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Martín-Rodríguez AJ, Fernández-Juárez V, Valeriano VD, Mihindukulasooriya I, Ceresnova L, Joffré E, Jensie-Markopoulos S, Moore ERB, Sjöling Å. A hotspot of diversity: novel Shewanella species isolated from Baltic Sea sediments delineate a sympatric species complex. Int J Syst Evol Microbiol 2024; 74. [PMID: 39150443 PMCID: PMC11329295 DOI: 10.1099/ijsem.0.006480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024] Open
Abstract
Two bacterial strains, SP1S1-4T and SP2S1-2T, were isolated from sediment samples collected in the Stockholm archipelago in November 2021. Following whole-genome sequencing, these strains were identified as tentatively belonging to two novel Shewanella genospecies, based on digital DNA-DNA hybridization, as implemented in the Type Strain Genome Server. Shewanella septentrionalis, Shewanella baltica and Shewanella hafniensis were, in this order and within a narrow genomic relatedness range, their closest genotypic relatives. Additional sampling and sequencing efforts led to the retrieval of distinct isolates that were monophyletic with SP1S1-4T and SP2S1-2T, respectively, based on phylogenomic analysis of whole-genome sequences. Comparative analyses of genome sequence data, which included blast-based average nucleotide identity, core genome-based and core proteome-based phylogenomics, in addition to MALDI-TOF MS-based protein profiling, confirmed the distinctness of the putative novel genospecies with respect to their closest genotypic relatives. A comprehensive phenotypic characterisation of SP1S1-4T and SP2S1-2T revealed only minor differences with respect to the type strains of S. septentrionalis, S. baltica and S. hafniensis. Based on the collective phylogenomic, proteomic, and phenotypic evidence presented here, we describe two novel genospecies within the genus Shewanella, for which the names Shewanella scandinavica sp. nov. and Shewanella vaxholmensis sp. nov. are proposed. The type strains are, respectively, SP2S1-2T (=CCUG 76457T=CECT 30688T), with a draft genome sequence of 5 041 805 bp and a G+C content of 46.3 mol%, and SP1S1-4T (=CCUG 76453T=CECT 30684T), with a draft genome sequence of 4 920147 bp and a G+C content of 46.0 mol%. Our findings suggest the existence of a species complex formed by the species S. baltica, S. septentrionalis, S. scandinavica sp. nov., and S. vaxholmensis sp. nov., with S. hafniensis falling in the periphery, where distinct genomic species clusters could be identified. However, this does not exclude the possibility of a continuum of genomic diversity within this sedimental ecosystem, as discussed herein with additional sequenced isolates.
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Affiliation(s)
- Alberto J Martín-Rodríguez
- Department of Clinical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Víctor Fernández-Juárez
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Valerie D Valeriano
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Indiwari Mihindukulasooriya
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Livia Ceresnova
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Enrique Joffré
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Gothenburg, Sweden
| | - Susanne Jensie-Markopoulos
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital and Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Åsa Sjöling
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Chemistry and Molecular Biology (CMB), University of Gothenburg, Gothenburg, Sweden
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Yasawong M, Rosyidah A, Songngamsuk T, Phatcharaharikarn M, Ganta P, Chanthasena P, Chudapongse N, Santapan N, Srisakvarangkool W, Kerdtoob S, Nantapong N. First draft genome sequence data of TA4-1, the type strain of Gram-positive bacterium Streptomyces chiangmaiensis. Data Brief 2024; 55:110611. [PMID: 38993230 PMCID: PMC11237854 DOI: 10.1016/j.dib.2024.110611] [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: 03/05/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 07/13/2024] Open
Abstract
TA4-1 is the type strain of Streptomyces chiangmaiensis. The TA4-1 strain was isolated from a stingless bee (Tetragonilla collina). Here we present the draft genome sequence data of S. chiangmaiensis TA4-1. The Illumina NextSeq 550 sequencer was used to generate paired-end reads from the genomic DNA of the pure culture of S. chiangmaiensis TA4-1. The draft genome sequence of strain TA4-1 consists of 776 contigs with a total size of 9,707,984 base pairs, an N50 of 32,937 base pairs, and a GC content of 69.73 %. Digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) analysis showed that S. yaanensis CGMCC 4.7035 had the highest dDDH value (32.7 %) and ANIm value (88.50 %) when compared with TA4-1. The presented data indicate the potential for a reference genome sequence in bacterial taxonomy, comparative genomics, and the investigation of bioactive compound biosynthesis in S. chiangmaiensis TA4-1. The draft genome sequence data have been deposited at NCBI under the Bioproject accession number PRJNA680432.
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Affiliation(s)
- Montri Yasawong
- Programme on Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - A'liyatur Rosyidah
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Thunwarat Songngamsuk
- Programme on Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Manassanan Phatcharaharikarn
- Programme on Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Phongsakorn Ganta
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panjamaphon Chanthasena
- Faculty of Allied Health Sciences, Nakhonratchasima College, Nakhon Ratchasima 30000, Thailand
| | - Nuannoi Chudapongse
- Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok 10160, Thailand
| | - Napatsorn Santapan
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wissarut Srisakvarangkool
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supavadee Kerdtoob
- Faculty of Allied Health Sciences, Nakhonratchasima College, Nakhon Ratchasima 30000, Thailand
| | - Nawarat Nantapong
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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103
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Powell J, Daly M, O'Connell NH, Dunne CP. Seek and you shall find: Yersinia enterocolitica in Ireland's drinking water. Ir J Med Sci 2024; 193:1885-1890. [PMID: 38381378 PMCID: PMC11294261 DOI: 10.1007/s11845-024-03641-5] [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: 01/25/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
INTRODUCTION Three Yersinia species were identified from samples of drinking water from diverse geographic regions of Ireland. Conventional commercial biochemical identification systems classified them as Yersinia enterocolitica. Since this organism is the most common cause of bacterial gastroenteritis in some countries, further investigation was warranted. The aim of the study was to provide a microbial characterisation of three Yersinia species, to determine their pathogenicity, and to review the incidence rate of Yersinia enterocolitica detection in our region. METHODS Organism identification was performed using conventional commercial diagnostic systems MALDI-TOF, API 20E, API 50CHE, TREK Sensititre GNID and Vitek 2 GN, and whole genome sequencing (WGS) was performed. Historical data for detections was extracted from the lab system for 2008 to 2023. RESULTS All three isolates gave "good" identifications of Yersinia enterocolitica on conventional systems. Further analysis by WGS matched two of the isolates with recently described Yersinia proxima, and the third was a member of the non-pathogenic Yersinia enterocolitica clade 1Aa. DISCUSSION Our analysis of these three isolates deemed them to be Yersinia species not known currently to be pathogenic, but determining this necessitated the use of next-generation sequencing and advanced bioinformatics. Our work highlights the importance of having this technology available to public laboratories, either locally or in a national reference laboratory. The introduction of molecular technologies for the detection of Yersinia species may increase the rate of detections. Accurate identification of significant pathogens in environmental, public health and clinical microbiology laboratories is critically important for the protection of society.
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Affiliation(s)
- James Powell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Maureen Daly
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Nuala H O'Connell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland.
- School of Medicine, University of Limerick, Limerick, Ireland.
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104
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Lin L, Tao M, He WM, Wu QH, Huang HK, Murero AK, Shao XL, Wang LM, Qian GL. Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing. PEST MANAGEMENT SCIENCE 2024; 80:3997-4005. [PMID: 38527976 DOI: 10.1002/ps.8103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay. RESULTS In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli. CONCLUSION Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Long Lin
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Min Tao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Wei-Mei He
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Qian-Hua Wu
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Hao-Kai Huang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Kavutu Murero
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiao-Long Shao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Li-Min Wang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Guo-Liang Qian
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
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105
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Meaney JS, Panchal AK, Wilcox AJ, diCenzo GC, Karas BJ. Identifying functional multi-host shuttle plasmids to advance synthetic biology applications in Mesorhizobium and Bradyrhizobium. Can J Microbiol 2024; 70:336-347. [PMID: 38564797 DOI: 10.1139/cjm-2023-0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ammonia availability has a crucial role in agriculture as it ensures healthy plant growth and increased crop yields. Since diazotrophs are the only organisms capable of reducing dinitrogen to ammonia, they have great ecological importance and potential to mitigate the environmental and economic costs of synthetic fertilizer use. Rhizobia are especially valuable being that they can engage in nitrogen-fixing symbiotic relationships with legumes, and they demonstrate great diversity and plasticity in genomic and phenotypic traits. However, few rhizobial species have sufficient genetic tractability for synthetic biology applications. This study established a basic genetic toolbox with antibiotic resistance markers, multi-host shuttle plasmids and a streamlined protocol for biparental conjugation with Mesorhizobium and Bradyrhizobium species. We identified two repABC origins of replication from Sinorhizobium meliloti (pSymB) and Rhizobium etli (p42d) that were stable across all three strains of interest. Furthermore, the NZP2235 genome was sequenced and phylogenetic analysis determined its reclassification to Mesorhizobium huakuii. These tools will enable the use of plasmid-based strategies for more advanced genetic engineering projects and ultimately contribute towards the development of more sustainable agriculture practices by means of novel nitrogen-fixing organelles, elite bioinoculants, or symbiotic association with nonlegumes.
