), Lenin Avenue, 125, Tula, 300026, Russia.
| | - V D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - M Gertsen
- Tula State Lev Tolstoy Pedagogical University (Lev Tolstoy University), Lenin Avenue, 125, Tula, 300026, Russia
| | - O Sizova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
| | - I Perelomova
- Tula State University, Lenin Avenue, 92, Tula, 300026, Russia
| | - S Kozmenko
- Tula State Lev Tolstoy Pedagogical University (Lev Tolstoy University), Lenin Avenue, 125, Tula, 300026, Russia
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - T Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Y Atroshchenko
- Tula State Lev Tolstoy Pedagogical University (Lev Tolstoy University), Lenin Avenue, 125, Tula, 300026, Russia
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11
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Bloomfield SJ, Palau R, Holden ER, Webber MA, Mather AE. Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection. BMC Microbiol 2024; 24:20. [PMID: 38212698 PMCID: PMC10782663 DOI: 10.1186/s12866-023-03153-9] [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: 07/09/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Pseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans. RESULTS A non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41-312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19-67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control. CONCLUSION The most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.
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Affiliation(s)
| | - Raphaёlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- University of East Anglia, Norwich, UK.
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12
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [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: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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13
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El Fakhouri K, Ramdani C, Aasfar A, Boulamtat R, Sijilmassi B, El Bouhssini M, Kadmiri IM. Isolation, identification and pathogenicity of local entomopathogenic bacteria as biological control agents against the wild cochineal Dactylopius opuntiae (Cockerell) on cactus pear in Morocco. Sci Rep 2023; 13:21647. [PMID: 38062128 PMCID: PMC10703873 DOI: 10.1038/s41598-023-48976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
The Opuntia ficus-indica (L.) cactus, a crucial crop in Morocco, is threatened by the wild cochineal, Dactylopius opuntiae (Cockerell). The aim of this research was to investigate the efficacy of nine bacterial strains against both D. opuntiae nymphs and adults females applied individually or after black soap in the laboratory, greenhouse, and field conditions. Using the partial 16S ribosomal DNA, the bacterial isolates were identified as Pseudomonas koreensis, Pseudomonas sp., Burkholderia sp. and Bacillus sp. Under laboratory conditions, the insecticidal activity of P. koreensis strain 66Ms.04 showed the level mortality (88%) of adult females' at 108 CFU/mL, 7 days after application. At a concentration of 108 CFU/mL, P. koreensis strain 66Ms.04 and Pseudomonas sp. (strains 37 and 5) caused 100% nymphs mortality rate three days after application. Under greenhouse conditions, the use of P. koreensis strain 66Ms.04 at 108 CFU/mL following the application of black soap (60 g/L) demonstrated the maximum levels of females and nymphs' mortalities with 80 and 91.25%, respectively, after 8 days of treatment. In field conditions, the combined application of the P. koreensis strain 66Ms.04 at 108 CFU/mL with black soap at 60 g/L, for an interval of 7 days, significantly increased the mortality of adult females to 93.33% at 7 days after the second application. These findings showed that the combined treatment of P. koreensis strain 66Ms.04 with black soap can be a potent and eco-friendly pesticide against D. opuntiae.
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Affiliation(s)
- Karim El Fakhouri
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco.
| | - Chaimae Ramdani
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Abderrahim Aasfar
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Rachid Boulamtat
- Entomology Laboratory, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Badreddine Sijilmassi
- Rhizobium Laboratory, Genetic Resources Section, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Mustapha El Bouhssini
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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14
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Gundersen MS, Fiedler AW, Bakke I, Vadstein O. The impact of phage treatment on bacterial community structure is minor compared to antibiotics. Sci Rep 2023; 13:21032. [PMID: 38030754 PMCID: PMC10687242 DOI: 10.1038/s41598-023-48434-5] [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: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 12/01/2023] Open
Abstract
Phage treatment is suggested as an alternative to antibiotics; however, there is limited knowledge of how phage treatment impacts resident bacterial community structure. When phages induce bacterial lysis, resources become available to the resident community. Therefore, the density of the target bacterium is essential to consider when investigating the effect of phage treatment. This has never been studied. Thus, we invaded microcosms containing a lake-derived community with Flavobacterium columnare strain Fc7 at no, low or high densities, and treated them with either the bacteriophage FCL-2, the antibiotic Penicillin or kept them untreated (3 × 3 factorial design). The communities were sampled over the course of one week, and bacterial community composition and density were examined by 16S rDNA amplicon sequencing and flow cytometry. We show that phage treatment had minor impacts on the resident community when the host F. columnare Fc7 of the phage was present, as it caused no significant differences in bacterial density α- and β-diversity, successional patterns, and community assembly. However, a significant change was observed in community composition when the phage host was absent, mainly driven by a substantial increase in Aquirufa. In contrast, antibiotics induced significant changes in all community characteristics investigated. The most crucial finding was a bloom of γ-proteobacteria and a shift from selection to ecological drift dominating community assembly. This study investigated whether the amount of a bacterial host impacted the effect of phage treatment on community structure. We conclude that phage treatment did not significantly affect the diversity or composition of the bacterial communities when the phage host was present, but introduced changes when the host was absent. In contrast, antibiotic treatment was highly disturbing to community structure. Moreover, higher amounts of the bacterial host of the phage increased the contribution of stochastic community assembly and resulted in a feast-famine like response in bacterial density in all treatment groups. This finding emphasises that the invader density used in bacterial invasion studies impacts the experimental reproducibility. Overall, this study supports that phage treatment is substantially less disturbing to bacterial communities than antibiotic treatments.
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Affiliation(s)
- Madeleine S Gundersen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Alexander W Fiedler
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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15
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Di DYW, Cao G, Zhong C, Yan T. Diversity of bla POM in carbapenem-resistant opportunistic pathogenic Pseudomonas otitidis in municipal wastewater. JOURNAL OF WATER AND HEALTH 2023; 21:560-570. [PMID: 37254905 PMCID: wh_2023_255 DOI: 10.2166/wh.2023.255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metallo-β-lactamases (MBLs) encoding carbapenem resistance in wastewater are a well-known serious threat to human health. Twelve Pseudomonas otitidis isolates obtained from a municipal wastewater treatment plant (WWTP) in Hawaii were found to possess a subclass B3 MBL - POM (P. otitidis MBL), with a minimum inhibition concentration (MIC) range of 8-16 mg/L. The unrooted neighbor-joining phylogenetic tree showed that these blaPOM genes isolated in wastewater samples (n = 12) were distinctly different from other reference genes isolated from clinical, freshwater, animal, and soil samples except for isolates MR7, MR8, and MR11. MR7, MR8, and MR11 were found to have 4, 3, and 3 amino acid substitutions when compared to the type strain MC10330T and were closely clustered to the clinical reference genes. The meropenem hydrolysis experiment showed that isolates with multiple amino acid substitutions completely hydrolyzed 64 mg/L of meropenem in 7 h. The emergence of the opportunistic pathogen P. otitidis chromosomally encoding blaPOM in the treated municipal wastewater is an alarming call for the spread of this MBL in the environment. Further studies are required to understand the mechanism and regulation of this carbapenem-resistant β-lactamase in order to fill in the knowledge gap.
