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Kardos G, Laczkó L, Kaszab E, Timmer B, Szarka K, Prépost E, Bányai K. Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes. Antibiotics (Basel) 2024; 13:573. [PMID: 39061255 PMCID: PMC11273654 DOI: 10.3390/antibiotics13070573] [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: 02/09/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 07/28/2024] Open
Abstract
The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae.
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Affiliation(s)
- Gábor Kardos
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- HUN-REN-UD Conservation Biology Research Group, H-4032 Debrecen, Hungary
| | - Eszter Kaszab
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1078 Budapest, Hungary
| | - Bálint Timmer
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- Department of Medical Microbiology and Immunology, University of Pécs, H-7624 Pécs, Hungary
| | - Krisztina Szarka
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Eszter Prépost
- Department of Health Industry, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Krisztián Bányai
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, H-1143 Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, H-1078 Budapest, Hungary
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Liu Q, Liu S, Zhou XQ, Liu YR. Assessing microbial degradation potential of methylmercury in different types of paddy soil through short-term incubation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122603. [PMID: 37748640 DOI: 10.1016/j.envpol.2023.122603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/03/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
The neurotoxic methylmercury (MeHg) in paddy soils can accumulate in rice grains. Microbial demethylation is an important pathway of MeHg degradation in soil, but the effect of soil type on microbial degradation of MeHg remains unclear. Therefore, we investigated MeHg degradation in eight typical paddy soils and analyzed the associations between soil physiochemical properties and microbial degradation efficiencies of MeHg. Results showed that MeHg was significantly degraded in unsterilized paddy soils, and the microbial degradation efficiency ranged from 10.8% to 64.6% after a 30-day incubation. The high microbial degradation efficiency of MeHg was observed in the soils with high levels of clay content, whereas relatively low degradation efficiency was found in the red paddy soils. We identified that Paenibacillaceae was the most important microbial predictor of MeHg degradation and was positively correlated with the degradation efficiency in the soils. The abundances of these microbial taxa associated with MeHg degradation were positively correlated with clay content. In addition, Eh, pH, and SOC could influence microbial degradation of MeHg by regulating certain microbial communities. Our results indicate that soil type is crucial in driving MeHg degradation, which has important implications for the mitigation of MeHg pollution in various croplands.
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Affiliation(s)
- Qin Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Siyuan Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Xin-Quan Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
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Matsumoto H, Qian Y, Fan X, Chen S, Nie Y, Qiao K, Xiang D, Zhang X, Li M, Guo B, Shen P, Wang Q, Yu Y, Cernava T, Wang M. Reprogramming of phytopathogen transcriptome by a non-bactericidal pesticide residue alleviates its virulence in rice. FUNDAMENTAL RESEARCH 2022; 2:198-207. [PMID: 38933150 PMCID: PMC11197535 DOI: 10.1016/j.fmre.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteria equipped with virulence systems based on highly bioactive small molecules can circumvent their host's defense mechanisms. Pathogens employing this strategy are currently threatening global rice production. In the present study, variations in the virulence of the highly destructive Burkholderia plantarii were observed in different rice-producing regions. The environment-linked variation was not attributable to any known host-related or external factors. Co-occurrence analyses indicated a connection between reduced virulence and 5-Amino-1,3,4-thiadiazole-2-thiol (ATT), a non-bactericidal organic compound. ATT, which accumulates in rice plants during metabolization of specific agrochemicals, was found to reduce virulence factor secretion by B. plantarii up to 88.8% and inhibit pathogen virulence by hijacking an upstream signaling cascade. Detailed assessment of the newly discovered virulence inhibitor resulted in mechanistic insights into positive effects of ATT accumulation in plant tissues. Mechanisms of virulence alleviation were deciphered by integrating high-throughput data, gene knockout mutants, and molecular interaction assays. TroK, a histidine protein kinase in a two-component system that regulates virulence factor secretion, is likely the molecular target antagonized by ATT. Our findings provide novel insights into virulence modulation in an important plant-pathogen system that relies on the host's metabolic activity and subsequent signaling interference.