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Affiliation(s)
- Jordyn S Meaney
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aakanx K Panchal
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Aiden J Wilcox
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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Kim S, Park MS, Kang I, Cho JC. Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream. Curr Microbiol 2024; 81:290. [PMID: 39085659 DOI: 10.1007/s00284-024-03814-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
A Gram-strain-negative, aerobic, yellow-colored, non-motile, and rod-shaped bacterial strain, designated IMCC34852T, was isolated from a freshwater stream in the Republic of Korea. Cellular growth occurred at 10-37 °C, pH 6.0-9.0, and with 0-0.5% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain IMCC34852T belonged to the genus Flavobacterium and that the strain was most closely related to F. cheonhonense ARSA-15 T (97.6%), F. buctense T7T (96.7%), F. silvisoli RD-2-33 T (96.1%), and F. paronense KNUS1T (96.1%). The whole-genome sequence of strain IMCC34852T was 3.2 Mbp in size, with a DNA G + C content 37.3%. The average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34852T and its related species were all below 79.8% and 22.7%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The major respiratory quinone of strain IMCC34852T was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:0 (32.6%), iso-C16:0 (11.7%), iso-C15:1 G (10.3%), and iso-C14:0 (6.7%). The major polar lipids of the strain were phosphatidylethanolamine, two unidentified aminolipids and six unidentified lipids. Based on these results, it was concluded that strain IMCC34852T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium rivulicola sp. nov is proposed. The type strain of the proposed novel species is IMCC34852T (= KACC 23133 T = KCTC 82066 T = NBRC 114419 T).
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Affiliation(s)
- Sumin Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Miri S Park
- Department of Biological Sciences, Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea
- Green & Biome Customizing Laboratory, GFC Co., Ltd., Hwasung, 18471, Gyeonggi-Do, Korea
| | - Ilnam Kang
- Department of Biological Sciences, Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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Otto SJ, Teichmann L, Fante N, Crauwels P, Grünberger A, Neddermann T, Riedel CU. High-throughput detection of potential bacteriocin producers in a large strain library using live fluorescent biosensors. Front Bioeng Biotechnol 2024; 12:1405202. [PMID: 39144483 PMCID: PMC11321961 DOI: 10.3389/fbioe.2024.1405202] [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: 03/22/2024] [Accepted: 07/03/2024] [Indexed: 08/16/2024] Open
Abstract
The global increase in antibiotic resistances demands for additional efforts to identify novel antimicrobials such as bacteriocins. These antimicrobial peptides of bacterial origin are already used widely in food preservation and promising alternatives for antibiotics in animal feed and some clinical setting. Identification of novel antimicrobials is facilitated by appropriate high throughput screening (HTS) methods. Previously, we have described a rapid, simple and cost-efficient assay based on live biosensor bacteria for detection of antimicrobial compounds that act on membrane integrity using the ratiometric pH-dependent fluorescent protein pHluorin2 (pHin2). Here, we use these biosensors to develop an integrated pipeline for high-throughput identification of bacteriocin producers and their biosynthetic gene clusters. We extend the existing portfolio of biosensors by generating pHin2 expressing strains of Escherichia coli, Bacillus cereus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus. These strains were characterized, and control experiments were performed to assess heterogeneity of these biosensors in response to known bacteriocins and develop a robust HTS system. To allow detection of compounds that inhibit target bacteria by inhibiting growth without disturbing membrane integrity, the HTS system was extended with a growth-dependent readout. Using this HTS system, we screened supernatants of a total of 395 strains of a collection of lactic acid bacteria. After two rounds of screening 19 strains of the collection were identified that produced antimicrobial activity against Listeria innocua and Listeria monocytogenes. Genomes of confirmed hits were sequenced and annotated. In silico analysis revealed that the identified strains encode between one and six biosynthetic gene clusters (BGCs) for bacteriocins. Our results suggest that pHin2 biosensors provides a flexible, cheap, fast, robust and easy to handle HTS system for identification of potential bacteriocins and their BGCs in large strain collections.
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Affiliation(s)
| | | | - Niklas Fante
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
| | | | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany
- Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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Saikat TA, Sayem Khan MA, Islam MS, Tasnim Z, Ahmed S. Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications. Heliyon 2024; 10:e34369. [PMID: 39114027 PMCID: PMC11305188 DOI: 10.1016/j.heliyon.2024.e34369] [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: 02/19/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.
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Affiliation(s)
| | - Md Abu Sayem Khan
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Zarin Tasnim
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sangita Ahmed
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
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Sermkaew N, Atipairin A, Wanganuttara T, Krobthong S, Aonbangkhen C, Yingchutrakul Y, Uchiyama J, Songnaka N. A Novel Bacitracin-like Peptide from Mangrove-Isolated Bacillus paralicheniformis NNS4-3 against MRSA and Its Genomic Insights. Antibiotics (Basel) 2024; 13:716. [PMID: 39200016 PMCID: PMC11350868 DOI: 10.3390/antibiotics13080716] [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: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/01/2024] Open
Abstract
The global rise of antimicrobial resistance (AMR) presents a critical challenge necessitating the discovery of novel antimicrobial agents. Mangrove microbes are valuable sources of new antimicrobial compounds. This study reports the discovery of a potent antimicrobial peptide (AMP) from Bacillus paralicheniformis NNS4-3, isolated from mangrove sediment, exhibiting significant activity against methicillin-resistant Staphylococcus aureus (MRSA). The AMP demonstrated a minimum inhibitory concentration ranging from 1 to 16 µg/mL in the tested bacteria and exhibited bactericidal effects at higher concentrations. Structural analysis revealed a bacitracin-like configuration and the peptide acted by disrupting bacterial membranes in a time- and concentration-dependent manner. The AMP maintained stability under heat, proteolytic enzymes, surfactants, and varying pH treatments. The ten biosynthetic gene clusters (BGCs) of secondary metabolites were found in the genome. Detailed sequence comparison of the predicted bacitracin BGC indicated distinct DNA sequences compared to previously reported strains. Although the antibiotic resistance genes were found, this strain was susceptible to antibiotics. Our findings demonstrated the potential of Bacillus paralicheniformis NNS4-3 and its AMP as a promising agent in combating AMR. The genetic information could be pivotal for future applications in the healthcare industry, emphasizing the need for continued exploration of marine microbial diversity in drug discovery.
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Affiliation(s)
- Namfa Sermkaew
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Apichart Atipairin
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Thamonwan Wanganuttara
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Nuttapon Songnaka
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand; (N.S.); (A.A.); (T.W.)
- Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
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Lee H, Chaudhary DK, Kim DU. Agromyces silvae sp. nov., Rathayibacter soli sp. nov., and Nocardioides terrisoli sp. nov., Isolated from Soil. J Microbiol Biotechnol 2024; 34:1475-1483. [PMID: 38973386 PMCID: PMC11294650 DOI: 10.4014/jmb.2404.04007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 07/09/2024]
Abstract
Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11T, SW19T, and YR1T, were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11T, SW19T, and YR1T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11T was closely affiliated with Agromyces cavernae SYSU K20354T (98.1%), strain SW19T showed the closest affiliation with Rathayibacter rubneri ZW T2_19T (97.0%), and strain YR1T was most closely related to Nocardioides marmorisolisilvae KIS18-7T (98.0%). The genome sizes of strains W11T, SW19T, and YR1T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA-DNA hybridization values of W11T, SW19T, and YR1T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11T were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. In strain SW19T, they were summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω 9c), anteiso-C17:0, and anteiso-C15:0. Strain YR1T exhibited C18:1ω 9c, C18:0 10-methyl, TBSA, and anteiso-C15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11T, SW19T, and YR1T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11T (=KCTC 49818T =NBRC 115999T), Rathayibacter soli sp. nov., with the type strain SW19T (=KCTC 49860T =NBRC 116108T), and Nocardioides terrisoli sp. nov., with the type strain YR1T (=KCTC 49863T =NBRC 116165T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 26339, Republic of Korea
| | | | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 26339, Republic of Korea
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Maltseva PY, Plotnitskaya NA, Krivoruchko AV, Beletskiy AV, Rakitin AL, Mardanov AV, Ivshina IB. Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer. Genes (Basel) 2024; 15:992. [PMID: 39202353 PMCID: PMC11354180 DOI: 10.3390/genes15080992] [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: 07/04/2024] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.