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Affiliation(s)
- Doris Yoong Wen Di
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA E-mail: ; D.Y.W.D. and G.X.C contributed equally to the manuscript
| | - Guangxiang Cao
- School of Biomedical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, China; D.Y.W.D. and G.X.C contributed equally to the manuscript
| | - Chuanqing Zhong
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan 250101, China
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA E-mail: ; Water Resources Research Center, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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16
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Huang Q, Huang Y, Li B, Li X, Guo Y, Jiang Z, Liu X, Yang Z, Ning Z, Xiao T, Jiang C, Hao L. Metagenomic analysis characterizes resistomes of an acidic, multimetal(loid)-enriched coal source mine drainage treatment system. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130898. [PMID: 36731323 DOI: 10.1016/j.jhazmat.2023.130898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/07/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal(loid) contaminations caused by mine activities are potential hot spots of antibiotic resistance genes (ARGs) because of heavy metal(loid)-induced co-selection of ARGs and heavy metal(loid) resistance genes (MRGs). This study used high-throughput metagenomic sequencing to analyze the resistome characteristics of a coal source acid mine drainage passive treatment system. The multidrug efflux mechanism dominated the antibiotic resistome, and a highly diverse heavy metal(loid) resistome was dominated by mercury-, iron-, and arsenic--associated resistance. Correlation analysis indicated that mobile gene elements had a greater influence on the dynamic of MRGs than ARGs. Among the metagenome-assembled genomes, six potential pathogens carrying multiple resistance genes resistant to several antibiotics and heavy metal(loid)s were recovered. Pseudomonas spp. contained the highest numbers of resistance genes, with resistance to two types of antibiotics and 12 types of heavy metal(loid)s. Thus, high contents of heavy metal(loid)s drove the co-selection of ARGs and MRGs. The occurrence of potential pathogens containing multiple resistance genes might increase the risk of ARG dissemination in the environment.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuan Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaoling Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhenni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Tangfu Xiao
- Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, PR China.
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17
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Quddus S, Liaqat Z, Azam S, Haq MU, Ahmad S, Alharbi M, Khan I. Identification of Efflux Pump Mutations in Pseudomonas aeruginosa from Clinical Samples. Antibiotics (Basel) 2023; 12:antibiotics12030486. [PMID: 36978353 PMCID: PMC10044530 DOI: 10.3390/antibiotics12030486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Efflux pumps are a specialized tool of antibiotic resistance used by Pseudomonas aeruginosa to expel antibiotics. The current study was therefore conducted to examine the expression of MexAB-OprM and MexCD-OprJ efflux pump genes. In this study, 200 samples were collected from Khyber Teaching Hospital (KTH) and Hayatabad Medical Complex (HMC) in Peshawar, Pakistan. All the isolates were biochemically identified by an Analytical Profile Index kit and at the molecular level by Polymerase Chain Reaction (PCR) utilizing specific primers for the OprL gene. A total of 26 antibiotics were tested in the current study using the guidelines of the Clinical and Laboratory Standard Institute (CLSI) and high-level resistance was shown to amoxicillin-clavulanic acid (89%) and low-level to chloramphenicol (1%) by the isolates. The antibiotic-resistant efflux pump genes MexA, MexB, OprM, MexR, MexC, MexD, OprJ, and NfxB were detected in 178 amoxicillin-clavulanic acid-resistant isolates. Mutations were detected in MexA, MexB, and OprM genes but no mutation was found in the MexR gene as analyzed by I-Mutant software. Statistical analysis determined the association of antibiotics susceptibility patterns by ANOVA: Single Factor p = 0.05. The in silico mutation impact on the protein structure stability was determined via the Dynamut server, which revealed the mutations might increase the structural stability of the mutants. The docking analysis reported that MexA wild protein showed a binding energy value of −6.1 kcal/mol with meropenem and the mexA mutant (E178K) value is −6.5 kcal/mol. The mexB wild and mutant binding energy value was −5.7 kcal/mol and −8.0 kcal/mol, respectively. Efflux pumps provide resistance against a wide range of antibiotics. Determining the molecular mechanisms of resistance in P. aeruginosa regularly will contribute to the efforts against the spread of antibiotic resistance globally.
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Affiliation(s)
- Sonia Quddus
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Zainab Liaqat
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Sadiq Azam
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
| | - Sajjad Ahmad
- Department of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24060, USA
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ibrar Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
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18
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Reyes BMD, Fonseca PLC, Heming NM, Conceição LBDA, Nascimento KTDS, Gramacho KP, Arevalo-Gardini E, Pirovani CP, Aguiar ERGR. Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species. Front Microbiol 2023; 13:1053562. [PMID: 36817107 PMCID: PMC9936985 DOI: 10.3389/fmicb.2022.1053562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/23/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized. Methods Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri. Results Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements. Discussion To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.
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Affiliation(s)
| | - Paula Luize Camargos Fonseca
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Neander Marcel Heming
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | | | - Karina Peres Gramacho
- Centro de Pesquisas do Cacau, Comissão Executivo do Plano da Lavoura Cacaueira, CEPEC/CEPLAC, Rodovia Ilhéus-Itabuna, Ilhéus, Brazil
| | - Enrique Arevalo-Gardini
- Instituto de Cultivos Tropicales, Tarapoto, Peru,Universidad Nacional Autónoma de Alto Amazonas, Yurimaguas, Peru
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,*Correspondence: Eric Roberto Guimarães Rocha Aguiar, ✉
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Abreu-Acosta N, Pino-Vera R, Izquierdo-Rodríguez E, Afonso O, Foronda P. Zoonotic Bacteria in Anolis sp., an Invasive Species Introduced to the Canary Islands (Spain). Animals (Basel) 2023; 13:414. [PMID: 36766304 PMCID: PMC9913382 DOI: 10.3390/ani13030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Lizards belonging to the genus Anolis are native to America and have been introduced in many parts of the world. In this work, a gastrointestinal microbiological analysis from Anolis sp. introduced to Tenerife, Canary Island, was carried out. A total of 74 individuals were analyzed by culture and molecular tools. Pseudomonas spp. was the most prevalent bacteria isolated (64.3%), followed by enteropathogenic Escherichia coli with at least one of the investigated virulent genes (stx1, stx2, and eae) (44.6%). The stx2 gene was more prevalent which differs to that reported in other reptiles, probably due to wastewater transmission. Campylobacter spp. was detected in 32.4% of the animals, highlighting the detection of C. jejuni and C. fetus by their relevance to public health. The zoonotic Staphylococcus lugdunensis, found in 14.9% of the animals, was firstly detected in reptiles. Vibrio sp. which is more associated with aquatic environments was found in 10.8% of the lizards in this study, with Vibrio cholerae being found in two of the animals. The prevalence of Salmonella sp. (5.4%) was low, compared with other studies carried out in reptiles. These results indicate that Anolis sp. in Tenerife could be playing a role in the maintenance and spread of the pathogens detected, being a possible risk factor for public health and biodiversity conservation.
