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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Wang N, Zheng X, Leptihn S, Li Y, Cai H, Zhang P, Wu W, Yu Y, Hua X. Characteristics and phylogenetic distribution of megaplasmids and prediction of a putative chromid in Pseudomonas aeruginosa. Comput Struct Biotechnol J 2024; 23:1418-1428. [PMID: 38616963 PMCID: PMC11015739 DOI: 10.1016/j.csbj.2024.04.002] [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: 10/08/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
Research on megaplasmids that contribute to the spread of antimicrobial resistance (AMR) in Pseudomonas aeruginosa strains has grown in recent years due to the now widely used technologies allowing long-read sequencing. Here, we systematically analyzed distinct and consistent genetic characteristics of megaplasmids found in P. aeruginosa. Our data provide information on their phylogenetic distribution and hypotheses tracing the potential evolutionary paths of megaplasmids. Most of the megaplasmids we found belong to the IncP-2-type, with conserved and syntenic genetic backbones carrying modules of genes associated with chemotaxis apparatus, tellurite resistance and plasmid replication, segregation, and transmission. Extensively variable regions harbor abundant AMR genes, especially those encoding β-lactamases such as VIM-2, IMP-45, and KPC variants, which are high-risk elements in nosocomial infection. IncP-2 megaplasmids act as effective vehicles transmitting AMR genes to diverse regions. One evolutionary model of the origin of megaplasmids claims that chromids can develop from megaplasmids. These chromids have been characterized as an intermediate between a megaplasmid and a chromosome, also containing core genes that can be found on the chromosome but not on the megaplasmid. Using in silico prediction, we identified the "PABCH45 unnamed replicon" as a putative chromid in P. aeruginosa, which shows a much higher similarity and closer phylogenetic relationship to chromosomes than to megaplasmids while also encoding plasmid-like partition genes. We propose that such a chromid could facilitate genome expansion, allowing for more rapid adaptations to novel ecological niches or selective conditions, in comparison to megaplasmids.
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Affiliation(s)
- Nanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zheng
- Department of Nephrology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sebastian Leptihn
- HMU Health and Medical University, Am Anger 64/73 – 99084, Erfurt, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) Translational Phage-Network, Inhoffenstraße 7 – 38124, Braunschweig, Germany
- University of Southern Denmark,Department of Biochemistry and Molecular Biology, Campusvej 55 – 5230, Odense, Denmark
| | - Yue Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhao Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Siderius NL, Sapula SA, Hart BJ, Hutchings JL, Venter H. Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species. Microbiol Res 2024; 288:127867. [PMID: 39163716 DOI: 10.1016/j.micres.2024.127867] [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: 05/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
BACKGROUND Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing. AIM To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs. METHODS Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution. RESULTS ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants. CONCLUSION E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.
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Affiliation(s)
- Naomi L Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Sylvia A Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Bradley J Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Joshua L Hutchings
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
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Lin R, Li H, Wu H, Ren H, Kong X, Lu Z. Resting for viability: Gordonia polyisoprenivorans ZM27, a robust generalist for petroleum bioremediation under hypersaline stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124618. [PMID: 39067736 DOI: 10.1016/j.envpol.2024.124618] [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: 04/12/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The intrinsic issue associated with the application of microbes for practical pollution remediation involves maintaining the expected activity of engaged strains or consortiums as effectively as that noted under laboratory conditions. Faced with various stress factors, degraders with dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic and halotolerant strain, Gordonia polyisoprenivorans ZM27, was isolated via stimulation with resuscitation-promoting factor (Rpf). Long-term exposure to dual stresses of 10% NaCl and starvation induced ZM27 to enter a viable but nonculturable (VBNC)-like state, and ZM27 cells could be resuscitated upon Rpf stimulation. Notable changes in both morphological and physiological characteristics between VBNC-like ZM27 cells and resuscitated cells confirmed the response to Rpf and their robust resistance against harsh environments. Whole-genome sequencing and analysis indicated ZM27 could be a generalist degrader with dormancy ability. Subsequently, VBNC-like ZM27 was applied in a soil microcosm experiment to investigate the practical application potential under harsh conditions. VBNC-like ZM27 combined with Rpf stimulation exhibited the most effective biodegradation performance, and the initial n-hexadecane content (1000 mg kg-1) decreased by 63.29% after 14-day incubation. Based on 16S rRNA amplicon sequencing and analysis, Gordonia exhibited a positive response to Rpf stimulation. The relative abundance of genus Gordonia was negatively correlated with that of Alcanivorax, a genus of obligate hydrocarbon degrader with the greatest abundance during soil incubation. Based on the degradation profile and community analysis, generalist Gordonia may be more efficient in hydrocarbon degradation than specialist Alcanivorax under harsh conditions. The characteristics of ZM27, including its sustainable culturability under long-term stress, response to Rpf and robust performance in soil microcosms, are valuable for the remediation of petroleum pollution under stressful conditions. Our work validated the importance of dormancy and highlighted the underestimated role of low-activity degraders in petroleum remediation.
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Affiliation(s)
- Renzhang Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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Huo Y, Zhang D, Wang X, Xu G, Dai M, Zhang S. Biofunctional attributes and storage study of milk fermented by Enterococcus italicus. Int J Food Microbiol 2024; 423:110844. [PMID: 39068860 DOI: 10.1016/j.ijfoodmicro.2024.110844] [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: 04/14/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Lactic acid bacteria are probiotics in the intestines and have been widely used as natural antioxidants in the food industry. In this study, Enterococcus italicus FM5 with strong antioxidant ability was isolated from fresh milk. The safety evaluation showed that E. italicus FM5 was sensitive to ampicillin, chloramphenicol, erythromycin, vancomycin, rifampicin, and tetracycline, and was not hemolytic. Meanwhile, the whole genome information and biofunctional attributes of this strain were determined and analyzed. Subsequently, E. italicus FM5 was co-cultured with traditional yogurt starters (Streptococcus thermophilus and Lactobacillus bulgaricus) to make fermented milk. The results showed that the addition of E. italicus FM5 could improve the oxygen free radical scavenging ability of the fermented milk, and the scavenging rates of DPPH, ABTS, OH-, and O2- radicals reaching up to 95.54 %, 88.35 %, 93.65 %, and 60.29 %, respectively. Furthermore, the addition of E. italicus FM5 reduced the curd time and improved the water holding capacity of the fermented milk. Besides, the growth of Lb. bulgaricus was significantly promoted when co-cultured with E. italicus FM5, thus the survival cells were increased compared with the traditional fermentation processes. Therefore, this study emphasized the potential to manufacture fermented milk by the co-cultivation of E. italicus with traditional yogurt starters.
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Affiliation(s)
- Yingxin Huo
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Daolei Zhang
- Department of Bioengineering, Shandong Polytechnic, Jinan 250104, China
| | - Xiaona Wang
- Shandong Freda Biotech Co., Ltd, Jinan 250101, China
| | - Guangyao Xu
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Meixue Dai
- College of Life Science, Shandong Normal University, Jinan 250358, China
| | - Susu Zhang
- College of Life Science, Shandong Normal University, Jinan 250358, China.
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Plomp N, Harmsen HJM. Description of Faecalibacterium wellingii sp. nov. and two Faecalibacterium taiwanense strains, aiding to the reclassification of Faecalibacterium species. Anaerobe 2024; 89:102881. [PMID: 38925221 DOI: 10.1016/j.anaerobe.2024.102881] [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: 04/05/2024] [Revised: 06/09/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVES The genus Faecalibacterium is one of the most important butyrate producers in the human intestinal tract and has been widely linked to health. Recently, several different species have been described, but still more phylogroups have been identified, suggesting that additional species may exist. Four strains HTF-FT, HTF-128, HTF-75H and HTF-76H, representing two different phylogenetic clusters, are evaluated in this study. METHODS Phylogenomic analysis was performed using whole-genome sequences and 16S rRNA gene sequences. Chemotaxonomic analysis was done based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Physiological and phenotypical characteristics of these strains were also determined. All characteristics of these strains were compared with other validly published species within the genus Faecalibacterium. RESULTS On a genomic level, the strains HTF-FT and HTF-128 shared an average nucleotide identity (ANI) of <95.0 % and digital DNA-DNA hybridization (dDDH) of <70.0 with other Faecalibacterium species, while between HTF-FT and HTF-128 the ANI-value was 97.18 % and the dDDH was 76.8 %. HTF-75H and HTF-76H had an ANI and dDDH value of 100 % (99.96 %) and 100 % (99.99 %) respectively. Both HTF-75H and HTF-76H were closely related to Faecalibacterium taiwanense HLW78T. 16S rRNA gene and chemotaxonomic analysis were in accordance with the genomic data, confirming that HTF-FT and HTF-128 represent a novel Faecalibacterium species and HTF-75H and HTF-76H belong to F. taiwanense. CONCLUSIONS Faecalibacterium strains HTF-FT (=DSM 117771T = NCIMB 15531T) and HTF-128 represent a novel species. The name Faecalibacterium wellingii with HTF-FT as type strain is proposed. Two novel isolates HTF-75H (=DSM 17770 = NCIMB 15530) and HTF-76H are described in this study and belong to the recently described Faecalibacterium taiwanense.