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Affiliation(s)
- Polina Yu. Maltseva
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Natalia A. Plotnitskaya
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Anastasiia V. Krivoruchko
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Aleksey V. Beletskiy
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Irina B. Ivshina
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
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Maw ZA, Grunwald AL, Haltli BA, Cartmell C, Kerr RG. Discovery of the Lipopeptides Albubactins A-H from Streptomyces albidoflavus RKJM0023 via Chemical Elicitation with Rhamnolipids and Synthesis of Albubactin A. JOURNAL OF NATURAL PRODUCTS 2024; 87:1682-1693. [PMID: 38940698 DOI: 10.1021/acs.jnatprod.3c01234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The marine tunicate-derived Streptomyces albidoflavus RKJM0023 was cultured in the presence of a rhamnolipid mixture in an effort to elicit the production of silent natural products. MS/MS-based molecular networking analysis enhanced with nonparametric statistics highlighted the upregulation of a molecular cluster (Kruskal-Wallis p = 1.6 e-6 for 1) in which no MS/MS features had library matches. Targeted isolation of these features resulted in the discovery of nine new N-acylated lipopeptides, albubactins A-H (1-8) each containing a unique glutamine tripeptide and a C-terminal ethyl ester moiety. Three related albubactin acids A-C (9-11) lacking the ethyl ester were also identified. NMR spectroscopy and UPLC-HR-ESI-MS/MS demonstrated that the albubactins were obtained as mixtures that shared a common m/z and differed only in their acylated terminal groups. Due to the complex spectroscopic elucidation with many overlapping shifts, a total synthesis of albubactin A (1) was completed and used to determine the absolute configuration of the new albubactins.
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Affiliation(s)
- Zacharie A Maw
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
| | - Alyssa L Grunwald
- Nautilus Biosciences, Croda Canada, Charlottetown, PEI C1A 4P3, Canada
| | - Bradley A Haltli
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
- Nautilus Biosciences, Croda Canada, Charlottetown, PEI C1A 4P3, Canada
| | - Christopher Cartmell
- Department of Pharmacology, College of Medicine; Comprehensive Center for Pain and Addiction, University of Arizona, Tucson, AZ 85724, United States
| | - Russell G Kerr
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
- Department of Chemistry, Faculty of Science, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
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Bucka-Kolendo J, Kiousi DE, Dekowska A, Mikołajczuk-Szczyrba A, Karadedos DM, Michael P, Galanis A, Sokołowska B. Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance. Int J Mol Sci 2024; 25:8144. [PMID: 39125715 PMCID: PMC11312215 DOI: 10.3390/ijms25158144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.
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Affiliation(s)
- Joanna Bucka-Kolendo
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Agnieszka Dekowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Anna Mikołajczuk-Szczyrba
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Dimitrios Marinos Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Panagiotis Michael
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
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Xie J, Yin D, Ou J, Lu B, Liao S, Yang D, Zhang H, Shen N. A new strain of Rhodococcus indonesiensis T22.7.1 T and its functional potential for deacetylation of chitin and chitooligsaccharides. Front Microbiol 2024; 15:1427143. [PMID: 39113839 PMCID: PMC11303147 DOI: 10.3389/fmicb.2024.1427143] [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: 05/03/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Chitin, abundant in marine environments, presents significant challenges in terms of transformation and utilization. A strain, T22.7.1T, with notable chitin deacetylation capabilities, was isolated from the rhizosphere of Acanthus ebracteatus in the North Sea of China. Comparative 16S rDNA sequence analysis showed that the new isolate had the highest sequence similarity (99.79%) with Rhodococcus indonesiensis CSLK01-03T, followed by R. ruber DSM 43338T, R. electrodiphilus JC435T, and R. aetherivorans 10bc312T (98.97%, 98.81%, and 98.83%, respectively). Subsequent genome sequencing and phylogenetic analysis confirmed that strain T22.7.1T belongs to the R. indonesiensis species. However, additional taxonomic characterization identified strain T22.7.1T as a novel type strain of R. indonesiensis distinct from CSLK01-03T. Methods This study refines the taxonomic description of R. indonesiensis and investigates its application in converting chitin into chitosan. The chitin deacetylase (RiCDA) activity of strain T22.7.1T was optimized, and the enzyme was isolated and purified from the fermentation products. Results Through optimization, the RiCDA activity of strain T22.7.1T reached 287.02 U/mL, which is 34.88 times greater than the original enzyme's activity (8.0 U/mL). The natural CDA enzyme was purified with a purification factor of 31.83, and the specific activity of the enzyme solution reached 1200.33 U/mg. RiCDA exhibited good pH and temperature adaptability and stability, along with a wide range of substrate adaptabilities, effectively deacetylating chitin, chitooligosaccharides, N-acetylglucosamine, and other substrates. Discussion Product analysis revealed that RiCDA treatment increased the deacetylation degree (DD) of natural chitin to 83%, surpassing that of commercial chitosan. Therefore, RiCDA demonstrates significant potential as an efficient deacetylation tool for natural chitin and chitooligosaccharides, highlighting its applicability in the biorefining of natural polysaccharides.
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Affiliation(s)
- Junjie Xie
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Doudou Yin
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Junchao Ou
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Bo Lu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Siming Liao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Hongyan Zhang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Naikun Shen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
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Samadpour M, Benoit L, Myoda S, Hans B, Nadala C, Kim SH, Themeli E, Cantera R, Nguyen T, Richter H. Microbiological survey and genomic analysis of Cronobacter sakazakii strains isolated from US households and retail foods. Appl Environ Microbiol 2024; 90:e0070024. [PMID: 38953659 PMCID: PMC11267904 DOI: 10.1128/aem.00700-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Cronobacter species are opportunistic pathogens that are capable of causing morbidity and mortality, particularly in infants. Although the transmission dynamics involved in Cronobacter infections remain largely unknown, contaminated powdered infant formula (PIF) has been linked to 30% of Cronobacter sakazakii cases involving invasive illness in infants. As several lines of evidence have implicated the domestic environment in PIF contamination, we undertook a microbiological survey of homes (N = 263) across the US. Cronobacter spp. and C. sakazakii were isolated from 36.1% and 24.7% of US homes, respectively, with higher recovery rates observed for floor and kitchen surfaces. Multi-locus sequence typing indicated that the dominant strain was C. sakazakii ST4, the sequence type most commonly associated with neonatal meningitis. For comparison purposes, retail foods (N = 4,009) were also surveyed, with the highest contamination frequencies (10.1%-26.3%) seen for nut products, seeds, and grains/baked goods/flours. The sequence type profile of isolates recovered from homes mirrored that of isolates recovered from retail foods, with increased representation of ST1, ST4, ST13, ST17, and ST40. Analysis of 386 whole genomic sequences revealed significant diversity. Redundancies were only observed for isolates recovered from within the same domicile, and there were no identical matches with sequences archived at the NCBI pathogen database. Genes coding for putative virulence and antibiotic resistance factors did not segregate with clinically significant sequence types. Collectively, these findings support the possibility that contamination events occurring within the home should not be overlooked as a contributor to community-onset Cronobacter infections. IMPORTANCE Cronobacter sakazakii is an opportunistic pathogen that can cause significant morbidity and mortality in neonates. Its transmission dynamics are poorly understood, though powered infant formula (PIF) is thought to be the major transmission vehicle. How the PIF becomes contaminated remains unknown. Our survey shows that roughly 1/4 of US homes are contaminated with Cronobacter sakazakii, particularly in the kitchen setting. Our analyses suggest that the domestic environment may contribute to contamination of PIF and provides insights into mitigating the risk of transmission.
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Affiliation(s)
- Mansour Samadpour
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Lora Benoit
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Sam Myoda
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Bada Hans
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Cesar Nadala
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Seong Hong Kim
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Eni Themeli
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Ruth Cantera
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Truyen Nguyen
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
| | - Hans Richter
- IEH Laboratories and Consulting Group Inc., Lake Forest Park, Washington, USA
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Mian G, Belfiore N, Marcuzzo P, Spinelli F, Tomasi D, Colautti A. Counteracting Grey Mould ( Botrytis cinerea) in Grapevine 'Glera' Using Three Putative Biological Control Agent Strains ( Paraburkholderia sp., Pseudomonas sp., and Acinetobacter sp.): Impact on Symptoms, Yield, and Gene Expression. Microorganisms 2024; 12:1515. [PMID: 39203358 PMCID: PMC11356063 DOI: 10.3390/microorganisms12081515] [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: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
This study examined the potential use of three bacterial strains-Paraburkholderia sp. strain CRV74, Pseudomonas sp. strain CRV21, and Acinetobacter sp. strain CRV19-as biocontrol agents of Botrytis cinerea in grapevine. These strains were selected for their ability to inhibit B. cinerea growth in vitro and used in field conditions for the control of grey mould symptoms in 'Glera' grapes. To this end, after inoculating these microorganisms onto plants sprayed with B. cinerea spores, the final yield, the physicochemical characteristics of the must, disease incidence, and the possible influence on the expression of plant-defence proteins were evaluated. Strain CRV21 resulted as being the most effective in combating grey mould (-20% of disease incidence). Although yield was not affected, significantly different values of total soluble solids content was observed. Additionally, a significant up-regulation of the genes PR-1, PR-5, β-1,3-glucanase, and class III chitinase was observed. These findings highlight the potential application of strains with anti-botrytis activity as sustainable alternatives to chemical defence for the control of this pathogen.