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Affiliation(s)
- Néstor Abreu-Acosta
- Nertalab S.L.U. Santa Cruz de Tenerife, Tenerife, 38001 Canary Islands, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
| | - Román Pino-Vera
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
- Department Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
| | - Elena Izquierdo-Rodríguez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
- Department Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
| | - Oscar Afonso
- Área de Medio Ambiente, Gestión y Planeamiento Territorial y Ambiental (Gesplan), Santa Cruz de Tenerife, Tenerife, 38200 Canary Islands, Spain
| | - Pilar Foronda
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
- Department Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Tenerife, 38200 Canary Islands, Spain
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20
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A Review of Pseudomonas aeruginosa Metallophores: Pyoverdine, Pyochelin and Pseudopaline. BIOLOGY 2022; 11:biology11121711. [PMID: 36552220 PMCID: PMC9774294 DOI: 10.3390/biology11121711] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
P. aeruginosa is a common Gram-negative bacterium found in nature that causes severe infections in humans. As a result of its natural resistance to antibiotics and the ability of biofilm formation, the infection with this pathogen can be therapeutic challenging. During infection, P. aeruginosa produces secondary metabolites such as metallophores that play an important role in their virulence. Metallophores are metal ions chelating molecules secreted by bacteria, thus allowing them to survive in the host under metal scarce conditions. Pyoverdine, pyochelin and pseudopaline are the three metallophores secreted by P. aeruginosa. Pyoverdines are the primary siderophores that acquire iron from the surrounding medium. These molecules scavenge and transport iron to the bacterium intracellular compartment. Pyochelin is another siderophore produced by this bacterium, but in lower quantities and its affinity for iron is less than that of pyoverdine. The third metallophore, pseudopaline, is an opine narrow spectrum ion chelator that enables P. aeruginosa to uptake zinc in particular but can transport nickel and cobalt as well. This review describes all the aspects related to these three metallophore, including their main features, biosynthesis process, secretion and uptake when loaded by metals, in addition to the genetic regulation responsible for their synthesis and secretion.
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21
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Yang K, Wang L, Cao X, Gu Z, Zhao G, Ran M, Yan Y, Yan J, Xu L, Gao C, Yang M. The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA. Int J Mol Sci 2022; 23:13690. [PMID: 36430193 PMCID: PMC9698649 DOI: 10.3390/ijms232213690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
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Affiliation(s)
- Kaixin Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lishuang Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xinghong Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaorui Gu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guowei Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengqu Ran
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chunhui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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22
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Rudra B, Duncan L, Shah AJ, Shah HN, Gupta RS. Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36355412 DOI: 10.1099/ijsem.0.005542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The strains of
Pseudomonas aeruginosa
exhibit considerable differences in their genotypic and pathogenic properties. To clarify their evolutionary/taxonomic relationships, comprehensive phylogenomic and comparative genomic studies were conducted on the genome sequences of 212
P
.
aeruginosa
strains covering their genetic diversity. In a phylogenomic tree based on 118 conserved proteins, the analysed strains formed two distinct clades. One of these clades, Clade-1, encompassing >70 % of the strains including the type strain DSM 50071T, represents the species P. aeruginosa sensu stricto. Clade-2, referred to in earlier work as the outlier group, with NCTC 13628T as its type strain, constitutes a novel species level lineage. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the strains from Clade-1 and Clade-2 are in the range of 93.4–93.7, 95.1–95.3 and 52–53 %, respectively. The 16S rRNA gene of
P. aeruginosa
DSM 50071T also shows 98.3 % similarity to that of NCTC 13628T. These values are lower than the suggested cut-off values for species distinction, indicating that the Clade-2 strains (NCTC 13628T) constitute a new species. We also report the identification of 12 conserved signature indels in different proteins and 24 conserved signature proteins that are exclusively found in either Clade-1 or Clade-2, providing a reliable means for distinguishing these clades. Additionally, in contrast to swimming motility, twitching motility is only present in Clade-1 strains. Based on earlier work, the strains from these two clades also differ in their pathogenic mechanisms (presence/absence of Type III secretion system), production of biosurfactants, phenazines and siderophores, and several other genomic characteristics. Based on the evidence from different studies, we propose that the Clade-2 strains constitute a novel species for which the name Pseudomonas paraeruginosa is proposed. The type strain is NCTC 13628T (=PA7T=ATCC 9027T). The description of
Pseudomonas aeruginosa
is also emended to include information for different molecular markers specific for this species.
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
| | - Louise Duncan
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NH, UK
| | - Ajit J Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Haroun N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
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23
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Gerasimchuk AI, Ivasenko DA, Kasymova AA, Frank YA. Selective cultivation of bacterial strains with lipolytic and hydrocarbon-oxidizing activity from bottom sediments of the Ob River, Western Siberia. Vavilovskii Zhurnal Genet Selektsii 2022; 26:449-457. [PMID: 36128566 PMCID: PMC9450031 DOI: 10.18699/vjgb-22-55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
Bacteria play a key role in biogeochemical cycles in natural and anthropogenic ecosystems. In river ecosystems, bacteria intensively colonize silt sediments. Microorganisms are essential for energy conversion, biogeochemical nutrient cycling, pollutant degradation, and biotransformation of organic matter; therefore, bottom sediments can be a source of metabolically diverse microorganisms, including those with promise for industrial biotechnologies. The aim of this work was to isolate and study pure cultures of microorganisms – producers of industrially important enzymes and decomposers of organic matter – from bottom sediments of the Ob River. Pork fat and diesel fuel were used as substrates to obtain enrichment and pure cultures for selective cultivation of bacteria with lipolytic and hydrocarbon-oxidizing activity. A total of 21 pure cultures were isolated. The phylogenetic position of the obtained bacterial isolates was determined based on the analysis of 16S rRNA gene sequences. The strains isolated on selective media belonged to representatives of the genera Pseudomonas and Aeromonas (Gammaproteobacteria), and the genus Microvirgula (Betaproteobacteria). The ability of strains to grow on culture media containing pork fat, olive oil and diesel fuel was analyzed. The lipolytic activity of the isolates was evidenced by cultivation on a diagnostic medium containing 1 % tributyrin. The phylogenetic and metabolic diversity of the cultivated non-pathogenic bacterial strains with lipolytic and oil-oxidizing activity revealed in the study indicates the biotechnological potential of the isolates. The most promising strains were M. aerodenitrificans sp. LM1 and P. lini sp. KGS5K3, which not only exhibited lipolytic activity on the diagnostic medium with tributyrin in a wide temperature range, but also utilized diesel fuel, pork fat and olive oil.