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Affiliation(s)
- Niels Plomp
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands.
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Makiura T, Matsutani M, Tseng HC, Fujimoto N, Ohnishi A. Succinate-mediated symbiosis between Dialister hominis and an uncharacterized Segatella-like pectinophile. Anaerobe 2024; 89:102883. [PMID: 39038530 DOI: 10.1016/j.anaerobe.2024.102883] [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: 03/30/2024] [Revised: 06/27/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
OBJECTIVES Syntrophy has been documented between pectinophiles and methanol-utilizing bacteria, along with instances of cross-feeding between pectinophiles and methanogens. However, studies on the ecology of pectinophiles in anaerobic digestion (AD) are lacking. Therefore, in this study, we aimed to elucidate the ecology of pectinophiles by isolating novel pectinophile forms and conducting a comprehensive analysis of their physiology and ecology. METHODS Complex microbial communities from AD systems were enriched in a pectin-containing medium; subsequently, specific strains were isolated using a pectinophile isolation method. The carbon source assimilation and growth ability of the isolates, along with their symbiotic relationships, were evaluated using batch tests. RESULTS Strain LPYR103-Pre exhibited 16S rRNA gene sequence similarity and average nucleotide identity values of 94.3 % and 77.9 %, respectively, compared to its closest related species, Segatella cerevisiae. Strain LPYR103-Pre demonstrated attenuated growth in the presence of eight common sugars but exhibited remarkably high growth in the presence of pectin, d-galacturonate, and d-glucuronate, with succinate being identified as a primary metabolite. Accumulation of succinate inhibited the growth of strain LPYR103-Pre. However, this growth impediment was alleviated by Dialister hominis LPYG114-Dih, whose growth required succinate. CONCLUSIONS Our results elucidate the specific carbon source requirements of the Segatella-like strain LPYR103-Pre and succinate-mediated symbiosis involving D. hominis. These findings provide new insights into the degradation of pectin and its degradation products during AD, contributing to the identification of unknown pectinophiles.
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Affiliation(s)
- Tomoki Makiura
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Hou-Chia Tseng
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Naoshi Fujimoto
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akihiro Ohnishi
- Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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Bigey F, Menatong Tene X, Wessner M, Pradal M, Aury JM, Cruaud C, Neuvéglise C. Differential adaptation of the yeast Candida anglica to fermented food. Food Microbiol 2024; 123:104584. [PMID: 39038890 DOI: 10.1016/j.fm.2024.104584] [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: 03/03/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
A single strain of Candida anglica, isolated from cider, is available in international yeast collections. We present here seven new strains isolated from French PDO cheeses. For one of the cheese strains, we achieved a high-quality genome assembly of 13.7 Mb with eight near-complete telomere-to-telomere chromosomes. The genomes of two additional cheese strains and of the cider strain were also assembled and annotated, resulting in a core genome of 5966 coding sequences. Phylogenetic analysis showed that the seven cheese strains clustered together, away from the cider strain. Mating-type locus analysis revealed the presence of a MATa locus in the cider strain but a MATalpha locus in all cheese strains. The presence of LINE retrotransposons at identical genome position in the cheese strains, and two different karyotypic profiles resulting from chromosomal rearrangements were observed. Together, these findings are consistent with clonal propagation of the cheese strains. Phenotypic trait variations were observed within the cheese population under stress conditions whereas the cider strain was found to have a much greater capacity for growth in all conditions tested.
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Affiliation(s)
- Frédéric Bigey
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, 91057, France
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10
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Li DH, Zheng N, Liu ZH, Dong XR, Zhao C, Yan SG, Xie BB. Complete genome sequence of the 4-hydroxybenzoate-degrading bacterium Gymnodinialimonas sp. 57CJ19, a potential novel species from intertidal sediments. Mar Genomics 2024; 77:101135. [PMID: 39179312 DOI: 10.1016/j.margen.2024.101135] [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: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/26/2024]
Abstract
A bacterium Gymnodinialimonas sp. 57CJ19, was isolated from the intertidal sediments of Aoshan Bay, and further assays showed that it has the ability to degrade the antibacterial preservative 4-hydroxybenzoate. The complete genome sequence was sequenced, and phylogenomic analyses indicated that strain 57CJ19 represents a potential novel species in the genus Gymnodinialimonas (family Rhodobacteraceae). Its genome contains a 3,861,607-bp circular chromosome with 61.25% G + C content. Gene prediction revealed 3716 protein-encoding genes, 41 tRNA genes, 3 rrn operons, and 3 non-coding RNA genes. Functional annotation revealed a complete metabolic pathway for 4-hydroxybenzoate. The genome sequence of strain 57CJ19 provides new insights into the potential and underlying genomic basis of aromatic compound pollutant degradation by marine bacteria.
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Affiliation(s)
- Dong-Hui Li
- School of Bioengineering, Shandong Provincial Key Laboratory of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Ning Zheng
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhen-Hai Liu
- School of Bioengineering, Shandong Provincial Key Laboratory of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xiao-Rui Dong
- School of Bioengineering, Shandong Provincial Key Laboratory of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Chen Zhao
- School of Bioengineering, Shandong Provincial Key Laboratory of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Shi-Gan Yan
- School of Bioengineering, Shandong Provincial Key Laboratory of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Bin-Bin Xie
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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11
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Yuan Q, Wang S, Wang S, Zhong Y, Jiang L. Genome sequence of Sulfurimonas sp. C5, a potential chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a mangrove sediment. Microbiol Resour Announc 2024:e0047424. [PMID: 39315832 DOI: 10.1128/mra.00474-24] [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: 05/12/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Sulfurimonas sp. strain C5 (MCCC 1A19556) is a strain with potential chemolithoautotrophic sulfur-oxidizing function, which is isolated from a mangrove sediment sample collected from Quanzhou Bay, Fujian Province, China. This report describes the genome sequence of strain C5, which possesses the gene sets for the sulfur-oxidizing pathway.
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Affiliation(s)
- Qing Yuan
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Shufang Wang
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - ShaSha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Yangsheng Zhong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
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12
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Song ST, Li CY, Gu CT. Lacticaseibacillus jixiensis sp. nov., Isolated from Traditional Chinese Pickle. Curr Microbiol 2024; 81:374. [PMID: 39316138 DOI: 10.1007/s00284-024-03902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 09/15/2024] [Indexed: 09/25/2024]
Abstract
A novel lactic acid bacterial strain (designated N163-3-2T), isolated from traditional Chinese pickle ('Suan cai'), was characterized using a polyphasic approach. Strain N163-3-2T was most closely related to the type strains of Lacticaseibacillus baoqingensis, Lacticaseibacillus manihotivorans, and Lacticaseibacillus porcinae, having 97.9-98.4% 16S rRNA gene, 82.0-85.1% pheS, 87.5-87.8% rpoA, and 85.8-86.7% concatenated pheS and rpoA sequence similarities. Strain N163-3-2T had 74.4-81.7% ANI, 22.6-23.9% dDDH, and 74.0-75.1% AAI values with L. baoqingensis 47-3T, L. manihotivorans DSM 13343T and L. porcinae JCM 19617T, less than the threshold for species demarcation (95-96%, 70% and 95-96%, respectively), indicating that strain N163-3-2T represented a novel species of the genus Lacticaseibacillus. Based upon the data obtained in the present study, a novel species, Lacticaseibacillus jixiensis sp. nov., is proposed, and the type strain is N163-3-2T (= CCTCC AB 2024125T = JCM 36999T).