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Affiliation(s)
- Giovanni Mian
- Department of Agricultural and Food Sciences, Alma Mater Studiorum Università di Bologna, 40129 Bologna, Italy; (G.M.); (F.S.)
| | - Nicola Belfiore
- Council for Agricultural and Economics-Research-Centre for Viticulture and Oenology, Viale Aprile, 26, 31015 Conegliano, Italy; (N.B.); (P.M.)
| | - Patrick Marcuzzo
- Council for Agricultural and Economics-Research-Centre for Viticulture and Oenology, Viale Aprile, 26, 31015 Conegliano, Italy; (N.B.); (P.M.)
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum Università di Bologna, 40129 Bologna, Italy; (G.M.); (F.S.)
| | - Diego Tomasi
- Consorzio Tutela del Vino Conegliano Valdobbiadene Prosecco, Piazza Libertà, 7, 31053 Pieve di Soligo, Italy;
| | - Andrea Colautti
- Department of Agricultural, Food, Environmental and Animal Science (Di4A), University of Udine, 33100 Udine, Italy
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Khan IU, Saqib M, Amin A, Manzoor S, Ahmed I, Liu RR, Jiao JY, Zhi XY, Li WJ. Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China. Antonie Van Leeuwenhoek 2024; 117:103. [PMID: 39042225 DOI: 10.1007/s10482-024-02001-8] [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: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.
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Affiliation(s)
- Inam Ullah Khan
- Faculty of Veterinary and Animal Sciences, Institute of Microbiology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Muhammad Saqib
- Department of Zoology, Gomal University, Tank Campus, 29050, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500, Pakistan
| | - Sadia Manzoor
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Zhang W, Zheng L, Xie J, Su X, Zhang M, Huang H, Schmitz-Esser S, Du S, Yang Y, Xie J, Zhang Q, Yu S, Guo Q, Wang H, Zhang L, Yang K, Hou R. The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline. mSystems 2024; 9:e0052024. [PMID: 38920380 PMCID: PMC11265448 DOI: 10.1128/msystems.00520-24] [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: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Some lactic acid bacteria (LAB) can provide significant health benefits, which are critically important for the conservation of endangered animals, such as giant pandas. However, little is known about the diversity and culturability of LAB in the giant panda gut microbiota. To understand the roles of LAB in giant panda conservation, it is critical to culture bacterial strains of interest. In this study, we established a pipeline to culture bacterial strains using enrichment of target bacteria with different liquid media and growth conditions. Then, the strains were isolated in solid media to study their functions. Using 210 samples from the culture enrichment method and 138 culture-independent samples, we obtained 1120 amplicon sequencing variants (ASVs) belonging to Lactobacillales. Out of the 1120 ASVs, 812 ASVs from the culture enrichment approach were twofold more diverse than 336 ASVs from the culture-independent approach. Many ASVs of interest were not detected in the culture-independent approach. Using this pipeline, we isolated many relevant bacterial strains and established a giant panda gut bacteria strain collection that included strains with low-abundance in culture-independent samples and included most of the giant panda LAB described by other researchers. The strain collection consisted of 60 strains representing 35 species of 12 genera. Thus, our pipeline is powerful and provides guidance in culturing gut microbiota of interest in hosts such as the giant panda.IMPORTANCECultivation is necessary to screen strains to experimentally investigate microbial traits, and to confirm the activities of novel genes through functional characterization studies. In the long-term, such work can aid in the identification of potential health benefits conferred by bacteria and this could aid in the identification of bacterial candidate strains that can be applied as probiotics. In this study, we developed a pipeline with low-cost and user-friendly culture enrichment to reveal the diversity of LAB in giant pandas. We compared the difference between culture-independent and culture enrichment methods, screened strains of interest that produced high concentrations of short-chain fatty acids (SCFAs), and we investigated the catalog of virulence factors, antibiotic resistance, butyrate and lactate synthesis genes of the strains at a genomic level. This study will provide guidance for microbiota cultivation and a foundation for future research aiming to understand the functions of specific strains.
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Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Lijun Zheng
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Junjin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xiaoyan Su
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu, Sichuan, China
| | - He Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | | | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
| | - Yu Yang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Jiqin Xie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qinrong Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Shuran Yu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Qiang Guo
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Hairui Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Kong Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
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Molina D, Carrión–Olmedo JC, Jarrín–V P, Tenea GN. Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits ( Physalis peruviana L.). Front Microbiol 2024; 15:1392333. [PMID: 39104589 PMCID: PMC11298459 DOI: 10.3389/fmicb.2024.1392333] [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: 02/27/2024] [Accepted: 07/09/2024] [Indexed: 08/07/2024] Open
Abstract
Introduction Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question. Methods This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes. Results The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood). Conclusion Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.
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Affiliation(s)
- Diana Molina
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
| | - Julio C. Carrión–Olmedo
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Innovación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Pablo Jarrín–V
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Innovación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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Kumari S, Kumar A, Lepcha A, Kumar R. Cold-adapted Exiguobacterium sibiricum K1 as a potential bioinoculant in cold regions: Physiological and genomic elucidation of biocontrol and plant growth promotion. Gene 2024; 916:148439. [PMID: 38583819 DOI: 10.1016/j.gene.2024.148439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
The scarcity of soil nutrient availability under cold conditions of Himalayan regions needs a sustainable approach for better crop yields. The cold-adapted bacteria, Exiguobacterium sibiricum K1, with the potential to produce several plant growth-promoting (PGP) attributes, nitrogen fixation, indole acetic acid production, phosphate and potassium solubilization at 10 °C can provide an opportunity to promote crop yield improvement in an eco-friendly way under cold conditions. The bacterium also exhibited biocontrol activity against two phytopathogens and produced siderophore (53.0 ± 0.5 % psu). The strain's PGP properties were investigated using a spinach-based bioassay under controlled conditions. The bacterized seeds showed a notable increase in germination rate (23.2 %), shoot length (65.3 %), root length (56.6 %), leaf area (73.7 %), number of leaflets (65.2 %), and dry matter (65.2 %). Additionally, the leaf analysis indicated elevated chlorophyll pigments, i.e., chlorophyll a (55.5 %), chlorophyll b (42.8 %), carotenoids (35.2 %), percentage radical scavenging activity (47.4 %), and leaf nutrient uptake such as nitrogen (23.4 %), calcium (60.8 %), potassium (62.3 %), and magnesium (28.9 %). Moreover, the whole-genome sequencing and genome mining endorsed various biofertilisation-related genes, including genes for potassium and phosphate solubilization, iron and nitrogen acquisition, carbon dioxide fixation, and biocontrol ability of Exiguobacterium sibiricum K1. Overall, this study highlights the role of Exiguobacterium sibiricum K1 as a potential bioinoculant for improving crop yield under cold environments.
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Affiliation(s)
- Sareeka Kumari
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Anil Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Ayush Lepcha
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rakshak Kumar
- High Altitude Microbiology Laboratory (HAM-LAB), Biotechnology Division, CSIR -Institute of Himalayan and Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India; Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
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Millán-López S, Zurita-Artaloitia JM, Silva-Jiménez H, Pardo-López L, Sanchez-Flores A. Genomic sequence of three hydrocarbonoclastic pseudomonadaceae strains isolated from marine sediments of the port of Rosarito, Baja California, Mexico. Microbiol Resour Announc 2024; 13:e0033524. [PMID: 38916305 PMCID: PMC11256838 DOI: 10.1128/mra.00335-24] [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: 04/02/2024] [Accepted: 05/24/2024] [Indexed: 06/26/2024] Open
Abstract
We report the draft genome sequence of three marine bacteria belonging to Pseudomonas and Stutzerimonas genera, with hydrocarbonoclastic metabolism for oil and monoaromatic hydrocarbon degradation. The genomic information of these organisms contributes to the knowledge of natural and polluted marine environments with ubiquitous presence of hydrocarbons as a selective pressure.
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Affiliation(s)
- Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan M. Zurita-Artaloitia
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Ramzan R, Ali A, Farooq M, Ali H, Khaliq S, Rashid MH. Draft genome sequence of extracellular enzyme-producing Bacillus paralicheniformis strain NBG-07. Microbiol Resour Announc 2024; 13:e0009624. [PMID: 38860803 PMCID: PMC11256837 DOI: 10.1128/mra.00096-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024] Open
Abstract
The genome of Bacillus paralicheniformis strain NBG-07 was sequenced using Illumina sequencing due to its ability to produce thermostable enzymes of industrial importance. The strain was isolated from the soil. Annotation of the draft genome revealed genes involved in the production of different enzymes, including alpha-amylase, protease, cellulase, and laccase.