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24
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Hu S, Li X, Yin X, Li R, Zhang R, Zang J, Liu Y. Species-specific identification of Pseudomonas based on 16S-23S rRNA gene internal transcribed spacer (ITS) and its combined application with next-generation sequencing. BMC Microbiol 2022; 22:188. [PMID: 35915434 PMCID: PMC9341087 DOI: 10.1186/s12866-022-02607-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Pseudomonas species are widely distributed in the human body, animals, plants, soil, fresh water, seawater, etc. Pseudomonas aeruginosa is one of the main pathogens involved in nosocomial infections. It can cause endocarditis, empyema, meningitis, septicaemia and even death. However, the Pseudomonas classification system is currently inadequate and not well established. Results In this study, the whole genomes of 103 Pseudomonas strains belonging to 62 species available in GenBank were collected and the specificity of the 16S–23S ribosomal RNA internal transcribed spacer (ITS) sequence was analysed. Secondary structures of ITS transcripts determining where the diversity bases were located were predicted. The alignment results using BLAST indicated that the ITS sequence is specific for most species in the genus. The remaining species were identified by additional frequency analyses based on BLAST results. A double-blind experiment where 200 ITS sequences were randomly selected indicated that this method could identify Pseudomonas species with 100% sensitivity and specificity. In addition, we applied a universal primer to amplify the Pseudomonas ITS of DNA extracts from fish samples with next-generation sequencing. The ITS analysis results were utilized to species-specifically identify the proportion of Pseudomonas species in the samples. Conclusions The present study developed a species-specific method identification and classification of Pseudomonas based on ITS sequences combined NGS. The method showed its potential application in other genera. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02607-w.
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Affiliation(s)
- Shuqian Hu
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Xiang Li
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Xin Yin
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Runmeng Li
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Ruiyang Zhang
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Junhao Zang
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Yin Liu
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
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25
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Circella E, Casalino G, Camarda A, Schiavone A, D'Amico F, Dimuccio MM, Pugliese N, Ceci E, Romito D, Bozzo G. <em>Pseudomonas fluorescens</em> group bacteria as responsible for chromatic alteration on rabbit carcasses. Possible hygienic implications. Ital J Food Saf 2022; 11:9998. [PMID: 35795461 PMCID: PMC9251874 DOI: 10.4081/ijfs.2022.9998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/21/2022] [Indexed: 11/23/2022] Open
Abstract
Bacteria belonging to the genus Pseudomonas are ubiquitous and characterized by a high adaptation capability to different environmental conditions and wide range of temperatures. They may colonize food, sometimes causing alteration. Quite recently, a blue pigmentation due to Pseudomonas fluorescens has been widely reported in mozzarella cheese. In this report, we describe a blue coloration occurred on rabbit meat stored in the refrigeration cell of a slaughterhouse. The alteration was observed after about 72 hours of storage at 4-6°C. Bacteriological analyses were performed, and a microorganism included in the Pseudomonas fluorescens group was identified. The experimental contamination was planned, using a bacterial suspension with 1×108 UFC/ml load to spread on rabbit carcasses. The blue pigmentation appeared after 24 hours of storage in a cell with the same conditions of temperature. The bacterium was reisolated and identified as responsible for the alteration on meat. These findings highlight the importance of considering the members of the genus Pseudomonas and, more specifically, of the P. fluorescens group when the microbiological quality of food is to be ascertained. In fact, even if these bacteria are not considered a public health problem, their presence should be monitored by food industry operators in self-control plans because they may cause alteration in food. In fact, any altered product should be withdrawn from the market in agreement with Regulation (EC) No 178/2002 of the European Parliament and of the Council.
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26
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Zhang N, He J, Muhammad A, Shao Y. CRISPR/Cas9–Mediated Genome Editing for Pseudomonas fulva, a Novel Pseudomonas Species with Clinical, Animal, and Plant–Associated Isolates. Int J Mol Sci 2022; 23:ijms23105443. [PMID: 35628253 PMCID: PMC9145825 DOI: 10.3390/ijms23105443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022] Open
Abstract
As one of the most widespread groups of Gram–negative bacteria, Pseudomonas bacteria are prevalent in almost all natural environments, where they have developed intimate associations with plants and animals. Pseudomonas fulva is a novel species of Pseudomonas with clinical, animal, and plant–associated isolates, closely related to human and animal health, plant growth, and bioremediation. Although genetic manipulations have been proven as powerful tools for understanding bacterial biological and biochemical characteristics and the evolutionary origins, native isolates are often difficult to genetically manipulate, thereby making it a time–consuming and laborious endeavor. Here, by using the CRISPR–Cas system, a versatile gene–editing tool with a two–plasmid strategy was developed for a native P. fulva strain isolated from the model organism silkworm (Bombyx mori) gut. We harmonized and detailed the experimental setup and clarified the optimal conditions for bacteria transformation, competent cell preparation, and higher editing efficiency. Furthermore, we provided some case studies, testing and validating this approach. An antibiotic–related gene, oqxB, was knocked out, resulting in the slow growth of the P. fulva deletion mutant in LB containing chloramphenicol. Fusion constructs with knocked–in gfp exhibited intense fluorescence. Altogether, the successful construction and application of new genetic editing approaches gave us more powerful tools to investigate the functionalities of the novel Pseudomonas species.
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Affiliation(s)
- Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Abrar Muhammad
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Hangzhou 310058, China
- Correspondence: ; Fax: +86-571-88982757
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27
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Abstract
A novel Gram-stain-negative, rod-shaped, aerobic and motile bacterium designated strain UL073T was isolated from a forest soil of an island, and subjected to taxonomic characterization. Strain UL073T grew at 10–37 °C (optimum, 30 °C), at pH 5.0–10.0 (optimum, pH 7.0) and in the presence of 0–3 % NaCl (optimum, 0 %), respectively. Strain UL073T showed the highest sequence similarity to
Pseudomonas lalkuanensis
PE08T based on 16S rRNA gene analysis with a sequence similarity of 98.08 %, which was well below the suggested cutoff for species distinction. The 16S rRNA gene tree as well as the multilocus sequence analysis and genome-based trees indicated the independent taxonomic position of strain UL073T, and the orthologous average nucleotide identity and in silico DNA–DNA hybridization values between strain UL073T and related species were no higher than 84.7 and 28.3% respectively, thus confirming the distinctive taxonomic position of the strain. The chemotaxonomic properties were consistent with those of the genus, as the major fatty acids of the strain were a summed feature consisting of C18 : 1 ω7c/C18 : 1 ω6c (31.4 %), another summed feature consisting of C16 : 1 ω7c/C16 : 1 ω6c (23.1 %), and C16 : 0 (22.0 %), the major respiratory quinone was ubiquinone 9, and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genome size and DNA G+C content of strain UL073T were 4.87 Mbp and 65.9 mol%. On the basis of phenotypic and phylogenetic evidence, strain UL073T should be classified as representing a novel species of
Pseudomonas
, for which the name Pseudomonas insulae sp. nov. (type strain=UL073T=KCTC 82407T=JCM 34511T) is proposed.
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28
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Khanal M, Timilsina S, Bhatta BP, Bophela K, Coutinho T, Cochran K, Malla S. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int J Syst Evol Microbiol 2022; 72. [PMID: 35442877 DOI: 10.1099/ijsem.0.005311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20T (99.3 %), Pseudomonas corrugata CFBP 2431T (99.2 %), and Pseudomonas viciae 11K1T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172T represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172T (=NCIMB 15426T=CIP 112022T).