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Affiliation(s)
- Si-Tong Song
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin, 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China.
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13
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Yao L, Liu GH, Zhang SY, Gao P, Rensing C, Yang QE, Zhou SG. Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential. Antonie Van Leeuwenhoek 2024; 118:6. [PMID: 39292388 DOI: 10.1007/s10482-024-02017-0] [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: 07/01/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024]
Abstract
Two facultatively aerobic strains, designated SGZ-02T and SGZ-792T, were isolated from plant Pennisetum sp., exhibiting the highest 16S rRNA gene sequence similarities with the type strains of Sphingomonas zeae LMG 28739T (98.6%) and Massilia forsythiae NBRC 114511T (98.4%), respectively. SGZ-02T grew between 5 and 45 °C, pH 5.0-11.0 and tolerated NaCl concentrations of 0-4% (w/v), whereas SGZ-792T thrived at 5-40 °C, pH 5.0-11.0 and NaCl tolerance to 0-3.5% (w/v). The major quinone of SGZ-02T was ubiquinone-10, with the dominant fatty acids being C16:0 (13.5%), Summed Feature 3 (6.3%), C14:02-OH (5.3%) and Summed Feature 8 (66.3%). SGZ-792T predominantly contained ubiquinone-8, with major fatty acids being C16:0 (20.3%), Summed Feature 3 (5.0%) and Summed Feature 8 (54.7%). Average nucleotide identity and digital DNA-DNA hybridization values between two strains and their closest references strains were below the bacterial species threshold. Based on genotypic and phenotypic characteristics, strains SGZ-02T and SGZ-792T are proposed as novel species within the genera Sphingomonas and Massilia, respectively. The suggested names for the new species are Sphingomonas fuzhouensis sp. nov. (SGZ-02T = GDMCC 1.4033T = JCM 36769T) and Massilia phyllosphaerae sp. nov. (SGZ-792T = GDMCC 1.4211T = JCM 36643T), respectively.
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Affiliation(s)
- Ling Yao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, 35003, People's Republic of China.
| | - Shu-Yi Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Peng Gao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, 350002, People's Republic of China.
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14
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Salmaso N, Cerasino L, Pindo M, Boscaini A. Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps. FEMS Microbiol Ecol 2024; 100:fiae117. [PMID: 39227168 PMCID: PMC11412076 DOI: 10.1093/femsec/fiae117] [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: 04/03/2024] [Revised: 08/19/2024] [Accepted: 09/02/2024] [Indexed: 09/05/2024] Open
Abstract
Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Italy
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Leonardo Cerasino
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Italy
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach, 1, 38098 San Michele all'Adige, Italy
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15
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Guo HR, Wang F, Yu HY, Wang CX, Wang Z, Fang BZ, Li X, Li WJ. Yunchengibacter salinarum gen. nov., sp. nov., a novel bacterium of the family Kordiimonadaceae isolated from sediment in Yuncheng salt lake. Antonie Van Leeuwenhoek 2024; 118:4. [PMID: 39269642 DOI: 10.1007/s10482-024-02011-6] [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: 03/28/2024] [Accepted: 08/16/2024] [Indexed: 09/15/2024]
Abstract
A Gram-stain-negative, aerobic, motile and rod-shaped bacterium, the color of the bacterial colony ranges from light yellow to yellow, designated YC-2023-2T, was isolated from sediment sample of Yuncheng salt lake. Growth occurred at 15-45℃ (optimum 37℃), pH 6.0-9.0 (optimum pH 7.0-8.0) and with 0-8.0% NaCl (w/v, optimum 2.0%). The phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC-2023-2T belonged to the family Kordiimonadaceae. The closely related members were Gimibacter soli 6D33T (92.38%), Kordiimonas lipolytica M41T (91.88%), Eilatimonas milleporae DSM 25217T (91.88%) and Kordiimonas gwangyangensis JCM 12864T (91.84%). The genome of strain YC-2023-2T was 2957513 bp, and the genomic DNA G+C content was 63.91%. The main respiratory quinone was Q-10 and the major fatty acids (>10%) were iso-C15:0, C16:0, C19:0 cyclo ω8c, Summed Feature 8 (C18:1 ω6c or C18:1 ω7c) and Summed Feature 9 (iso-C17:1 ω9c or C16:0 10-methyl). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, unidentified glycolipid, unidentified lipid, and two unidentified aminolipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain YC-2023-2T is proposed to represent a novel species of a novel genus named Yunchengibacter salinarum gen. nov., sp. nov., within the family Kordiimonadaceae. The type strain is YC-2023-2T (= GDMCC 1.4502T = KCTC 8546T).
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Affiliation(s)
- Hao-Ran Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China
| | - Fan Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China
| | - Hui-Ying Yu
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, Yuncheng University, Yuncheng, 044000, Shanxi, People's Republic of China
| | - Chuan-Xu Wang
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, Yuncheng University, Yuncheng, 044000, Shanxi, People's Republic of China
| | - Zhuo Wang
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, Yuncheng University, Yuncheng, 044000, Shanxi, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, Xinjiang, People's Republic of China
| | - Xin Li
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, Yuncheng University, Yuncheng, 044000, Shanxi, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, Xinjiang, People's Republic of China.
- 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, People's Republic of China.
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16
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Delesalle VA, King MAK, Rozario TJ, Wolf ND, Stewart CJ, DeMato LF, Trafford KF, Adhikari S, Dinh VT, Caputo G, Hunter A, Licata M, Modell M, Bhalla S. Complete genomes of two cluster AK Arthrobacter phages isolated from soil samples in Newburgh, NY, United States. Microbiol Resour Announc 2024:e0071624. [PMID: 39264183 DOI: 10.1128/mra.00716-24] [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: 07/03/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Two phages belonging to Arthrobacter phage cluster AK were isolated from soil samples collected in Newburgh, NY in 2021. Both are lytic with a genome organization typical of siphoviruses except for two genes encoding minor tail proteins with pyocin-knob domains found early in the genome, before the terminase gene.
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Affiliation(s)
| | - Mariah A K King
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Tabitha J Rozario
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Noah D Wolf
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Connor J Stewart
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Luke F DeMato
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Kevin F Trafford
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Saiman Adhikari
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Van T Dinh
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Gina Caputo
- Department of Biology, Mount Saint Mary College, Newburgh, New York, USA
| | - Ashley Hunter
- Department of Biology, Mount Saint Mary College, Newburgh, New York, USA
| | - Michelle Licata
- Department of Biology, Mount Saint Mary College, Newburgh, New York, USA
| | - Misun Modell
- Department of Biology, Mount Saint Mary College, Newburgh, New York, USA
| | - Suparna Bhalla
- Department of Biology, Mount Saint Mary College, Newburgh, New York, USA
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17
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Wang TY, Li CY, Wang H, Gu CT. Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov., and Streptococcus parasalivarius sp. nov., isolated from Traditional Chinese Pickle. Curr Microbiol 2024; 81:351. [PMID: 39261326 DOI: 10.1007/s00284-024-03871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/22/2024] [Indexed: 09/13/2024]
Abstract
Four Gram-stain-positive bacterial strains (designated 475-2T, 46-6BT, 778-2T and A810-3), isolated from traditional Chinese pickle, were characterized using a polyphasic taxonomic approach. Strain 475-2T was most closely related to the type strain of Lapidilactobacillus achengensis, having 99.9% 16S rRNA gene sequence similarity, 94.1-95.1% average nucleotide identity (ANI) and 57.6% digital DNA-DNA hybridization (dDDH) values. Strain 46-6BT was most closely related to the type strain of Secundilactobacillus similis, having 99.8% 16S rRNA gene sequence similarity, 94.3-94.9% ANI and 58.9-59.2% dDDH values. Strains 778-2T and A810-3 were phylogenetically related to the type strains of Streptococcus salivarius, Streptococcus thermophilus and Streptococcus vestibularis, having 99.7-99.9% 16S rRNA gene sequence similarities, 89.1-94.4% ANI and 39.0-55.5% dDDH values. Based upon the data obtained in the present study, three novel species, Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov. and Streptococcus parasalivarius sp. nov., are proposed and the type strains are 475-2T (= JCM 36613T = CCTCC AB 2023258T = LMG 33412T), 46-6BT (= JCM 36612T = CCTCC AB 2023259T = LMG 33411T) and 778-2T (= JCM 36614T = CCTCC AB 2023257T = LMG 33413T), respectively.