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Affiliation(s)
- Rubab Ramzan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Asad Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Hamid Rashid
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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Dao VHT, Nguyen LT, Tran PMT, Nguyen TX, Le HHT, Dinh ST. Whole-genome sequence of Micrococcus sp. strain HOU01 isolated from potato root. Microbiol Resour Announc 2024; 13:e0026824. [PMID: 38916298 PMCID: PMC11256776 DOI: 10.1128/mra.00268-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Endophytes play important roles in potato production. The whole genome of endophytic Micrococcus sp. Strain HOU01, isolated from potato root grown at Vietnam National University of Agriculture, Hanoi, Vietnam, was sequenced using Oxford Nanopore's PromethION platform. The complete circular genome is 2,552,707 bp with a GC content of 72.5%.
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Affiliation(s)
| | - Loan To Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
| | - Phuong Minh Thi Tran
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Truong Xuan Nguyen
- Institute of Agrobiology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | | | - Son Truong Dinh
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
- Institute of Agrobiology, Vietnam National University of Agriculture, Hanoi, Vietnam
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Wang X, Pan H, Zhou H, Feng Z, Li A, Guan X. Draft genome of Pseudomonas sp. XK-1, a marine bacterium capable of degrading lignin and Mn(II) oxidation. Microbiol Resour Announc 2024; 13:e0041124. [PMID: 38864618 PMCID: PMC11256819 DOI: 10.1128/mra.00411-24] [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: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
We report the draft genome sequence of marine bacteria, Pseudomonas sp. XK-1. Strain XK-1 could facilitate Mn(II) oxidation with lignin as the sole carbon source. The genome length of XK-1 is 4,751,776 bp, with a G + C content of 62.61%. Genome analyses reveal the carbon and manganese cycling driven by bacteria.
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Affiliation(s)
- Xukang Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Zhongqing Feng
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, Panjin, China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Xiaoyan Guan
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
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Stegman N, Steiling M, Jackson B, Sedano C, Putonti C. Draft genome assembly of Lactobacillus johnsonii UMB3423 from a voided urine sample. Microbiol Resour Announc 2024; 13:e0033324. [PMID: 38832771 PMCID: PMC11256846 DOI: 10.1128/mra.00333-24] [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: 03/30/2024] [Accepted: 05/02/2024] [Indexed: 06/05/2024] Open
Abstract
While the urogenital microbiota of asymptomatic females is often dominated by species of Lactobacillus, Lactobacillus johnsonii is not a common member. It is more frequently found in the gastrointestinal tract. Here, we present the draft genome sequence of L. johnsonii UMB3423, which was isolated from a voided urine sample.
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Affiliation(s)
- Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Maria Steiling
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Briana Jackson
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Cerena Sedano
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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Půža V, Machado RAR. Systematics and phylogeny of the entomopathogenic nematobacterial complexes Steinernema-Xenorhabdus and Heterorhabditis-Photorhabdus. ZOOLOGICAL LETTERS 2024; 10:13. [PMID: 39020388 PMCID: PMC11256433 DOI: 10.1186/s40851-024-00235-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/08/2024] [Indexed: 07/19/2024]
Abstract
Entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, along with their bacterial symbionts from the genera Xenorhabdus and Photorhabdus, respectively, are important biological control agents against agricultural pests. Rapid progress in the development of genomic tools has catalyzed a transformation of the systematics of these organisms, reshaping our understanding of their phylogenetic and cophlylogenetic relationships. In this review, we discuss the major historical events in the taxonomy and systematics of this group of organisms, highlighting the latest advancements in these fields. Additionally, we synthesize information on nematode-bacteria associations and assess the existing evidence regarding their cophylogenetic relationships.
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Affiliation(s)
- Vladimír Půža
- Institute of Entomology, Biology centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic.
- Faculty of Agriculture and Technology, University of South Bohemia, Studentská 1668, České Budějovice, 37005, Czech Republic.
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Neuchâtel, 2000, Switzerland.
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da Silva Santos D, Freitas NSA, de Morais MA, Mendonça AA. Liquorilactobacillus: A Context of the Evolutionary History and Metabolic Adaptation of a Bacterial Genus from Fermentation Liquid Environments. J Mol Evol 2024:10.1007/s00239-024-10189-6. [PMID: 39017924 DOI: 10.1007/s00239-024-10189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
In the present work, we carried out a comparative genomic analysis to trace the evolutionary trajectory of the bacterial species that make up the Liquorilactobacillus genus, from the identification of genes and speciation/adaptation mechanisms in their unique characteristics to the identification of the pattern grouping these species. We present phylogenetic relationships between Liquorilactobacillus and related taxa such as Bacillus, basal lactobacilli and Ligilactobacillus, highlighting evolutionary divergences and lifestyle transitions across different taxa. The species of this genus share a core genome of 1023 genes, distributed in all COGs, which made it possible to characterize it as Liquorilactobacillus sensu lato: few amino acid auxotrophy, low genes number for resistance to antibiotics and general and specific cellular reprogramming mechanisms for environmental responses. These species were divided into four clades, with diversity being enhanced mainly by the diversity of genes involved in sugar metabolism. Clade 1 presented lower (< 70%) average amino acid identity with the other clades, with exclusive or absent genes, and greater distance in the genome compared to clades 2, 3 and 4. The data pointed to an ancestor of clades 2, 3 and 4 as being the origin of the genus Ligilactobacillus, while the species of clade 1 being closer to the ancestral Bacillus. All these traits indicated that the species of clade 1 could be soon separated in a distinct genus.
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Affiliation(s)
- Dayane da Silva Santos
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | - Marcos Antonio de Morais
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
| | - Allyson Andrade Mendonça
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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Romanenko L, Bystritskaya E, Savicheva Y, Eremeev V, Otstavnykh N, Kurilenko V, Velansky P, Isaeva M. Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan. Microorganisms 2024; 12:1413. [PMID: 39065181 PMCID: PMC11278836 DOI: 10.3390/microorganisms12071413] [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: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA-DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed.
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Yuliya Savicheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Viacheslav Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Peter Velansky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
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Elgayar FA, Gouda MK, Badran AA, El Halfawy NM. Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt. BMC Microbiol 2024; 24:256. [PMID: 38987681 PMCID: PMC11234735 DOI: 10.1186/s12866-024-03389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic. METHODS In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate. RESULTS The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer. CONCLUSIONS This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.
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Affiliation(s)
- Fatma A Elgayar
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Mona K Gouda
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Alaa Aboelnour Badran
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nancy M El Halfawy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt.
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Kumar P, Verma A, Yadav P, Das J, Kumar L, Krishnamurthi S. Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172995. [PMID: 38719044 DOI: 10.1016/j.scitotenv.2024.172995] [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: 12/14/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Lalit Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
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Gandham P, Vadla N, Saji A, Srinivas V, Ruperao P, Selvanayagam S, Saxena RK, Rathore A, Gopalakrishnan S, Thakur V. Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Sci Rep 2024; 14:15934. [PMID: 38987320 PMCID: PMC11237095 DOI: 10.1038/s41598-024-66835-y] [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: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.
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Affiliation(s)
- Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Nandini Vadla
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Angeo Saji
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India.
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania.
| | - Vivek Thakur
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
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Van Le V, Ko SR, Nguyen LTT, Kim JC, Shin Y, Kim K, Ahn CY. Undibacterium cyanobacteriorum sp. nov., an auxin-producing bacterium isolated from fresh water during cyanobacterial bloom period. Antonie Van Leeuwenhoek 2024; 117:99. [PMID: 38985203 DOI: 10.1007/s10482-024-01992-8] [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: 12/12/2023] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
A novel Gram-negative, white-pigmented, and auxin-producing strain, 20NA77.5T, was isolated from fresh water during cyanobacterial bloom period. Pairwise comparison of the 16S rRNA gene sequences showed that strain 20NA77.5T belonged to the genus Undibacterium and exhibited the highest sequence similarity to the type strains of Undibacterium danionis (98.00%), Undibacterium baiyunense (97.93%), Undibacterium macrobrachii (97.92%), and Undibacterium fentianense (97.71%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain 20NA77.5T and its related type strains were below 79.93 and 23.80%, respectively. The predominant fatty acids (> 10% of the total fatty acids) were C16:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The genomic DNA G + C content of strain 20NA77.5T was found to be 48.61%. Based on the phylogenetic distinctness, chemotaxonomic features, and phenotypic features, strain 20NA77.5T is considered to represent a novel species of the genus Undibacterium, for which the name Undibacterium cyanobacteriorum sp. nov is proposed. The type strain is 20NA77.5T (= KCTC 8005T = LMG 33136T).
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yuna Shin
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Kyunghyun Kim
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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Poddar BJ, Khardenavis AA. Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04980-w. [PMID: 38980659 DOI: 10.1007/s12010-024-04980-w] [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] [Accepted: 06/05/2024] [Indexed: 07/10/2024]
Abstract
In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.