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA.,Present address: Charles River Laboratories, Newark, DE, USA
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Khumbuzile Bophela
- Department of Plant and Soil Sciences, University of Pretoria, 0002 Pretoria, South Africa
| | - Teresa Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa
| | - Kimberly Cochran
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
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29
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Association between Consumption of Fluoroquinolones and Carbapenems and Their Resistance Rates in Pseudomonas aeruginosa in Argentina. Interdiscip Perspect Infect Dis 2022; 2022:3924212. [PMID: 35154314 PMCID: PMC8828346 DOI: 10.1155/2022/3924212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Background. Irrational use of antimicrobials (ATMs) triggers microbial resistance (AMR) which has severe consequences for human health. ATM consumption varies among countries and within each territory. These data should be known, in order to perform local policies towards AMR reduction. This work aimed to expose the association of the level of consumption of carbapenems and fluoroquinolones with their resistance rates in Pseudomonas aeruginosa in Argentina. Method. Consumption of antimicrobials was expressed by defined daily dose (DDD)/1000 inhabitants for each ATM during one year period, discriminating by each country region. Resistance of P. aeruginosa to carbapenems/fluoroquinolones groups was recorded. Consumption/resistance ratio “R” was calculated for each region of the country, comparing results with other countries. Results. P. aeruginosa resistance rate to fluoroquinolone (F) was 26.4% in blood samples and 29.7% in urine samples, whereas resistance rates to carbapenems (C) were 19.9 and 17.7% in blood and urine, respectively. Correlation between consumption and resistance was demonstrated for both antimicrobials (C : R = 0.58;
and F : R = 0.77;
). Great fluctuations of resistance levels were seen among regions within the country, always correlating resistance with areas in which a higher level of ATM consumption was detected. Conclusion. P. aeruginosa resistance to fluoroquinolone/carbapenems in Argentina directly correlated with antimicrobial consumption levels. A great heterogeneity in resistance profile was observed among areas where ATMs were widely used. Global data at the national level might mask local realities that require specific health policies in order to control the irrational use of ATMs.
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30
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Zhang P, Dong X, Zhou K, Zhu T, Liang J, Shi W, Gao M, Feng C, Li Q, Zhang X, Ren P, Lu J, Lin X, Li K, Zhu M, Bao Q, Zhang H. Characterization of a Novel Chromosome-Encoded AmpC β-Lactamase Gene, blaPRC–1, in an Isolate of a Newly Classified Pseudomonas Species, Pseudomonas wenzhouensis A20, From Animal Farm Sewage. Front Microbiol 2021; 12:732932. [PMID: 34975778 PMCID: PMC8719060 DOI: 10.3389/fmicb.2021.732932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022] Open
Abstract
In this work, we characterized a novel chromosome-encoded AmpC β-lactamase gene, blaPRC–1, in an isolate of a newly classified Pseudomonas species designated Pseudomonas wenzhouensis A20, which was isolated from sewage discharged from an animal farm in Wenzhou, China. Susceptibility testing, molecular cloning, and enzyme kinetic parameter analysis were performed to determine the function and enzymatic properties of the β-lactamase. Sequencing and comparative genomic analysis were conducted to clarify the phylogenetic relationship and genetic context of the blaPRC–1 gene. PRC-1 is a 379-amino acid AmpC β-lactamase with a molecular weight of 41.48 kDa and a predicted pI of 6.44, sharing the highest amino acid identity (57.7%) with the functionally characterized AmpC β-lactamase PDC-211 (ARX71249). blaPRC–1 confers resistance to many β-lactam antibiotics, including penicillins (penicillin G, amoxicillin, and amoxicillin-clavulanic acid) and cephalosporins (cefazolin, ceftriaxone, and cefotaxime). The kinetic properties of PRC-1 were compatible with those of a typical class C β-lactamase showing hydrolytic activities against β-lactam antibiotics, and the hydrolytic activity was strongly inhibited by avibactam. The genetic context of blaPRC–1 was relatively conserved, and no mobile genetic element was predicted in its surrounding region. Identification of a novel β-lactamase gene in an unusual environmental bacterium reveals that there might be numerous unknown resistance mechanisms in bacterial populations, which may pose potential risks to human health due to universal horizontal gene transfer between microorganisms. It is therefore of great value to carry out extensive research on the mechanism of antibiotic resistance.
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Affiliation(s)
- Peiyao Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kexin Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tingting Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jialei Liang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ping Ren
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
- *Correspondence: Mei Zhu,
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Ministry of Education, Wenzhou Medical University, Wenzhou, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Qiyu Bao,
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Hailin Zhang,
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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32
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Oberlé K, Bouju-Albert A, Helsens N, Pangga G, Prevost H, Magras C, Calvez S. No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2021; 132:1738-1750. [PMID: 34719087 PMCID: PMC9299046 DOI: 10.1111/jam.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022]
Abstract
AIMS Study the relationship between antibiotic resistance patterns of Pseudomonas isolated from farmed rainbow trout fillets and farm or transformation process locations. METHODS AND RESULTS Pseudomonas strains were isolated from rainbow trout sampled in two differently located farms and filleted in laboratory or in a processing factory. One hundred and twenty-five isolates were confirmed as belonging to Pseudomonas using CFC selective media, Gram staining, oxidase test and quantitative polymerase chain reaction methods. Fifty-one isolates from separate fish fillets were further identified using MALDI-TOF mass spectrometry, and the minimal inhibitory concentrations (MIC) of 11 antibiotics were also determined by microdilution method. Most of the isolates belonged to the Pseudomonas fluorescens group (94.1%), and no relationship was established between antibiotic resistance patterns and sampling locations (farms or filleting areas). Multiple resistance isolates with high MIC values (from 64 µg ml-1 to more than 1024 µg ml-1 ) were identified. CONCLUSIONS Antibiotic resistance patterns found in Pseudomonas isolates were not influenced by farms or transformation process locations. Seven isolates were found highly resistant to four different antibiotic classes. SIGNIFICANCE AND IMPACT OF THE STUDY This study does not provide evidence of a relationship between farm or transformation process locations on antibiotic resistance patterns of Pseudomonas population.