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Affiliation(s)
- Ting-Yu Wang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin, 150030, PR China
| | - Hao Wang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China.
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18
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Oh KK, Cho GS, Franz CMAP. Draft genome sequences of Klebsiella spp. isolated from produce and agricultural water in South Korea. Microbiol Resour Announc 2024; 13:e0011024. [PMID: 39162444 PMCID: PMC11385959 DOI: 10.1128/mra.00110-24] [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: 02/05/2024] [Accepted: 06/28/2024] [Indexed: 08/21/2024] Open
Abstract
This report outlines the draft genome sequences of six Klebsiella spp. strains from South Korea's agricultural produce and environments. Genome sizes ranged from 5.25 to 6.21 Mbp with 55.64% to 57.55% GC content. Each strain contained multiple plasmid sequences identified by PlasmidFinder, indicating significant antimicrobial resistance.
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Affiliation(s)
- Kwang-Kyo Oh
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße, Kiel, Germany
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19
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Hirsch AM, Khan N, Humm E, Rubbi M, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. Genome of Dietzia cinnamea 55, a desert-isolated microbe with plant growth-promoting properties for grain crops. Microbiol Resour Announc 2024:e0025724. [PMID: 39254331 DOI: 10.1128/mra.00257-24] [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: 03/20/2024] [Accepted: 07/30/2024] [Indexed: 09/11/2024] Open
Abstract
Here, we report the genome sequence of Dietzia cinnamea 55, isolated from the Negev Desert, Israel. D. cinnamea 55 was found to promote the growth of several cereal crops (corn, wheat, and pearl millet) in greenhouse and field studies.
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Affiliation(s)
- Ann M Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Noor Khan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Ethan Humm
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Mila Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Giorgia Del Vecchio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Sung Min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
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20
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Tran DM, Huynh TU, Do TO, Nguyen AD. Isolation, Plant Growth-Promoting Properties, and Whole-Genome Sequence of a Novel Paenibacillus Species. J Basic Microbiol 2024; 64:e2400119. [PMID: 38894514 DOI: 10.1002/jobm.202400119] [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: 03/02/2024] [Revised: 04/27/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus Paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA-DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - To Uyen Huynh
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
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21
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Chen X, Xia J, Fu X, Lai Q, Wang J, Du Y, Liu X, Li G, Tang X, Shao Z. Aequorivita flava sp. nov., isolated from deep-sea sediments. Int J Syst Evol Microbiol 2024; 74. [PMID: 39230938 DOI: 10.1099/ijsem.0.006513] [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: 09/05/2024] Open
Abstract
Three Gram-stain-negative, aerobic, non-motile, chemoheterotrophic, short-rod-shaped bacteria, designated CDY1-MB1T, CDY2-MB3, and BDY3-MB2, were isolated from three marine sediment samples collected in the eastern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus Aequorivita and close to the type strain of Aequorivita vitellina F4716T (with similarities of 98.0-98.1%). Strain CDY1-MB1T can grow at 15-37 °C (optimum 30 °C) and in media with pH 6-9 (optimum, pH 7), and tolerate up to 10% (w/v) NaCl. The predominant cellular fatty acids of strain CDY1-MB1T were iso-C15 : 0 (20.7%) and iso-C17 : 0 3-OH (12.8%); the sole respiratory quinone was menaquinone 6; the major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. The digital DNA-DNA hybridization/average nucleotide identity values between strains CDY1-MB1T, CDY2-MB3, and BDY3-MB2 and A. vitellina F4716T were 24.7%/81.6-81.7%, thereby indicating that strain CDY1-MB1T should represent a novel species of the genus Aequorivita. The genomic DNA G+C contents were 37.6 % in all three strains. Genomic analysis showed the presence of genes related to nitrogen and sulphur cycling, as well as metal reduction. The genetic traits of these strains indicate their possible roles in nutrient cycling and detoxification processes, potentially shaping the deep-sea ecosystem's health and resilience. Based upon the consensus of phenotypic and genotypic analyses, strain CDY1-MB1T should be classified as a novel species of the genus Aequorivita, for which the name Aequorivita flava sp. nov. is proposed. The type strain is CDY1-MB1T (=MCCC 1A16935T=KCTC 102223T).
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Affiliation(s)
- Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
- School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, PR China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Yaping Du
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
- School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, PR China
- School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, PR China
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Zhao SB, Liu L, Lian FB, Du ZJ. Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 39235837 DOI: 10.1099/ijsem.0.006512] [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: 09/06/2024] Open
Abstract
Two bacterial strains, Y60-23T and HN-65T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23T exhibited 96.0% similarity to its most related type strain Hyphobacterium vulgare KCTC 52487T, while strain HN-65T exhibited 97.3% similarity to its most related type strain Hyphobacterium indicum 2ED5T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23T and HN-65T belonged to the genus Hyphobacterium. Cells of strains Y60-23T and HN-65T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23T were C18 : 1 ω7c and C17 : 0, while those of strain HN-65T were iso-C17 : 1 ω9c, iso-C17 : 0 and C18 : 1 ω7c. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23T and HN-65T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus Hyphobacterium, for which the names Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov. were proposed with the type strains Y60-23T (=MCCC 1H01433T=KCTC 8172T) and HN-65T (=MCCC 1H01434T=KCTC 8169T), respectively.
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Affiliation(s)
- Shi-Bo Zhao
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Le Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Feng-Bai Lian
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Shandong University-Weihai Research Institute of Industrial Technology, Weihai, Shandong, 264209, PR China
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Seo H, Yoon Y, Kim S, Ghorbanian F, Tajdozian H, Jo S, Barman I, Lee S, Lee Y, Rahim MA, Hossain MS, Lee S, Song HY. Anti-tuberculosis effect of microbiome therapeutic PMC205 in extensively drug-resistant pulmonary tuberculosis in vivo. Int J Antimicrob Agents 2024; 64:107274. [PMID: 39002701 DOI: 10.1016/j.ijantimicag.2024.107274] [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: 06/15/2023] [Revised: 06/05/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis, and the increase in antibiotic resistance threatens humankind. Therefore, there is an urgent need to develop new anti-tuberculosis drugs that can overcome the limitations of existing drugs. Here, we report the anti-tuberculosis effect of microbiome therapeutic PMC205, a strain of Bacillus subtilis. METHODS The anti-tuberculosis activity of probiotics was evaluated in mouse models of lethal and latent pulmonary tuberculosis induced by high or low-dose infection of the extensively drug-resistant strain. Probiotics were administered by inhalation, and the burden of M. tuberculosis in the lungs, along with mortality and clinical observations, were monitored for 12 weeks and 8 months, respectively. For an in-depth understanding, analysis of the microbiome and inflammatory profile of the lung microenvironment and induction of autophagy in vitro were explored. RESULTS After inhalation administration of PMC205 for 3 months, the survival rate was 100%, unlike all deaths in the saline-treated group, and the burden of M. tuberculosis in the lungs was reduced by log 1.3 in the 8-month latent tuberculosis model. Moreover, PMC205 induced recovery of disrupted lung microflora, increased butyric acid, and suppressed excessive inflammation. It also promoted autophagy. CONCLUSIONS These results confirm PMC205's anti-tuberculosis effect, suggesting that it can be developed as an adjuvant to current antibiotic therapy to solve the drug-resistant tuberculosis problem.
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Affiliation(s)
- Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si, Chungnam, Republic of Korea
| | - Youjin Yoon
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si, Chungnam, Republic of Korea
| | - Fatemeh Ghorbanian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Hanieh Tajdozian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Sujin Jo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Indrajeet Barman
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Soyeon Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Youngkyoung Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Md Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Mohammed Solayman Hossain
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea
| | - Saebim Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea; Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si, Chungnam, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si, Chungnam, Republic of Korea; Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si, Chungnam, Republic of Korea.