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Affiliation(s)
- Bhagyashri J Poddar
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Wetzstein N, Diricks M, Anton TB, Andres S, Kuhns M, Kohl TA, Schwarz C, Lewin A, Kehrmann J, Kahl BC, Schmidt A, Zimmermann S, Jansson MK, Baron SA, Schulthess B, Hogardt M, Friesen I, Niemann S, Wichelhaus TA. Clinical and genomic features of Mycobacterium avium complex: a multi-national European study. Genome Med 2024; 16:86. [PMID: 38982539 PMCID: PMC11232273 DOI: 10.1186/s13073-024-01359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. METHODS Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. RESULTS Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). CONCLUSIONS This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas B Anton
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany
| | - Sönke Andres
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Martin Kuhns
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Carsten Schwarz
- Division of Cystic Fibrosis, CF Center Westbrandenburg, Campus Potsdam, Klinikum Potsdam, Potsdam, Germany
| | - Astrid Lewin
- Unit Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Annika Schmidt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Moritz K Jansson
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sophie A Baron
- Faculté de Médecine Et de Pharmacie, IRD, APHM, Aix Marseille Univ, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bettina Schulthess
- National Reference Laboratory for Mycobacteria, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
- German National Consiliary Laboratory On Cystic Fibrosis Bacteriology, Frankfurt Am Main, Germany
| | - Inna Friesen
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
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Lu YT, Wu YY, Li YN, Zheng WY, Liu WZ. Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis. Arch Microbiol 2024; 206:342. [PMID: 38967823 DOI: 10.1007/s00203-024-04069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
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Affiliation(s)
- Yi-Ting Lu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Yi-Yi Wu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
- Department of Pharmaceutical Laboratory, Anhui Sunhere Pharmaceutical Excipients Co., Ltd, Huainan, Anhui Province, 232000, China
| | - Wei-Yi Zheng
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
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Alghamdi AK, Parween S, Hirt H, Saad MM. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina. BMC Genomics 2024; 25:672. [PMID: 38969999 PMCID: PMC11225332 DOI: 10.1186/s12864-024-10555-0] [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: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.
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Affiliation(s)
- Amal Khalaf Alghamdi
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
| | - Maged M Saad
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Böer T, Schüler MA, Lüschen A, Eysell L, Dröge J, Heinemann M, Engelhardt L, Basen M, Daniel R, Poehlein A. Isolation and characterization of novel acetogenic strains of the genera Terrisporobacter and Acetoanaerobium. Front Microbiol 2024; 15:1426882. [PMID: 39021630 PMCID: PMC11253131 DOI: 10.3389/fmicb.2024.1426882] [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: 05/02/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Due to their metabolic versatility in substrate utilization, acetogenic bacteria represent industrially significant production platforms for biotechnological applications such as syngas fermentation, microbial electrosynthesis or transformation of one-carbon substrates. However, acetogenic strains from the genera Terrisporobacter and Acetoanaerobium remained poorly investigated for biotechnological applications. We report the isolation and characterization of four acetogenic Terrisporobacter strains and one Acetoanaerobium strain. All Terrisporobacter isolates showed a characteristic growth pattern under a H2 + CO2 atmosphere. An initial heterotrophic growth phase was followed by a stationary growth phase, where continuous acetate production was indicative of H2-dependent acetogenesis. One of the novel Terrisporobacter isolates obtained from compost (strain COMT) additionally produced ethanol besides acetate in the stationary growth phase in H2-supplemented cultures. Genomic and physiological characterizations showed that strain COMT represented a novel Terrisporobacter species and the name Terrisporobacter vanillatitrophus is proposed (=DSM 116160T = CCOS 2104T). Phylogenomic analysis of the novel isolates and reference strains implied the reclassification of the T. petrolearius/T. hibernicus phylogenomic cluster to the species T. petrolearius and of the A. noterae/A. sticklandii phylogenomic cluster to the species A. sticklandii. Furthermore, we provide first insights into active prophages of acetogens from the genera Terrisporobacter and Acetoanaerobium.
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Affiliation(s)
- Tim Böer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Miriam Antonia Schüler
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Alina Lüschen
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lena Eysell
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Jannina Dröge
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lisa Engelhardt
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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Samudio Oggero A, Valdez Borda M, Félix Pablos CM, Leguizamón G, Morínigo FM, González Caballero V, Farías A, Nakayama H, de los Santos Villalobos S. Draft genome sequence of Agrobacterium pusense strain CMT1: A promising growth-promoting bacterium isolated from nodules of soybean ( Glycine max L. Merrill) crops for the One Health approach in Paraguay. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100259. [PMID: 39076833 PMCID: PMC11284674 DOI: 10.1016/j.crmicr.2024.100259] [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: 07/31/2024] Open
Abstract
Strain CMT1 was isolated from nodules of non-inoculated Roundup Ready (RR) soybean plants (Glycine max L. Merrill), which were collected in fields in Itauguá, Paraguay. The genome of this strain had 338,984,909 bp; 59.2 % G + C content; 377648 bp N50; 5 L50; 55 contigs; 51 RNAs and 5,272 predicted coding DNA sequences (CDS) distributed in 327 subsystems. Based on overall genome-relatedness indices (OGRIs), this strain was taxonomically affiliated with Agrobacterium pusense. Based on genome mining, strain CMT1 is a promising plant growth-promoting bacterium that could be validated in agricultural fields for increasing soybean yield and quality, diminishing the economic, environmental, and health costs of non-sustainable food production.
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Affiliation(s)
- Antonio Samudio Oggero
- Universidad Nacional de Asunción. Centro Multidisciplinario de Investigaciones Tecnológicas. Campus Universitario, San Lorenzo, Central, Paraguay
| | - Magalí Valdez Borda
- Universidad Nacional de Asunción. Centro Multidisciplinario de Investigaciones Tecnológicas. Campus Universitario, San Lorenzo, Central, Paraguay
| | | | - Gladis Leguizamón
- Universidad Columbia del Paraguay. Carrera de Ingeniería Agronómica. Asunción, Central, Paraguay
| | - Fernando Mathías Morínigo
- Universidad Nacional de Asunción. Centro Multidisciplinario de Investigaciones Tecnológicas. Campus Universitario, San Lorenzo, Central, Paraguay
| | | | - Ariel Farías
- Universidad Nacional de Asunción. Centro Multidisciplinario de Investigaciones Tecnológicas. Campus Universitario, San Lorenzo, Central, Paraguay
| | - Héctor Nakayama
- Universidad Nacional de Asunción. Centro Multidisciplinario de Investigaciones Tecnológicas. Campus Universitario, San Lorenzo, Central, Paraguay
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Behrendt U, Burghard V, Wende S, Ulrich K, Wolf J, Neumann-Schaal M, Ulrich A. Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus. Syst Appl Microbiol 2024; 47:126516. [PMID: 38772267 DOI: 10.1016/j.syapm.2024.126516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
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Affiliation(s)
- Undine Behrendt
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Valentin Burghard
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Sonja Wende
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Kristina Ulrich
- Johann Heinrich Von Thünen Institute, Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany.
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
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140
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Schäfer L, Jehle JA, Kleespies RG, Wennmann JT. Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms. J Invertebr Pathol 2024; 205:108121. [PMID: 38705355 DOI: 10.1016/j.jip.2024.108121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
The oak processionary moth (OPM) Thaumetopoea processionea is a pest of oak trees and poses health risks to humans due to the urticating setae of later instar larvae. For this reason, it is difficult to rear OPM under laboratory conditions, carry out bioassays or examine larvae for pathogens. Biological control targets the early larval instars and is based primarily on commercial preparations of Bacillus thuringiensis ssp. kurstaki (Btk). To test the entomopathogenic potential of other spore-forming bacteria, a user-friendly bioassay system was developed that (i) applies bacterial spore suspensions by oak bud dipping, (ii) targets first instar larvae through feeding exposure and (iii) takes into account their group-feeding behavior. A negligible mortality in the untreated control proved the functionality of the newly established bioassay system. Whereas the commercial Btk HD-1 strain was used as a bioassay standard and confirmed as being highly efficient, a Bacillus wiedmannii strain was ineffective in killing OPM larvae. Larvae, which died during the infection experiment, were further subjected to Nanopore sequencing for a metagenomic approach for entomopathogen detection. It further corroborated that B.wiedmannii was not able to infect and establish in OPM, but identified potential insect pathogenic species from the genera Serratia and Pseudomonas.