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Affiliation(s)
| | | | - Nicolas Helsens
- INRAE, Oniris, BIOEPAR, Nantes, France.,INRAE, Oniris, SECALIM, Nantes, France
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33
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Wan Y, Ma R, Zhang H, Li L, Chai L, Qi R, Liu W, Li J, Li Y, Zhan K. Different Non-cage Housing Systems Alter Duodenal and Cecal Microbiota Composition in Shendan Chickens. Front Vet Sci 2021; 8:728538. [PMID: 34692808 PMCID: PMC8526545 DOI: 10.3389/fvets.2021.728538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022] Open
Abstract
Housing systems are among the most important non-genetic factors affecting hen production performance and intestinal microbes. With increased interest in animal welfare, cage-free laying hen housing systems have become common, providing behavioral freedom and health benefits. The present study aimed to compare the effects of plastic net housing system (NRS) and floor litter housing system (LRS) on the composition and function of the duodenal and cecal microbiota in Shendan chicken, one of the most popular laying hen strains in China. The associations between the differential microbiota abundance and production traits and intestinal morphological parameters were determined. Compared with the LRS, the NRS improved the laying rate (p < 0.05) and increased the villus height (VH) of the duodenum (p < 0.05) and the VH-to-crypt depth ratio (VCR) of the cecum (p < 0.05). Alpha diversity analysis showed that LRS chickens had a significantly higher diversity and richness than NRS chickens. Beta diversity analysis demonstrated differences in the microbiota composition based on housing systems. Within the cecum, Proteobacteria and Kiritimatiellaeota were significantly more abundant in the LRS than in the NRS (p < 0.05), while Bacteroidetes were significantly less abundant in the LRS (p < 0.05). Phascolarctobacterium and Ruminococcaceae_UCG-005 were significantly less abundant in the LRS (p < 0.05) compare to the NRS. Within the duodenum, Lactobacillus was significantly less abundant in the LRS (p < 0.05) than in the NRS, while Pseudomonas was significantly more abundant in the LRS (p < 0.05). Cecal Phascolarctobacterium and Ruminococcaceae_UCG-005 were significantly positively correlated with eggshell strength (R = 0.608, p < 0.01) and egg weight (R = 0.526, p < 0.05), respectively. Duodenal Lactobacillus was significantly positively correlated with VH and VCR (R = 0.548 and 0.565, p < 0.05), while Pseudomonas was significantly negatively correlated with the Haugh unit (R = -0.550, p < 0.05). In conclusion, there are differences in the cecal and duodenal microbiota compositions of Shendan laying hens reared in different non-cage housing systems, and the NRS was superior to the LRS in improving the laying performance and intestinal morphology and microecological environment.
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Affiliation(s)
- Yi Wan
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Ruiyu Ma
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Hongyi Zhang
- Hubei Shendan Health Food Co., Ltd., Anlu, China
| | - Ling Li
- Hubei Shendan Health Food Co., Ltd., Anlu, China
| | - Lilong Chai
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Renrong Qi
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Wei Liu
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Junying Li
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Yan Li
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
| | - Kai Zhan
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei, China
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34
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Bashir A, Sun Y, Yu X, Sun X, Li L. Nematicidal effects of 2-methyl-aconitate isomerase from the phytopathogen Pseudomonas syringae MB03 on the model nematode Caenorhabditis elegans. J Invertebr Pathol 2021; 185:107669. [PMID: 34560108 DOI: 10.1016/j.jip.2021.107669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 10/24/2022]
Abstract
The pathogenicity of a common phytopathogenic bacterium, Pseudomonas syringae, against animal model hosts, such as mice and Caenorhabditis elegans, has been recently revealed. However, most of the virulence determinants associated with pathogenesis remain elusive. In the current study, we performed predictive analysis of virulence factors against C. elegans in the genome of the wild-type P. syringae strain MB03. Nine predicted nematicidal proteins were expressed and purified in recombinant Escherichia coli strains and were evaluated to define their toxicity against C. elegans in liquid killing assays. Next, we focused on one essential 2-methyl citrate cycle protein, PrpF03, which showed the highest lethal activity against C. elegans compared to the other tested proteins with a half lethal concentration (LC50) of 155.3 (123.4-176.6) µg mL-1 and a half lethal time (LT50) of 3.72 (1.64-4.85) days. Purified PrpF03 also caused adverse effects on the brood size, growth, and motility of C. elegans. Moreover, the PrpF03 protein exhibited pathological activity towards the intestinal tract of C. elegans. We surmise that the PrpF03 protein functions as a virulence factor when it blocks the average circulation of the 2-methyl citrate cycle of C. elegans by accumulating 2-methyl citrate in the gut of C. elegans, which damages and restrains the growth of intestinal tissues that ultimately kill C. elegans. The discovery of specific nematicidal activities of PrpF03 provides a better understanding of the mechanisms of phytopathogenic P. syringae against nematodes and could aid in developing nematode pest-controlling agents in agriculture.
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Affiliation(s)
- Anum Bashir
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaowen Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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35
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Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546867 DOI: 10.1099/ijsem.0.005011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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36
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Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. BIOLOGY 2021; 10:782. [PMID: 34440014 PMCID: PMC8389581 DOI: 10.3390/biology10080782] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
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37
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Pang Y, Zhang Y, Chen M, Lu W, Chen M, Yan Y, Lin M, Zhang W, Zhou Z. Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea. Antonie van Leeuwenhoek 2021; 114:1791-1804. [PMID: 34392431 DOI: 10.1007/s10482-021-01639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/05/2021] [Indexed: 11/28/2022]
Abstract
A bacterial lipase producing bacterium, designated SCS 2-3, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA sequence revealed that strain SCS2-3 belonged to the genus Pseudomonas and had 98.56% similarity to P. xinjiangensis NRRL B-51270T as the closest relative strain. MLSA using four protein-coding genes (dnaK, gyrA, recA, and rpoB) showed strain SCS 2-3 to form a separate branch. ANI and in silico DDH values between strain SCS 2-3 and related type strains of Pseudomonas were less than 81.51% and 23.80%, respectively. Genome comparison showed that strain SCS 2-3 shared 1875 core gene families with other eight closely related type strains in Pseudomonas, and the number of strain-unique genes was 263. Through gene annotations, genes related to lipase were found in the genome. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SCS 2-3 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nanhaiensis sp. nov. is proposed. The type strain is SCS 2-3T (= GDMCC 1.2219T = JCM 34440T).
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Affiliation(s)
- Yu Pang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yage Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mengru Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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38
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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Lejal E, Chiquet J, Aubert J, Robin S, Estrada-Peña A, Rue O, Midoux C, Mariadassou M, Bailly X, Cougoul A, Gasqui P, Cosson JF, Chalvet-Monfray K, Vayssier-Taussat M, Pollet T. Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions. MICROBIOME 2021; 9:153. [PMID: 34217365 PMCID: PMC8254910 DOI: 10.1186/s40168-021-01051-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/17/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions. METHODS Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community. RESULTS Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus. CONCLUSIONS We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.
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Affiliation(s)
- E Lejal
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - J Chiquet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - J Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - S Robin
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - A Estrada-Peña
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - O Rue
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - C Midoux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, PROSE, Université Paris-Saclay, Antony, France
| | - M Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - X Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - A Cougoul
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - P Gasqui
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - J F Cosson
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - K Chalvet-Monfray
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | | | - T Pollet
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, Montpellier, France.