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24
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Li D, Phurbu D, Zhang X, Liu ZX, Wang R, Zheng YY, Zhou YG, Yu YJ, Xue L, Li AH. Virgibacillus tibetensis sp. nov., isolated from salt lake on the Tibetan plateau of China. Int J Syst Evol Microbiol 2024; 74. [PMID: 39312295 DOI: 10.1099/ijsem.0.006525] [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: 09/25/2024] Open
Abstract
One bacterial strain, designated as C22-A2T, was isolated from Lake LungmuCo in Tibet. Cells of strain C22-A2T were long rod-shaped, Gram-stain-negative, non-spore-forming, with positive catalase and oxidase activity. Optimal growth occurred at 20-25 °C, pH 8.0 and with 3.0-7.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene and whole genome sequences revealed that strain C22-A2T belonged to the genus Virgibacillus, showing the highest 16S rRNA gene similarity to Virgibacillus halodenitrificans DSM 10037T (97.6%). The average nucleotide identity values between strain C22-A2T and the type strains of related species in the genus Virgibacillus were less than 74.4% and the digital DNA-DNA hybridization values were less than 20.2%, both below the species delineation thresholds of 95 and 70% respectively. The genome analysis revealed that strain C22-A2T harboured genes responsible for osmotic and oxidative stress, enabling it to adapt to its surrounding environment. In terms of biochemical and physiological characteristics, strain C22-A2T shared similar characteristics with the genus Virgibacillus, including the predominant cellular fatty acid anteiso-C15 : 0, the major respiratory quinone MK-7, as well as the polar lipids phosphatidylglycerol and diphosphatidylglycerol. Based on the comprehensive analysis of phylogenetic, phylogenomic, morphological, physiological and biochemical characteristics, strain C22-A2T is proposed to represent a novel species of the genus Virgibacillus, named as Virgibacillus tibetensis sp. nov. (=CGMCC 1.19202T=KCTC 43426T).
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Affiliation(s)
- Dongyang Li
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Dorji Phurbu
- Tibet Plateau Key Laboratory of Mycology, Tibet Plateau Institute of Biology, Lhasa, Tibet 850001, PR China
| | - Xuan Zhang
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Zi-Xuan Liu
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Rui Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Yan-Yan Zheng
- Tibet Plateau Key Laboratory of Mycology, Tibet Plateau Institute of Biology, Lhasa, Tibet 850001, PR China
| | - Yu-Guang Zhou
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Ya-Jing Yu
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
| | - Lu Xue
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ai-Hua Li
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, PR China
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Peña TA, Villarreal P, Agier N, De Chiara M, Barría T, Urbina K, Villarroel CA, Santos ARO, Rosa CA, Nespolo RF, Liti G, Fischer G, Cubillos FA. An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia. PLoS Genet 2024; 20:e1011396. [PMID: 39241096 PMCID: PMC11410238 DOI: 10.1371/journal.pgen.1011396] [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: 07/31/2024] [Revised: 09/18/2024] [Accepted: 08/14/2024] [Indexed: 09/08/2024] Open
Abstract
Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct Saccharomyces lineage in Nothofagus forests of coastal Patagonia. This lineage, designated Saccharomyces chiloensis sp. nov., exhibits 7% genetic divergence from its sister species S. uvarum, as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent S. uvarum population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to S. uvarum, which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from S. uvarum. In addition, we found unique structural variants between S. chiloensis sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that S. chiloensis sp. nov diverged from S. uvarum in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of S. chiloensis sp. nov. illustrates the uniqueness of Patagonia's coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of S. chiloensis sp. nov. is CBS 18620T.
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Affiliation(s)
- Tomas A Peña
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Villarreal
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | | | - Tomas Barría
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Kamila Urbina
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Carlos A Villarroel
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Ana R O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago, Chile
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Francisco A Cubillos
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Millenium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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Podosokorskaya OA, Elcheninov AG, Klyukina AA, Merkel AY. Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera. Syst Appl Microbiol 2024; 47:126541. [PMID: 39084153 DOI: 10.1016/j.syapm.2024.126541] [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: 02/27/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-coT, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75-100 °C and within a pH range of 5.4-8.2 with the optimum at 92 °C and pH 6.4-6.7. Strain 4213-coT was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-coT was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-coT formed a species-level phylogenetic lineage within Ignisphaera genus. Our phylogenomic analysis also supports the delineation of the Ignisphaera genus into a separate family Ignisphaeraceae, as recently published. Here we propose a novel species Ignisphaera cupida, sp. nov. with type strain 4213-coT (=JCM 39446T=VKM B-3715T=UQM 41593T). Ecogenomic analysis showed that representatives of the Ignisphaera are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of Ignisphaeraceae - a rather understudied archaeal group.
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Affiliation(s)
- Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Alexandra A Klyukina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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Wang W, Chen X, Ma J, Li W, Long Y. Activity of Streptomyces globosus OPF-9 against the important pathogen Alternaria longipes and biocontrol mechanisms revealed by multi-omic analyses. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 204:106094. [PMID: 39277405 DOI: 10.1016/j.pestbp.2024.106094] [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: 06/29/2024] [Revised: 08/13/2024] [Accepted: 08/17/2024] [Indexed: 09/17/2024]
Abstract
Plant diseases caused by fungal pathogens represent main threats to the yield and quality of agricultural products, and Alternaria longipes is one of the most important pathogens in agricultural systems. Biological control is becoming increasingly prevalent in the management of plant diseases due to its environmental compatibility and sustainability. In the present study, a bacterial strain, designated as OPF-9, was shown to effectively inhibit the pathogen A. longipes, which was identified as Streptomyces globosus. The culture conditions for OPF-9 were optimized through a stepwise approach and the fermentation broth acquired displayed an excellent inhibitory activity against A. longipes in vitro and in vivo. Further investigations suggested that the fermentation broth exhibited strong stability under a range of adverse environmental conditions. To reveal the molecular bases of OPF-9 in inhibiting pathogens, the whole-genome sequencing and assembly were conducted on this strain. It showed that the genome size of OPF-9 was 7.668 Mb, containing a chromosome and two plasmids. Multiple clusters of secondary metabolite synthesis genes were identified by genome annotation analysis. In addition, the fermentation broth of strain OPF-9 was analyzed by LC-MS/MS non-target metabolomic assay and the activity of potential antifungal substances was determined. Among the five compounds evaluated, pyrogallol displayed the most pronounced inhibitory activity against A. longipes, which was found to effectively inhibit the mycelial growth of this pathogen. Overall, this study reported, for the first time, a strain of S. globosus that effectively inhibits A. longipes and revealed the underlying biocontrol mechanisms by genomic and metabolomic analyses.
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Affiliation(s)
- Weizhen Wang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xuetang Chen
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Jiling Ma
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Wenzhi Li
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Youhua Long
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, PR China.
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Xiong LS, Fan MQ, Yang ZZ, Zuo SY, Yuan Q, Wang LS, Jiang CL, Wang XY, Jiang Y. Luteipulveratus flavus sp. nov. isolated from two lichen species. Int J Syst Evol Microbiol 2024; 74. [PMID: 39255010 DOI: 10.1099/ijsem.0.006518] [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: 09/11/2024] Open
Abstract
Two novel strains, YIM 133132T and YIM 133296, were isolated from lichen samples collected from Yunnan Province, Southwest PR China. YIM 133132T and YIM 133296 are aerobic, Gram-staining-positive, non-motile actinomycetes. They are also catalase-positive and oxidase-negative, and YIM 133132T formed flat yellowish colonies that were relatively dry on YIM38 agar medium. Flat yellowish colonies of YIM 133296 were also observed on YIM38 agar medium. YIM 133132T grew at 25-35 °C (optimum 25-30 °C), pH 6.0-9.0 (optimum pH 7.0) and in the presence of 0-8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains YIM 133132T and YIM 133296 represented members of the genus Luteipulveratus and exhibited high sequence similarity (96.93%) with Luteipulveratus halotolerans C296001T. The genomic DNA G+C content of both strains was 71.8%. The DNA-DNA hybridisation (dDDH) values between YIM 133132T and YIM 133296 were 85.1%, and the DNA-DNA hybridisation value between YIM 133132T and YIM 133296 and L. halotolerans C296001T was 23.4%. On the basis of the draft genome sequences, the average nucleotide identity (ANI) between strains YIM 133132T and YIM 133296 and L. halotolerans C296001T was 80.8%. The major menaquinones that were identified were MK-8(H4), MK-9 and MK-8(H2). The polar lipids were diphosphatidylglycerol and phosphatidylinositol. On the basis of the morphological, physiological, biochemical, genomic, phylogenetic and chemotaxonomic characteristics, strains YIM 133132T and YIM 133296 can be clearly distinguished from L. halotolerans C296001T, and the two strains represent a novel species for which the name L. flavus sp. nov. is proposed. The type strain is YIM 133132T (CGMCC= 1.61357T and KCTC= 49824T).