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Affiliation(s)
- Lea Schäfer
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
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141
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Grabner F M, Grabner H M, Schein H, Schrank A, Töglhofer M, Weidenholzer E, Rückert-Reed C, Busche T, Buchebner-Jance M. Lacticaseibacillus parahuelsenbergensis sp. nov., Lacticaseibacillus styriensis sp. nov. and Lacticaseibacillus zeae subsp. silagei subsp. nov., isolated from different grass and corn silage. Int J Syst Evol Microbiol 2024; 74:006441. [PMID: 38954457 PMCID: PMC11316572 DOI: 10.1099/ijsem.0.006441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
Four rod-shaped, non-motile, non-spore-forming, facultative anaerobic, Gram-stain-positive lactic acid bacteria, designated as EB0058T, SCR0080, LD0937T and SCR0063T, were isolated from different corn and grass silage samples. The isolated strains were characterized using a polyphasic approach and EB0058T and SCR0080 were identified as Lacticaseibacillus zeae by 16S rRNA gene sequence analysis. Based on whole-genome sequence-based characterization, EB0058T and SCR0080 were separated into a distinct clade from Lacticaseibacillus zeae DSM 20178T, together with CECT9104 and UD2202, whose genomic sequences are available from NCBI GenBank. The average nucleotide identity (ANI) values within the new subgroup are 99.9 % and the digital DNA-DNA hybridization (dDDH) values are 99.3-99.9 %, respectively. In contrast, comparison of the new subgroup with publicly available genomic sequences of L. zeae strains, including the type strain DSM 20178T, revealed dDDH values of 70.2-72.5 % and ANI values of 96.2-96.6 %. Based on their chemotaxonomic, phenotypic and phylogenetic characteristics, EB0058T and SCR0080 represent a new subspecies of L. zeae. The name Lacticaseibacillus zeae subsp. silagei subsp. nov. is proposed with the type strain EB0058T (=DSM 116376T=NCIMB 15474T). According to the results of 16S rRNA gene sequencing, LD0937T and SCR0063T are members of the Lacticaseibacillus group. The dDDH value between the isolates LD0937T and SCR0063T was 67.6 %, which is below the species threshold of 70 %, clearly showing that these two isolates belong to different species. For both strains, whole genome-sequencing revealed that the closest relatives within the Lacticaseibacillus group were Lacticaseibacillus huelsenbergensis DSM 115425 (dDDH 66.5 and 65.9 %) and Lacticaseibacillus casei DSM 20011T (dDDH 64.1 and 64.9 %). Based on the genomic, chemotaxonomic and morphological data obtained in this study, two novel species, Lacticaseibacillus parahuelsenbergensis sp. nov. and Lacticaseibacillus styriensis sp. nov. are proposed and the type strains are LD0937T (=DSM 116105T=NCIMB 15471T) and SCR0063T (=DSM 116297T=NCIMB 15473T), respectively.
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Affiliation(s)
- Monika Grabner F
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Monika Grabner H
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Hermine Schein
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Andrea Schrank
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | - Manuela Töglhofer
- Lactosan GmbH & Co.KG, Industriestraße West 5, 8605 Kapfenberg, Austria
| | | | | | - Tobias Busche
- Omics Core Facility NGS, Medical School OWL & CBTec, Bielefeld University, Bielefeld, Germany
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Menéndez E, Flores-Félix JD, Kaur S, diCenzo GC, Young JPW, Peix A, Velázquez E. Reclassification of type strains of Rhizobium indigoferae and Sinorhizobium kummerowiae into the species Rhizobium leguminosarum and Sinorhizobium meliloti, respectively. Int J Syst Evol Microbiol 2024; 74:006451. [PMID: 39037439 PMCID: PMC11316585 DOI: 10.1099/ijsem.0.006451] [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: 04/17/2024] [Accepted: 06/27/2024] [Indexed: 07/23/2024] Open
Abstract
The species Rhizobium indigoferae and Sinorhizobium kummerowiae were isolated from legume nodules and the 16S rRNA sequences of their respective type strains, CCBAU 71042T and CCBAU 71714T, were highly divergent from those of the other species of the genera Rhizobium and Sinorhizobium, respectively. However, the 16S rRNA gene sequences obtained for strains CCBAU 71042T and CCBAU 71714T several years after description, were different from the original ones, showing 100 % similarity to the type strains of Rhizobium leguminosarum and Sinorhizobium meliloti, respectively. Phylogenetic analyses of two housekeeping genes, recA and atpD, confirmed the high phylogenetic closeness of strains CCBAU 71042T and CCBAU 71714T to the respective type strains of R. leguminosarum and S. meliloti. In the present work, we compared the genomes of the type strains of R. indigoferae and S. kummerowiae available in several culture collections with those of the respective type strains of R. leguminosarum and S. meliloti, some of them obtained in this study. The calculated average nucleotide identity-blast and digital DNA-DNA hybridization values in both cases were higher than those recommended for species differentiation, supporting the proposal for the reclassification of the type strains of R. indigoferae and S. kummerowiae into the species R. leguminosarum and S. meliloti, respectively.
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Affiliation(s)
- Esther Menéndez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Grupo de Interacción Planta-Microorganismo, USAL, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
| | - José David Flores-Félix
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Sabhjeet Kaur
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | - George C. diCenzo
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
| | | | - Alvaro Peix
- Grupo de Interacción Planta-Microorganismo, USAL, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Grupo de Interacción Planta-Microorganismo, USAL, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
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143
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Saticioglu IB, Ay H, Altun S, Ajmi N, Gunduz ES, Gocmen H, Duman M. Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov. Syst Appl Microbiol 2024; 47:126518. [PMID: 38761464 DOI: 10.1016/j.syapm.2024.126518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 T and Flavobacterium bizetiae, 99.0 % for strain F-65 T and Flavobacterium branchiarum, 98.7 % for strain F-126 T and Flavobacterium tructae, 98.2 % for strain F-323 T and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 T and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 T shared 100 % identical 16S rRNA genes, while strains F-323 T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 T, F-65 T, F-70 T, F126T and F-323 T represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 T (=JCM 34194 T = KCTC 82254 T), Flavobacterium pisciphilum sp. nov. F-65 T (=JCM 34197 T = KCTC 82257 T), Flavobacterium flavipigmentatum sp. nov. F-70 T (Fl-33 = Fl-77 = JCM 34198 T = KCTC 82258 T), Flavobacterium lipolyticum sp. nov. F-126 T (JCM 34199 T = KCTC 82259 T) and Flavobacterium cupriresistens sp. nov. F-323 T (Fl-318 = JCM 34200 T = KCTC 82260 T), are proposed.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yildiz Technical University, Istanbul, 34220, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
| | - Nihed Ajmi
- Graduate School of Health Sciences, Bursa Uludag University, Bursa, 16059, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Huban Gocmen
- Department of Microbiology, Faculty of Veterinary Medicine, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
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Hahnke S, Giebel HA, Freese HM, Moraru C, Tindall BJ, Simon M, Brinkhoff T. Biogeography of Lentibacter algarum, description of a new strain isolated from the North Sea and emended genus and species descriptions. Int J Syst Evol Microbiol 2024; 74. [PMID: 39058551 DOI: 10.1099/ijsem.0.006472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024] Open
Abstract
A new heterotrophic, aerobic alphaproteobacterium, designated strain SH36 (=DSM 23330=LMG 25292), was obtained from a seawater sample collected in the open North Sea during a phytoplankton bloom. Analysis of the 16S rRNA gene sequence revealed affiliation of strain SH36 to the species Lentibacter algarum (family Roseobacteraceae), showing 100 and 99.9 % sequence similarity to the 16S rRNA genes of the strains L. algarum ZXM098 and ZXM100T. Digital DNA-DNA hybridization of strain SH36 with the type strain of L. algarum showed 98.0 % relatedness, confirming that strain SH36 can be classified within the same species. All three L. algarum strains were compared by physiological, morphological, chemotaxonomic, and genotypic characteristics. The strains showed only minor differences in the composition of fatty acids and polar lipids, but considerable physiological differences. Comparison of the 16S rRNA gene sequence of SH36 with sequences present in GenBank revealed that phylotypes with ≥98.65 % sequence identity to the type strain of L. algarum were found at different marine and estuarine locations of temperate and subtropic regions. Furthermore, by using a specific PCR approach L. algarum was detected throughout annual cycles at the offshore station at Helgoland Roads in the German Bight, indicating that this species is a permanent member of the microbial community in the North Sea.