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Lee J, Ju F, Maile-Moskowitz A, Beck K, Maccagnan A, McArdell CS, Dal Molin M, Fenicia F, Vikesland PJ, Pruden A, Stamm C, Bürgmann H. Unraveling the riverine antibiotic resistome: The downstream fate of anthropogenic inputs. WATER RESEARCH 2021; 197:117050. [PMID: 33784606 DOI: 10.1016/j.watres.2021.117050] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/20/2021] [Accepted: 03/12/2021] [Indexed: 05/12/2023]
Abstract
River networks are one of the main routes by which the public could be exposed to environmental sources of antibiotic resistance, that may be introduced e.g. via treated wastewater. In this study, we applied a comprehensive integrated analysis encompassing mass-flow concepts, chemistry, bacterial plate counts, resistance gene quantification and shotgun metagenomics to track the fate of the resistome (collective antibiotic resistance genes (ARGs) in a microbial community) of treated wastewater in two Swiss rivers at the kilometer scale. The levels of certain ARGs and the class 1 integron integrase gene (intI1) commonly associated with anthropogenic sources of ARGs decreased quickly over short distances (2-2.5 km) downstream of wastewater discharge points. Mass-flow analysis based on conservative tracers suggested this decrease was attributable mainly to dilution but ARG loadings frequently also decreased (e.g., 55.0-98.5 % for ermB and tetW) over the longest studied distances (6.8 and 13.7 km downstream). Metagenomic analysis confirmed that ARG of wastewater-origin did not persist in rivers after 5 ~ 6.8 km downstream distance. sul1 and intI1 levels and loadings were more variable and even increased sharply at 5 ~ 6.8 km downstream distance on one occasion. While input from agriculture and in-situ positive selection pressure for organisms carrying ARGs cannot be excluded, in-system growth of biomass is a more probable explanation. The potential for direct human exposure to the resistome of wastewater-origin thus appeared to typically abate rapidly in the studied rivers. However, the riverine aquatic resistome was also dynamic, as evidenced by the increase of certain gene markers downstream, without obvious sources of anthropogenic contamination. This study provides new insight into drivers of riverine resistomes and pinpoints key monitoring targets indicative of where human sources and exposures are likely to be most acute.
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Affiliation(s)
- Jangwoo Lee
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland; Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Andreas Maccagnan
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Christa S McArdell
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Marco Dal Molin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland; The Centre of Hydrogeology and Geothermics (CHYN), University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Fabrizio Fenicia
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Christian Stamm
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland.
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Timsy, Spanner T, Ulrich A, Kublik S, Foesel BU, Kolb S, Horn MA, Behrendt U. Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34016249 DOI: 10.1099/ijsem.0.004799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.
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Affiliation(s)
- Timsy
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Tobias Spanner
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Susanne Kublik
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Bärbel U Foesel
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Steffen Kolb
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Marcus A Horn
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
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Jang MJ, Kim SY, Ricke SC, Rhee MS, Kim SA. Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing. Food Res Int 2021; 144:110316. [PMID: 34053521 DOI: 10.1016/j.foodres.2021.110316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety.
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Affiliation(s)
- Min Ji Jang
- Department of Food Science and Engineering, Ewha Womans University, Seoul, South Korea
| | - Seo Young Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, South Korea
| | - Steven C Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Science, University of Wisconsin, Madison, WI, USA
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Sun Ae Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul, South Korea.
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Schlusselhuber M, Girard L, Cousin FJ, Lood C, De Mot R, Goux D, Desmasures N. Pseudomonas crudilactis sp. nov., isolated from raw milk in France. Antonie van Leeuwenhoek 2021; 114:719-730. [PMID: 33715105 DOI: 10.1007/s10482-021-01552-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022]
Abstract
Strains belonging to the Pseudomonas genus have been isolated worldwide from various biotic (humans, animals and plant tissues) and abiotic (food, soil, water and air) environments. Raw milk provides a favorable environment for the growth of a broad spectrum of microorganisms, including Pseudomonas. Here we present the description of Pseudomonas sp. UCMA 17988 isolated from raw milk, which was previously reported to produce new antimicrobial lipopeptides. MultiLocus Sequence Analysis of four housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), whole genome sequence comparison (orthoANI value, original ANI value and dDDH value), microscopy, FAME analysis, and biochemical tests were performed. Digital DNA-DNA hybridization and average nucleotide identity values between strain UCMA 17988 and its closest relatives, P. helmanticensis CECT 8548T (46.9%, 92.07%) and P. baetica CECT 7720T (26.8%, 88.50%), rate well below the designed threshold for assigning prokaryotic strains to the same species. In conclusion, strain UCMA 17988 belongs to a novel species, for which the name Pseudomonas crudilactis sp. nov (type strain UCMA 17988T = DSM 109949T = LMG 31804T) is proposed.
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Affiliation(s)
| | - Léa Girard
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | - Fabien J Cousin
- UNICAEN, UNIROUEN, ABTE, Normandie Univ, 14000, Caen, France
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium.,Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Leuven, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | - Didier Goux
- UNICAEN, Centre de Microscopie Appliquée á la Biologie, SF 4206 Interaction Cellule-Organisme-Environnement (ICORE), Normandie Univ, 14000, Caen, France.,ENSICAEN, UNICAEN, CNRS, CRISMAT, Normandie Univ, 14000, Caen, France
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Pozo MI, Mariën T, van Kemenade G, Wäckers F, Jacquemyn H. Effects of pollen and nectar inoculation by yeasts, bacteria or both on bumblebee colony development. Oecologia 2021; 195:689-703. [PMID: 33582870 DOI: 10.1007/s00442-021-04872-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
It is increasingly recognized that gut microbiota have a major effect on the physiology, biology, ecology and evolution of their animal hosts. Because in social insects, the gut microbiota is acquired through the diet and by contact with nest provisions, it can be hypothesized that regular supplementation of microorganisms to the diet will have an impact on the fitness of the consumer and on the development of the whole colony. To test this hypothesis, we investigated how supplementation of bacteria, yeasts, and combinations of the two to either pollen or nectar affected colony development in the social bumblebee Bombus terrestris. Three yeasts and three bacterial species that live at the flower-insect interface were used in the experiments and the development of bumblebee colonies was monitored over a period of 10 weeks. The results showed that administration of microbes via pollen had a stronger positive impact on colony development than when provided via sugar water. Supplementation of bacteria led, in general, to a faster egg laying, higher brood size and increased production of workers during the first weeks, whereas yeasts or a combination of yeasts and bacteria had less impact on colony development. However, the results differed between microbial species, with Wickerhamiella bombiphila and Rosenbergiella nectarea showing the strongest increase in colony development. Torulaspora delbrueckii induced early male production, which is likely a fitness cost. We conclude that the tested bacteria-yeast consortia did not result in better colony development than the interacting species alone.