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Affiliation(s)
- Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuan Qian
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Fan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kun Qiao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Dandan Xiang
- Key laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xinzhong Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Meng Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Bo Guo
- Shanghai International Studies University, Shanghai 200083, China
| | - Peilin Shen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Xiaoshan Agricultural Comprehensive Development Zone & Management Committee, Hangzhou 311200, China
| | - Qiangwei Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Liu H, Prajapati V, Prajapati S, Bais H, Lu J. Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes. Front Genet 2021; 12:724217. [PMID: 34659348 PMCID: PMC8514880 DOI: 10.3389/fgene.2021.724217] [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: 06/12/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Vimalkumar Prajapati
- Division of Microbiology and Environmental, Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, India
| | - Shobha Prajapati
- SVP-A School of Sardar Vallabhbhai National Institute of Technology, Surat, India
| | - Harsh Bais
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Morse KV, Richardson DR, Brown TL, Vangundy RD, Cahoon AB. Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession. PeerJ 2021; 9:e10757. [PMID: 33732542 PMCID: PMC7950216 DOI: 10.7717/peerj.10757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave's aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave.
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Waglechner N, Culp EJ, Wright GD. Ancient Antibiotics, Ancient Resistance. EcoSal Plus 2021; 9:eESP-0027-2020. [PMID: 33734062 PMCID: PMC11163840 DOI: 10.1128/ecosalplus.esp-0027-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.
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Affiliation(s)
- Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Elizabeth J. Culp
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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Eduardo-Correia B, Morales-Filloy H, Abad JP. Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players. Front Microbiol 2020; 10:3071. [PMID: 31998281 PMCID: PMC6965355 DOI: 10.3389/fmicb.2019.03071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs CzR/TcR in Betaproteobacteria, and CcR/TcR and EmR/SmR in Sphingobacteriia at the class level, while at the genus level, was found for CcR/TcR and NxR/TmR in Mesonia, CzR/TmR and EmR/KmR in Paenibacillus, and CcR/EmR and RpR/TcR in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.
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Affiliation(s)
- Benedito Eduardo-Correia
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - Héctor Morales-Filloy
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - José P Abad
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
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Fancello F, Multineddu C, Santona M, Deiana P, Zara G, Mannazzu I, Budroni M, Dettori S, Zara S. Bacterial Biodiversity of Extra Virgin Olive Oils and Their Potential Biotechnological Exploitation. Microorganisms 2020; 8:E97. [PMID: 31936728 PMCID: PMC7022595 DOI: 10.3390/microorganisms8010097] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Bacterial diversity of 15 extra virgin olive oils, obtained from different Italian varieties, including Frantoio, Coratina, Bosana, and Semidana, was analyzed in this study. All bacterial isolates were genotyped using RAPD and REP-PCR method and grouped by means of cluster analyses. Sequencing of 16S rDNA of 51 isolates, representative of 36 clusters, led to the identification of Bacillus spp., Brevibacillus spp., Micrococcus spp., Staphylococcus spp., Pantoea spp., Kocuria spp., Lysinbacillus spp., and Lactobacillus spp., most of which reported for first time in olive oils. Phenotypic characterization of the 51 isolates, some of which ascribed to potentially probiotic species, indicate that two of them have beta-glucosidase activity while 37% present lipolytic activity. Preliminary evaluation of probiotic potential indicates that 31% of the isolates show biofilm formation ability, 29% acidic pH resistance, and 25% bile salt resistance. Finally, 29% of the isolates were sensitive to antibiotics while the remaining 71%, that include bacterial species well-recognized for their ability to disseminate resistance genes in the environment, showed a variable pattern of antibiotic resistance. The results obtained underline that microbial diversity of extra virgin olive oils represents an unexpected sink of microbial diversity and poses safety issues on the possible biotechnological exploitation of this microbial biodiversity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Severino Zara
- Dipartimento di Agraria, Viale Italia 39, University of Sassari, 07100 Sassari, Italy; (F.F.); (C.M.); (M.S.); (P.D.); (G.Z.); (I.M.); (M.B.); (S.D.)