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Affiliation(s)
- Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg, Germany
- Present address: Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg, Germany
- Present address: Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141 Essen, Germany
| | - Brian J Tindall
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, D-26129 Oldenburg, Germany
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Jiao JY, Abdugheni R, Zhang DF, Ahmed I, Ali M, Chuvochina M, Dedysh SN, Dong X, Göker M, Hedlund BP, Hugenholtz P, Jangid K, Liu SJ, Moore ERB, Narsing Rao MP, Oren A, Rossello-Mora R, Rekadwad BN, Salam N, Shu W, Sutcliffe IC, Teo WFA, Trujillo ME, Venter SN, Whitman WB, Zhao G, Li WJ. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. Natl Sci Rev 2024; 11:nwae168. [PMID: 39071100 PMCID: PMC11275469 DOI: 10.1093/nsr/nwae168] [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: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 07/30/2024] Open
Abstract
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig D-38124, Germany
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Kamlesh Jangid
- Bioenergy Group, MACS Collection of Microorganisms, Agharkar Research Institute, Pune 411004, India
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Edward R B Moore
- Department of Infectious Disease, Institute for Biomedicine, and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40234, Sweden
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles 070190, Spain
| | - Bhagwan Narayan Rekadwad
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nimaichand Salam
- National Agri-Food Biotechnology Institute, Knowledge City, Mohali 140306, India
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca 37008, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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Velasquez MR, De Lay BD, Edmondson DG, Wormser GP, Norris SJ, Cafferky K, Munzer E, Rizk CC, Keller M. A Novel Treponema pallidum Subspecies pallidum Strain Associated With a Painful Oral Lesion Is a Member of a Potentially Emerging Nichols-Related Subgroup. Sex Transm Dis 2024; 51:486-492. [PMID: 38829929 DOI: 10.1097/olq.0000000000001971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
BACKGROUND Early syphilitic lesions are typically painless; however, several recent case studies have included patients with tender lesions and no evidence of concurrent infections. Here we present the manifestations and serological and molecular findings of a patient from New York State with a painful tongue lesion. METHODS The diagnosis of syphilis was based on a combination of physical examination, serologic, pathologic, and immunohistochemical findings. DNA obtained from a formalin-fixed, paraffin-embedded biopsy was used to characterize the infecting pathogen using polymerase chain reaction, multilocus sequence typing, and whole-genome sequencing methods. RESULTS Polymerase chain reaction and multilocus sequence typing of the biopsy specimen confirmed infection with T. pallidum subspecies pallidum ( T. pallidum ) of the Nichols cluster. Whole-genome sequencing analysis of this strain (herein called NYMC01) showed that it contained 17 unique single nucleotide variations and 4 more complex genetic differences; this novel genotype matched only 2 specimens, both from a patient in Seattle, Washington. The presence of this rare genotype in 2 geographically distinct locations suggests the potential emergence and spread of a new subgroup of the Nichols cluster. CONCLUSIONS To our knowledge, this is the first genomic sequence obtained from a T. pallidum strain linked to a painful lesion, and the third description of whole-genome sequencing of T. pallidum from formalin-fixed, paraffin-embedded tissue. Analysis of additional specimens may reveal that the NYMC01-related genotype represents an emerging T. pallidum subgroup and may also aid in determining whether the painful clinical presentation of primary syphilis is related to specific T. pallidum genotypes.
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Affiliation(s)
- Maria Rosa Velasquez
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
| | - Bridget D De Lay
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | - Diane G Edmondson
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | - Gary P Wormser
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
| | - Steven J Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, UT Health Houston, Houston, TX
| | | | | | | | - Marina Keller
- From the Department of Internal Medicine, Division of Infectious Diseases, New York Medical College, Westchester Medical Center, Valhalla, NY
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147
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Zhang S, Luo Y, Zhang K, Song Z, Ling L, Yu X, Sun Y, Li J, Xiang W, Wang X, Zhao J. Methylobacterium amylolyticum sp. nov. and Methylobacterium ligniniphilum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39008351 DOI: 10.1099/ijsem.0.006457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Two pink-pigmented bacteria, designated strains NEAU-140T and NEAU-KT, were isolated from field soil collected from Linyi, Shandong Province, PR China. Both isolates were aerobic, Gram-stain-negative, rod-shaped, and facultatively methylotrophic. 16S rRNA gene sequences analysis showed that these two strains belong to the genus Methylobacterium. Strain NEAU-140T exhibited high 16S rRNA gene sequence similarities to Methylobacterium radiotolerans NBRC 15690T (97.43 %) and Methylobacterium phyllostachyos NBRC 105206T (97.36 %). Strain NEAU-KT exhibited high 16S rRNA gene sequence similarities to M. phyllostachyos NBRC 105206T (99.00 %) and Methylobacterium longum DSM 23933T (98.72 %). A phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-140T formed a clade with Methylobacterium aerolatum (95.94 %), Methylobacterium persicinum (95.66 %) and Methylobacterium komagatae (96.87 %), and strain NEAU-KT formed a cluster with M. phyllostachyos and M. longum. The predominant fatty acid in both strains was C18 : 1 ω7c. Both strains contained ubiquinone Q-10 as the only respiratory quinone. The polar lipid profiles of both strains contained diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. Whole-genome phylogeny showed that strains NEAU-140T and NEAU-KT formed a phyletic line with M. aerolatum, M. persicinum, Methylobacterium radiotolerans, Methylobacterium fujisawaense, Methylobacterium oryzae, Methylobacterium tardum, M. longum and M. phyllostachyos. The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NEAU-140T and its closely related strains were lower than 82.62 and 25.90 %, respectively. The ANI and dDDH values between strain NEAU-KT and its closely related strains were lower than 86.29 and 31.7 %, respectively. The genomic DNA G+C contents were 71.63 mol% for strain NEAU-140T and 69.08 mol% for strain NEAU-KT. On the basis of their phenotypic and phylogenetic distinctiveness and the results of dDDH and ANI hybridization, these two isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium amylolyticum sp. nov. (type strain NEAU-140T=MCCC 1K08801T=DSM 110568T) and Methylobacterium ligniniphilum sp. nov. (type strain NEAU-KT=MCCC 1K08800T=DSM 110567T) are proposed.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Yanfang Luo
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Kun Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhengke Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Ling Ling
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiaoyan Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Yanan Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Jiaxin Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Plant Protection, Northeast Agricultural University, Harbin 150030, PR China
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148
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Boutroux M, Favre-Rochex S, Gorgette O, Touak G, Mühle E, Bouchier C, Chesneau O, Veyrier FJ, Clermont D, Rahi P. Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits. Int J Syst Evol Microbiol 2024; 74:006460. [PMID: 39023135 PMCID: PMC11316581 DOI: 10.1099/ijsem.0.006460] [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: 03/20/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
A taxogenomic study of three strains (3986T, 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis, and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella. Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria. According to this proposed AAI threshold, strains 3986T, 51.81, and JF 2415 were placed within the genus Neisseria. The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae. The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986T, 51.81, and JF 2415 represent a novel species within the genus Neisseria, for which the name Neisseria leonii sp. nov. is proposed (type strain 3986T=R726T=CIP 109994T=LMG 32907T).
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Affiliation(s)
- Martin Boutroux
- Institut Pasteur, Université Paris Cité, Center of Biological Resources of Institut Pasteur (CRBIP), 75015 Paris, France
| | - Sandrine Favre-Rochex
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Gorgette
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging Unit, 75015 Paris, France
| | - Gérald Touak
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Estelle Mühle
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Christiane Bouchier
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Olivier Chesneau
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Frédéric J. Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
| | - Praveen Rahi
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur (CIP), 75015 Paris, France
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149
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Irgang R, Saldarriaga-Córdoba M, Poblete-Morales M, Avendaño-Herrera R. Flavobacterium facile sp. nov., isolated from water system of Atlantic salmon ( Salmo salar) fry cultured in Chile. Int J Syst Evol Microbiol 2024; 74:006468. [PMID: 39058544 PMCID: PMC11281480 DOI: 10.1099/ijsem.0.006468] [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: 05/22/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Strain T-12T, an orange, Gram-stain-negative, non-motile, rod-shaped strain, was isolated in November 2013 from water samples collected from an Atlantic salmon (Salmo salar) fry culturing system at a fish farm in Chile. Phylogenetic analysis based on 16S rRNA sequences (1394 bp) revealed that strain T-12T belonged to the genus Flavobacterium, showing close relationships to Flavobacterium bernardetii F-372T (99.48 %) and Flavobacterium terrigena DS-20T (98.50 %). The genome size of strain T-12T was 3.28 Mb, with a G+C content of 31.1 mol%. Genome comparisons aligned strain T-12T with Flavobacterium bernardetii F-372T (GCA_011305415) and Flavobacterium terrigena DSM 17934T (GCA_900108955). The highest digital DNA-DNA hybridization (dDDH) values were 42.6 % with F. bernardetii F-372T (GCA_011305415) and 33.9 % with F. terrigena DSM 17934T (GCA_900108955). Pairwise average nucleotide identity (ANI) calculations were below the species cutoff, with the best results with F. bernardetii F-372T being: ANIb, 90.33 %; ANIm, 91.85 %; and TETRA, 0.997 %. These dDDH and ANI results confirm that strain T-12T represents a new species. The major fatty acids were iso-C15 : 0 and C15 : 1ω6с. Detected polar lipids included phospholipids (n=2), aminophospholipid (n=1), aminolipid (n=1) and unidentified lipids (n=2). The predominant respiratory quinone was menaquinone MK7 (80 %) followed by MK-6 (20 %). Phenotypic, chemotaxonomic, and genomic data support the classification of strain T-12T (=CECT 30410T=RGM 3222T) as representing a novel species of Flavobacterium, for which the name Flavobacterium facile sp. nov. is proposed.
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Affiliation(s)
- Rute Irgang
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Mónica Saldarriaga-Córdoba
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Escuela de Medicina Veterinaria & Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O´Higgins, Santiago, Chile
| | - Matías Poblete-Morales
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Valparaíso, Chile
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150
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Ercole TG, Kava VM, Petters-Vandresen DAL, Ribeiro RA, Hungria M, Galli LV. Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417. Curr Microbiol 2024; 81:247. [PMID: 38951210 DOI: 10.1007/s00284-024-03784-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024]
Abstract
Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.
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Affiliation(s)
- Tairine Graziella Ercole
- Postgraduate Program in Genetics, Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
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