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Affiliation(s)
- Lian-Shuang Xiong
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Ming-Qun Fan
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Zu-Zhen Yang
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Shu-Ya Zuo
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Qing Yuan
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Li-Song Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Cheng-Lin Jiang
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
| | - Xin-Yu Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Yi Jiang
- Yunnan Institute of Microbiology, State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming 650500, PR China
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Nagar DN, Mani K, Braganca JM. Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India. Sci Rep 2024; 14:20214. [PMID: 39215047 PMCID: PMC11364659 DOI: 10.1038/s41598-024-70149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.
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Affiliation(s)
- Devika N Nagar
- Dept of Biological Sciences, Birla Institute of Technology and Science, Pilani, K K Birla Goa Campus, NH 17B Zuarinagar, Goa, 403 726, India
| | - Kabilan Mani
- Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Judith M Braganca
- Dept of Biological Sciences, Birla Institute of Technology and Science, Pilani, K K Birla Goa Campus, NH 17B Zuarinagar, Goa, 403 726, India.
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Lee H, Chaudhary DK, Kim DU. Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil. J Microbiol Biotechnol 2024; 34:1636-1641. [PMID: 39086223 PMCID: PMC11380503 DOI: 10.4014/jmb.2404.04038] [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: 04/23/2024] [Revised: 05/16/2024] [Accepted: 05/31/2024] [Indexed: 08/02/2024]
Abstract
A Gram-stain-positive, aerobic, white-coloured, rod-shaped bacteria, designated as a strain dW9T, was isolated from soil. Strain dW9T was catalase-positive and oxidase-negative. Strain dW9T grew at temperature of 20-37°C and at pH of 5.0-7.0. Phylogenetic and 16S rRNA gene analysis indicated that strain dW9T belonged to the genus Paenibacillus with its closest relative being Paenibacillus filicis S4T (97.4% sequence similarity). The genome size of dW9T was 7,787,916 bp with DNA G+C content of 51.3%. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of dW9T with its closest relatives were found to be <22.0% and <74.0%, respectively. The only respiratory quinone was MK-7, and the major fatty acids were antiso-C15:0 and iso-C16:0. Overall, the comprehensive taxonomic analysis revealed that strain dW9T met all the fundamental criteria to be classified as a novel species within the genus Paenibacillus. Accordingly, we propose the name Paenibacillus gyeongsangnamensis sp. nov., with the type strain dW9T (=KCTC 43431T =NBRC 116022T).
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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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Nicotra D, Ghadamgahi F, Ghosh S, Anzalone A, Dimaria G, Mosca A, Massimino ME, Vetukuri RR, Catara V. Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome. FRONTIERS IN PLANT SCIENCE 2024; 15:1437947. [PMID: 39253574 PMCID: PMC11381245 DOI: 10.3389/fpls.2024.1437947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024]
Abstract
Introduction Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.
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Affiliation(s)
- Daniele Nicotra
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Farideh Ghadamgahi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Samrat Ghosh
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Alice Anzalone
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Giulio Dimaria
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Alexandros Mosca
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Maria Elena Massimino
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
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Tuong HM, Méndez SG, Vandecasteele M, Willems A, Iancheva A, Ngoc PB, Phat DT, Ha CH, Goormachtig S. A novel Microbacterium strain SRS2 promotes the growth of Arabidopsis and MicroTom (S. lycopersicum) under normal and salt stress conditions. PLANTA 2024; 260:79. [PMID: 39182196 DOI: 10.1007/s00425-024-04510-2] [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: 04/24/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
MAIN CONCLUSION Microbacterium strain SRS2 promotes growth and induces salt stress resistance in Arabidopsis and MicroTom in various growth substrates via the induction of the ABA pathway. Soil salinity reduces plant growth and development and thereby decreases the value and productivity of soils. Plant growth-promoting rhizobacteria (PGPR) have been shown to support plant growth such as in salt stress conditions. Here, Microbacterium strain SRS2, isolated from the root endosphere of tomato, was tested for its capability to help plants cope with salt stress. In a salt tolerance assay, SRS2 grew well up to medium levels of NaCl, but the growth was inhibited at high salt concentrations. SRS2 inoculation led to increased biomass of Arabidopsis and MicroTom tomato in various growth substrates, in the presence and in the absence of high NaCl concentrations. Whole-genome analysis revealed that the strain contains several genes involved in osmoregulation and reactive oxygen species (ROS) scavenging, which could potentially explain the observed growth promotion. Additionally, we also investigated via qRT-PCR, promoter::GUS and mutant analyses whether the abscisic acid (ABA)-dependent or -independent pathways for tolerance against salt stress were involved in the model plant, Arabidopsis. Especially in salt stress conditions, the plant growth-promotion effect of SRS2 was lost in aba1, abi4-102, abi3, and abi5-1 mutant lines. Furthermore, ABA genes related to salt stress in SRS2-inoculated plants were transiently upregulated compared to mock under salt stress conditions. Additionally, SRS2-inoculated ABI4::GUS and ABI5::GUS plants were slightly more activated compared to the uninoculated control under salt stress conditions. Together, these assays show that SRS2 promotes growth in normal and in salt stress conditions, the latter possibly via the induction of ABA-dependent and -independent pathways.
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Affiliation(s)
- Ho Manh Tuong
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, CauGiay, Hanoi, 100000, Vietnam
| | - Sonia García Méndez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium
| | - Michiel Vandecasteele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, 9000, Ghent, Belgium
| | - Anelia Iancheva
- AgroBioInstitute, Agricultural Academy, 1164, Sofia, Bulgaria
| | - Pham Bich Ngoc
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, CauGiay, Hanoi, 100000, Vietnam
| | - Do Tien Phat
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, CauGiay, Hanoi, 100000, Vietnam
| | - Chu Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, CauGiay, Hanoi, 100000, Vietnam
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
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Gentilhomme A, Sweet C, Hennon GMM, Collins RE. Genomic signatures of cold adaptation in the family Colwelliaceae. Extremophiles 2024; 28:39. [PMID: 39177827 DOI: 10.1007/s00792-024-01356-0] [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: 05/30/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Psychrophily is a phenotype describing microbial growth at low temperatures; elucidating the biomolecular and genomic adaptations necessary for survival in the cold is important for understanding life in extreme environments on Earth and in outer space. We used comparative genomics and temperature growth experiments of bacteria from the family Colwelliaceae to identify genomic factors correlated with optimal growth temperature (OGT). A phylogenomic analysis of 67 public and 39 newly sequenced strains revealed three main clades of Colwelliaceae. Temperature growth experiments revealed significant differences in mean OGT by clade, wherein strains of Colwelliaceae had similar growth rates at -1 °C but varied in their ability to tolerate 17 °C. Using amino acid compositional indices, a multiple linear regression model was constructed to predict the OGT of these organisms (RMSE 5.2 °C). Investigation of Colwelliaceae functional genes revealed a putative cold-adaptive gene cassette that was present in psychrophilic strains but absent in a closely related strain with a significantly higher OGT. This study also presents genomic evidence suggesting that the clade of Colwelliaceae containing Colwellia hornerae should be investigated as a new genus. These contributions offer key insights into the psychrophily phenotype and its underlying genomic foundation in the family Colwelliaceae.