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Draft Genome Sequences of Five Proteobacteria Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing. Microbiol Resour Announc 2019; 8:8/40/e00913-19. [PMID: 31582457 PMCID: PMC6776774 DOI: 10.1128/mra.00913-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five Proteobacteria isolated from Lechuguilla Cave in New Mexico. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess genomic potential for the biosynthesis of acyl-homoserine lactone. Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five Proteobacteria isolated from Lechuguilla Cave in New Mexico. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess genomic potential for the biosynthesis of acyl-homoserine lactone.
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10
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Wright GD. Environmental and clinical antibiotic resistomes, same only different. Curr Opin Microbiol 2019; 51:57-63. [DOI: 10.1016/j.mib.2019.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
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Chernov VM, Chernova OA, Mouzykantov AA, Lopukhov LL, Aminov RI. Omics of antimicrobials and antimicrobial resistance. Expert Opin Drug Discov 2019; 14:455-468. [DOI: 10.1080/17460441.2019.1588880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladislav M. Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Olga A. Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Alexey A. Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Leonid L. Lopukhov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Rustam I. Aminov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
- Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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Golkar T, Zieliński M, Berghuis AM. Look and Outlook on Enzyme-Mediated Macrolide Resistance. Front Microbiol 2018; 9:1942. [PMID: 30177927 PMCID: PMC6109786 DOI: 10.3389/fmicb.2018.01942] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
Since their discovery in the early 1950s, macrolide antibiotics have been used in both agriculture and medicine. Specifically, macrolides such as erythromycin and azithromycin have found use as substitutes for β-lactam antibiotics in patients with penicillin allergies. Given the extensive use of this class of antibiotics it is no surprise that resistance has spread among pathogenic bacteria. In these bacteria different mechanisms of resistance have been observed. Frequently observed are alterations in the target of macrolides, i.e., the ribosome, as well as upregulation of efflux pumps. However, drug modification is also increasingly observed. Two classes of enzymes have been implicated in macrolide detoxification: macrolide phosphotransferases and macrolide esterases. In this review, we present a comprehensive overview on what is known about macrolide resistance with an emphasis on the macrolide phosphotransferase and esterase enzymes. Furthermore, we explore how this information can assist in addressing resistance to macrolide antibiotics.
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Affiliation(s)
- Tolou Golkar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michał Zieliński
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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Geesink P, Tyc O, Küsel K, Taubert M, van de Velde C, Kumar S, Garbeva P. Growth promotion and inhibition induced by interactions of groundwater bacteria. FEMS Microbiol Ecol 2018; 94:5076029. [DOI: 10.1093/femsec/fiy164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/17/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patricia Geesink
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
| | - Charlotte van de Velde
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Swatantar Kumar
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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The evolution of substrate discrimination in macrolide antibiotic resistance enzymes. Nat Commun 2018; 9:112. [PMID: 29317655 PMCID: PMC5760710 DOI: 10.1038/s41467-017-02680-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
The production of antibiotics by microbes in the environment and their use in medicine and agriculture select for existing and emerging resistance. To address this inevitability, prudent development of antibiotic drugs requires careful consideration of resistance evolution. Here, we identify the molecular basis for expanded substrate specificity in MphI, a macrolide kinase (Mph) that does not confer resistance to erythromycin, in contrast to other known Mphs. Using a combination of phylogenetics, drug-resistance phenotypes, and in vitro enzyme assays, we find that MphI and MphK phosphorylate erythromycin poorly resulting in an antibiotic-sensitive phenotype. Using likelihood reconstruction of ancestral sequences and site-saturation combinatorial mutagenesis, supported by Mph crystal structures, we determine that two non-obvious mutations in combination expand the substrate range. This approach should be applicable for studying the functional evolution of any antibiotic resistance enzyme and for evaluating the evolvability of resistance enzymes to new generations of antibiotic scaffolds. New antibiotics with reduced potential for resistance are urgently needed. Here, the authors use a multidisciplinary approach to characterize substrate discrimination in macrolide resistance kinases and present a strategy for the prediction of mutations that expand the substrate range of antibiotic-inactivating enzymes.
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