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Affiliation(s)
- María I Pozo
- Biology Department, Plant Conservation and Population Biology, KU Leuven, 3001, Heverlee, Belgium.
| | - Toon Mariën
- Biology Department, Plant Conservation and Population Biology, KU Leuven, 3001, Heverlee, Belgium
| | - Gaby van Kemenade
- Biology Department, Plant Conservation and Population Biology, KU Leuven, 3001, Heverlee, Belgium.,Biobest Group, Research and Development, 2260, Westerlo, Belgium
| | - Felix Wäckers
- Biobest Group, Research and Development, 2260, Westerlo, Belgium
| | - Hans Jacquemyn
- Biology Department, Plant Conservation and Population Biology, KU Leuven, 3001, Heverlee, Belgium
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Antibiotic Resistance and Phylogeny of Pseudomonas spp. Isolated over Three Decades from Chicken Meat in the Norwegian Food Chain. Microorganisms 2021; 9:microorganisms9020207. [PMID: 33498315 PMCID: PMC7909287 DOI: 10.3390/microorganisms9020207] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas is ubiquitous in nature and a predominant genus in many foods and food processing environments, where it primarily represents major food spoilage organisms. The food chain has also been reported to be a potential reservoir of antibiotic-resistant Pseudomonas. The purpose of the current study was to determine the occurrence of antibiotic resistance in psychrotrophic Pseudomonas spp. collected over a time span of 26 years from retail chicken in Norway and characterize their genetic diversity, phylogenetic distribution and resistance genes through whole-genome sequence analyses. Among the 325 confirmed Pseudomonas spp. isolates by 16S rRNA gene sequencing, antibiotic susceptibility profiles of 175 isolates to 12 antibiotics were determined. A subset of 31 isolates being resistant to ≥3 antibiotics were whole-genome sequenced. The isolates were dominated by species of the P. fluorescens lineage. Isolates susceptible to all antibiotics or resistant to ≥3 antibiotics comprised 20.6% and 24.1%, respectively. The most common resistance was to aztreonam (72.6%), colistin (30.2%), imipenem (25.6%) and meropenem (12.6%). Resistance properties appeared relatively stable over the 26-year study period but with taxa-specific differences. Whole-genome sequencing showed high genome variability, where isolates resistant to ≥3 antibiotics belonged to seven species. A single metallo-betalactmase gene (cphA) was detected, though intrinsic resistance determinants dominated, including resistance–nodulation (RND), ATP-binding cassette (ABC) and small multidrug resistance (Smr) efflux pumps. This study provides further knowledge on the distribution of psychrotrophic Pseudomonas spp. in chicken meat and their antibiotic resistance properties. Further monitoring should be encouraged to determine food as a source of antibiotic resistance and maintain the overall favorable situation with regard to antibiotic resistance in the Norwegian food chain.
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Ruiz-Roldán L, de Toro M, Sáenz Y. Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny. Genes (Basel) 2021; 12:115. [PMID: 33477842 PMCID: PMC7832885 DOI: 10.3390/genes12010115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/10/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these isolates. Thus, the aim of this study was to analyze the resistome, virulome, and phylogenetic relationship of two P. mendocina strains, Ps542 and Ps799, isolated from a healthy Anas platyrhynchos fecal sample and a lettuce, respectively. Among all of the small number of P.mendocina genomes available in the National Center for Biotechnology Information (NCBI) repository, both strains were placed within one of two well-defined phylogenetic clusters. Both P. mendocina strains lacked antimicrobial resistance genes, but the Ps799 genome showed a MOBP3 family relaxase. Nevertheless, this study revealed that P. mendocina possesses an important number of virulence factors, including a leukotoxin, flagella, pili, and the Type 2 and Type 6 Secretion Systems, that could be responsible for their pathogenesis. More phenotypical and in vivo studies are needed to deepen the association with human infections and the potential P. mendocina pathogenicity.
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Affiliation(s)
- Lidia Ruiz-Roldán
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain;
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain;
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Zhao Y, Yang Y, He F, Wang C, Feng J, Zhang X. Pseudomonas xionganensis sp. nov., isolated from Baiyangdian Lake in Xiong'an New Area. Int J Syst Evol Microbiol 2021; 70:6052-6059. [PMID: 32996879 DOI: 10.1099/ijsem.0.004485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped bacterium, designated as strain R-22-3 w-18T, was isolated from Baiyangdian Lake in Xiong'an New Area, PR China. Growth was observed at 15-37 °C (optimum, 30 °C) and pH 7.0-10.0 (optimum, pH 8.0). 16S rRNA gene sequence analysis placed the strain in a separate branch in the Pseudomonas putida group, with Pseudomonas anguilliseptica DSM12111T as its closest phylogenetic relative (98.2 %). Whole-genome comparisons, using average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) analyses, confirmed low genome relatedness to the closely related Pseudomonas species [below the recommended thresholds of 95 % (ANI), 95 % (AAI) and 70 % (DDH) for species delineation]. Phenotypic characterization tests could also distinguish this strain from other related species of the genus Pseudomonas. Therefore, based on genetic and phenotypic evidence, it is clear that strain R-22-3 w-18T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas xionganensis sp. nov. is proposed. The type strain is R-22-3 w-18T (=CGMCC 1.17250T=KCTC 72658T).
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Affiliation(s)
- Yingying Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China.,College of Life Science, Institute of Life Science and Green Development, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation, Baoding, PR China
| | - Yunzhen Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Fei He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China.,College of Life Science, Institute of Life Science and Green Development, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation, Baoding, PR China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Xiumin Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Engineering Laboratory of Microbial Breeding and Preservation, Baoding, PR China
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Sakuraoka R, Someya N, Takeuchi K, Suzuki T, Morohoshi T. Comparative Genome Analysis Reveals Differences in Biocontrol Efficacy According to Each Individual Isolate Belonging to Rhizospheric Fluorescent Pseudomonads. Microbes Environ 2021; 36. [PMID: 34321367 PMCID: PMC8446755 DOI: 10.1264/jsme2.me21034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Biocontrol fluorescent pseudomonads produce a number of antibiotic organic compounds, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, and phenazine. We previously classified rhizospheric fluorescent pseudomonads harboring antibiotic biosynthetic gene clusters into 10 operational taxonomic units (OTUs). In the present study, we report the complete genome sequences of selected strains from these OTUs. The genetic diversity of antibiotic biosynthetic gene clusters and their surrounding sequences correlated with the OTU classification. In comparisons of the biocontrol activity and distribution of antibiotic biosynthetic gene clusters, we found that the pyrrolnitrin biosynthetic gene cluster more effectively controlled the growth of Rhizoctonia solani.
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Affiliation(s)
- Ryohei Sakuraoka
- Department of Innovation Systems Engineering, Graduate School of Engineering, Utsunomiya University
| | - Nobutaka Someya
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO)
| | | | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University
| | - Tomohiro Morohoshi
- Department of Innovation Systems Engineering, Graduate School of Engineering, Utsunomiya University
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50
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Characterization of the microbiota of commercially traded finfish fillets. Food Res Int 2020; 137:109373. [PMID: 33233075 DOI: 10.1016/j.foodres.2020.109373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 05/18/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023]
Abstract
The profile of human gut microbiota is known to be affected by diet and is linked to human health. Seafood is a highly consumed food and it accounts for a large proportion of food-borne illness. The objective of this study is to characterise the microbiota of fish fillets of various species sold in the Canadian market. We test 19 fish fillet samples from nine species in five fish families, ten of which were previously determined to be mislabeled as different species. The microbiota profiles were characterized using 16S rRNA gene high-throughput sequencing. Despite the complexities of the supply chain to produce these fillets, the major microbial groups were fairly consistent across samples. Significant differences in microbial taxa were observed between species, families, and based on labelling accuracy. Several putative spoilage and putative pathogenic taxa were identified. Studying food-associated microbiota can provide comprehensive information on food safety, authenticity, and traceability.
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