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Affiliation(s)
- Anais Gentilhomme
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, Fairbanks, Alaska, 99775, USA.
| | - Charles Sweet
- Chemistry Department, U.S. Naval Academy, 572M Holloway Road, Annapolis, MD, 21402-5026, USA
| | - Gwenn M M Hennon
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, Fairbanks, Alaska, 99775, USA
| | - R Eric Collins
- Center for Earth Observation Sciences, University of Manitoba, 520 Wallace Building, Winnipeg, MB, R3T 2N2, Canada
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Hong Tuan Ha AS, Mammeri A, Plainvert C, Charfi R, Poyart C, Tazi A, Mammeri H. Clinical emergence of a novel extended-spectrum variant deriving from the OXY-1 β-lactamase. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04922-8. [PMID: 39172287 DOI: 10.1007/s10096-024-04922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
The genomic comparison of two Klebsiella michiganensis clinical isolates recovered from the same patient, one resistant to piperacillin-tazobactam and intermediate to cefotaxime, the other resistant to ceftazidime but susceptible to piperacillin-tazobactam, revealed one mutation in the blaOXY-1-24 gene accounting for a L169M substitution in the Ω loop. Cloning experiment in Escherichia coli demonstrated the contribution of this mutation to the hydrolysis spectrum extension towards ceftazidime and cefepime, whereas the resistance to piperacillin-tazobactam was reduced. To the best of our knowledge, this study shows for the first time that ceftazidime resistance can occur in vivo from OXY-1 precursor by structural alteration.
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Affiliation(s)
- Anne-Sophie Hong Tuan Ha
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
| | - Alice Mammeri
- INSERM, CNRS, Institut Necker Enfants Malades, Université Paris Cité, , Paris, 75015, France
| | - Céline Plainvert
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Rym Charfi
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
| | - Claire Poyart
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Asmaa Tazi
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris Cité, Paris, France
| | - Hedi Mammeri
- Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Site Cochin, 27 rue du Faubourg Saint-Jacques, Paris, 75014, France.
- INSERM, CNRS, Institut Necker Enfants Malades, Université Paris Cité, , Paris, 75015, France.
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Li R, Yang P, Zhang H, Wang C, Zhao F, Liu J, Wang Y, Liang Y, Sun T, Xie X. Comparative Genomic and Functional Analysis of c-di-GMP Metabolism and Regulatory Proteins in Bacillus velezensis LQ-3. Microorganisms 2024; 12:1724. [PMID: 39203566 PMCID: PMC11357230 DOI: 10.3390/microorganisms12081724] [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: 06/22/2024] [Revised: 08/08/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Bacillus velezensis is a promising candidate for biocontrol applications. A common second messenger molecule, bis-(3,5)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has the ability to regulate a range of physiological functions that impact the effectiveness of biocontrol. However, the status of the c-di-GMP signaling pathway in biocontrol strain LQ-3 remains unknown. Strain LQ-3, which was isolated from wheat rhizosphere soil, has shown effective control of wheat sharp eyespot and has been identified as B. velezensis through whole-genome sequencing analyses. In this study, we investigated the intracellular c-di-GMP signaling pathway of LQ-3 and further performed a comparative genomic analysis of LQ-3 and 29 other B. velezensis strains. The results revealed the presence of four proteins containing the GGDEF domain, which is the conserved domain for c-di-GMP synthesis enzymes. Additionally, two proteins were identified with the EAL domain, which represents the conserved domain for c-di-GMP degradation enzymes. Furthermore, one protein was found to possess a PilZ domain, indicative of the conserved domain for c-di-GMP receptors in LQ-3. These proteins are called DgcK, DgcP, YybT, YdaK, PdeH, YkuI, and DgrA, respectively; they are distributed in a similar manner across the strains and belong to the signal transduction family. We selected five genes from the aforementioned seven genes for further study, excluding YybT and DgrA. They all play a role in regulating the motility, biofilm formation, and colonization of LQ-3. This study reveals the c-di-GMP signaling pathway associated with biocontrol features in B. velezensis LQ-3, providing guidance for the prevention and control of wheat sharp eyespot by LQ-3.
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Affiliation(s)
- Rong Li
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Panlei Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Hongjuan Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Chunjing Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Fang Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Jiehui Liu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Yanbin Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Yan Liang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Ting Sun
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
| | - Xiansheng Xie
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China; (R.L.); (H.Z.); (C.W.); (F.Z.); (J.L.); (Y.W.); (Y.L.); (T.S.)
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Yu T, Qin M, Shao Z, Zhao Y, Zeng X. Isolation of highly copper-resistant bacteria from deep-sea hydrothermal fields and description of a novel species Marinobacter metalliresistant sp. nov. Front Microbiol 2024; 15:1390451. [PMID: 39234539 PMCID: PMC11371751 DOI: 10.3389/fmicb.2024.1390451] [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: 02/23/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Introduction Hydrothermal vents, rich in heavy metals, provided a unique niche for heavy metal resistant microbes. However, knowledge about copper resistant microbes in deep sea hydrothermal vents is still limited. Methods The copper-resistant bacteria were isolated from deep-sea hydrothermal vent samples and conducted thorough physical, phylogenetic, and genomic analyses to elucidate their copper resistance capability and related genes. Results Twelve highly copper-resistant bacteria (up to 6-10 mM) were isolated from deep sea hydrothermal fields They were affiliated with the Pseudoalteromonas (4), Marinobacter (3), Halomonas (2), Psychrobacter (1), and Pseudomonas (1) genus in the α-Proteobacteria, and the Sphingomonas (1) genus in the β-Proteobacteria. The presence of copper in the medium obviously induced the amount of polysaccharides and proteins in the crude extracellular polymeric substances (EPS) produced by Halomonas sp. CuT 3-1, Pseudoalteromonas sp. CuT 4-3 and Marinobacter metalliresistant CuT 6, which could absorb 40 to 50 mg•g-1 copper. We further described a novel species, Marinobacter metalliresistant sp. nov. CuT 6T, which exhibited a higher copper resistance and encoded more heavy metal resistance-related genes than other Marinobacter species. Discussion It revealed that the copper resistance capability exhibited by these strains in hydrothermal fields is likely attributed to the production of exopolymeric substances, such as polysaccharides and proteins, as well as active transport or efflux mechanisms for heavy metals.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Meng Qin
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yuemei Zhao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Faculty of Marine Biology, Xiamen Ocean Vocational College, Xiamen, China
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Truong QL, Wang L, Nguyen TA, Nguyen HT, Le AD, Nguyen GV, Vu AT, Hoang PT, Le TT, Nguyen HT, Nguyen HTT, Lai HLT, Bui DAT, Huynh LMT, Madera R, Li Y, Retallick J, Matias-Ferreyra F, Nguyen LT, Shi J. A Non-Hemadsorbing Live-Attenuated Virus Vaccine Candidate Protects Pigs against the Contemporary Pandemic Genotype II African Swine Fever Virus. Viruses 2024; 16:1326. [PMID: 39205300 PMCID: PMC11359042 DOI: 10.3390/v16081326] [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: 06/28/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
African swine fever (ASF) is a highly contagious and severe hemorrhagic transboundary swine viral disease with up to a 100% mortality rate, which leads to a tremendous socio-economic loss worldwide. The lack of safe and efficacious ASF vaccines is the greatest challenge in the prevention and control of ASF. In this study, we generated a safe and effective live-attenuated virus (LAV) vaccine candidate VNUA-ASFV-LAVL3 by serially passaging a virulent genotype II strain (VNUA-ASFV-L2) in an immortalized porcine alveolar macrophage cell line (3D4/21, 50 passages). VNUA-ASFV-LAVL3 lost its hemadsorption ability but maintained comparable growth kinetics in 3D4/21 cells to that of the parental strain. Notably, it exhibited significant attenuation of virulence in pigs across different doses (103, 104, and 105 TCID50). All vaccinated pigs remained healthy with no clinical signs of African swine fever virus (ASFV) infection throughout the 28-day observation period of immunization. VNUA-ASFV-LAVL3 was efficiently cleared from the blood at 14-17 days post-infection, even at the highest dose (105 TCID50). Importantly, the attenuation observed in vivo did not compromise the ability of VNUA-ASFV-LAVL3 to induce protective immunity. Vaccination with VNUA-ASFV-LAVL3 elicited robust humoral and cellular immune responses in pigs, achieving 100% protection against a lethal wild-type ASFV (genotype II) challenge at all tested doses (103, 104, and 105 TCID50). Furthermore, a single vaccination (104 TCID50) provided protection for up to 2 months. These findings suggest that VNUA-ASFV-LAVL3 can be utilized as a promising safe and efficacious LAV candidate against the contemporary pandemic genotype II ASFV.
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Affiliation(s)
- Quang Lam Truong
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Lihua Wang
- Center on Biologics Development and Evaluation, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (L.W.); (R.M.); (Y.L.)
| | - Tuan Anh Nguyen
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Hoa Thi Nguyen
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Anh Dao Le
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Giap Van Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (G.V.N.); (L.M.T.H.)
| | - Anh Thi Vu
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Phuong Thi Hoang
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Trang Thi Le
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Huyen Thi Nguyen
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Hang Thu Thi Nguyen
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Huong Lan Thi Lai
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Dao Anh Tran Bui
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Le My Thi Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (G.V.N.); (L.M.T.H.)
| | - Rachel Madera
- Center on Biologics Development and Evaluation, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (L.W.); (R.M.); (Y.L.)
| | - Yuzhen Li
- Center on Biologics Development and Evaluation, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (L.W.); (R.M.); (Y.L.)
| | - Jamie Retallick
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (J.R.); (F.M.-F.)
| | - Franco Matias-Ferreyra
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (J.R.); (F.M.-F.)
| | - Lan Thi Nguyen
- Key Laboratory of Veterinary Biotechnology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Gia Lam, Ha Noi 12406, Vietnam; (T.A.N.); (H.T.N.); (A.D.L.); (A.T.V.); (P.T.H.); (T.T.L.); (H.T.N.); (H.T.T.N.); (H.L.T.L.); (D.A.T.B.)
| | - Jishu Shi
- Center on Biologics Development and Evaluation, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (L.W.); (R.M.); (Y.L.)
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Versmessen N, Mispelaere M, Vandekerckhove M, Hermans C, Boelens J, Vranckx K, Van Nieuwerburgh F, Vaneechoutte M, Hulpiau P, Cools P. Average Nucleotide Identity and Digital DNA-DNA Hybridization Analysis Following PromethION Nanopore-Based Whole Genome Sequencing Allows for Accurate Prokaryotic Typing. Diagnostics (Basel) 2024; 14:1800. [PMID: 39202288 PMCID: PMC11353866 DOI: 10.3390/diagnostics14161800] [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: 05/31/2024] [Revised: 07/31/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Whole-genome sequencing (WGS) is revolutionizing clinical bacteriology. However, bacterial typing remains investigated by reference techniques with inherent limitations. This stresses the need for alternative methods providing robust and accurate sequence type (ST) classification. This study optimized and evaluated a GridION nanopore sequencing protocol, adapted for the PromethION platform. Forty-eight Escherichia coli clinical isolates with diverse STs were sequenced to assess two alternative typing methods and resistance profiling applications. Multi-locus sequence typing (MLST) was used as the reference typing method. Genomic relatedness was assessed using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (DDH), and cut-offs for discriminative strain resolution were evaluated. WGS-based antibiotic resistance prediction was compared to reference Minimum Inhibitory Concentration (MIC) assays. We found ANI and DDH cut-offs of 99.3% and 94.1%, respectively, which correlated well with MLST classifications and demonstrated potentially higher discriminative resolution than MLST. WGS-based antibiotic resistance prediction showed categorical agreements of ≥ 93% with MIC assays for amoxicillin, ceftazidime, amikacin, tobramycin, and trimethoprim-sulfamethoxazole. Performance was suboptimal (68.8-81.3%) for amoxicillin-clavulanic acid, cefepime, aztreonam, and ciprofloxacin. A minimal sequencing coverage of 12× was required to maintain essential genomic features and typing accuracy. Our protocol allows the integration of PromethION technology in clinical laboratories, with ANI and DDH proving to be accurate and robust alternative typing methods, potentially offering superior resolution. WGS-based antibiotic resistance prediction holds promise for specific antibiotic classes.
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Affiliation(s)
- Nick Versmessen
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Marieke Mispelaere
- Department of Bio-Medical Sciences, HOWEST University of Applied Sciences, 8000 Bruges, Belgium
| | | | - Cedric Hermans
- Department of Bio-Medical Sciences, HOWEST University of Applied Sciences, 8000 Bruges, Belgium
| | - Jerina Boelens
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
- Department of Laboratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Filip Van Nieuwerburgh
- NXTGNT, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Paco Hulpiau
- Department of Bio-Medical Sciences, HOWEST University of Applied Sciences, 8000 Bruges, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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Nurkanto A, Masrukhin, Erdian Tampubolon JC, Ewaldo MF, Putri AL, Ratnakomala S, Setiawan R, Fathoni A, Palupi KD, Rahmawati Y, Waluyo D, Prabandari EE, Pujiyanto S, Sumii Y, Agusta A, Shibata N, Matsumoto S, Nozaki T. Exploring Indonesian actinomycete extracts for anti-tubercular compounds: Integrating inhibition assessment, genomic analysis, and prediction of its target by molecular docking. Heliyon 2024; 10:e35648. [PMID: 39170210 PMCID: PMC11336835 DOI: 10.1016/j.heliyon.2024.e35648] [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] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
Tuberculosis (TB) is the foremost cause of infectious fatality globally. The primary global challenge in combatting TB lies in addressing the emergence of drug-resistant variants of the disease. However, the number of newly approved agents for treating TB has remained remarkably low over recent decades. Hence, research endeavors for discovering novel anti-TB agents are always needed. In the present study, we screened over 1,500 culture extracts from actinomycetes isolated in Indonesia for their inhibitory activity against Mycobacterium smegmatis used as a surrogate in the primary screening. The initial screening yielded approximately 6.2 % hit extracts, with a selection criterion of >80 % growth inhibition. The confirmed hit extracts were subsequently subjected to growth inhibition assay against Mycobacterium bovis and Mycobacterium tuberculosis. Approximately 20 % of the hit extracts that showed growth inhibition also exhibited efficacy against M. bovis BCG and M. tuberculosis H37Rv pathogenic strain. An active compound was successfully purified from a large-scale culture of the most potent representative extract by high-performance liquid chromatography and thin-layer chromatography. The structure of the active compound was elucidated by mass spectrometry and nuclear magnetic resonance. This compound displayed structural similarities to actinomycin group and exhibited robust inhibition, with IC50 values of 0.74, 0.02, and 0.07 μg/mL against M. smegmatis, M. bovis, and M. tuberculosis, respectively. The Actinomycetes strain A612, which produced the active compound, was taxonomically classified by phylogenetic analysis of 16s rRNA gene and whole genome sequencing data as Streptomyces parvus. Computational genome analysis utilizing anti-SMASH 7.0 unveiled that S. parvus A612 strain harbors 40 biosynthetic gene clusters with the potential to produce 16 known (with >70 % similarity) and 24 unknown compounds. A non-ribosomal peptide synthesis (NRPS) gene cluster associated with actinomycin D biosynthesis was also identified, boasting an 85 % similarity. Molecular docking analysis of actinomycin D and 21 potential M. tuberculosis targets revealed possible interactions with multiple targets. The purified active compound inhibited recombinant M. tuberculosis shikimate kinase (MtSK), which validated the results obtained from the docking analysis.
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Affiliation(s)
- Arif Nurkanto
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Masrukhin
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Muhammad Farrel Ewaldo
- Master's Programme in Biomedical Science, Faculty of Medicine, University of Indonesia, West Java, Indonesia
| | - Ade Lia Putri
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Shanti Ratnakomala
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Ruby Setiawan
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Ahmad Fathoni
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Kartika Dyah Palupi
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Yulia Rahmawati
- Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environmental, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Danang Waluyo
- Research Center for Vaccine and Drug, Research Organization for Health, National Research and Innovation Agency (BRIN), Banten, Indonesia
| | - Erwahyuni Endang Prabandari
- Research Center for Vaccine and Drug, Research Organization for Health, National Research and Innovation Agency (BRIN), Banten, Indonesia
| | - Sri Pujiyanto
- Department of Biology, Faculty of Science and Mathematics, Diponegoro University, Central Java, Indonesia
| | - Yuji Sumii
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Andria Agusta
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), West Java, Indonesia
| | - Norio Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, University of Airlangga, Surabaya, East Java, Indonesia
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Jaglan AB, Verma R, Vashisth M, Virmani N, Bera BC, Vaid RK, Anand T. A novel lytic phage infecting MDR Salmonella enterica and its application as effective food biocontrol. Front Microbiol 2024; 15:1387830. [PMID: 39211316 PMCID: PMC11358711 DOI: 10.3389/fmicb.2024.1387830] [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: 02/18/2024] [Accepted: 07/01/2024] [Indexed: 09/04/2024] Open
Abstract
Salmonella enterica is a foodborne pathogen associated with both typhoid and non-typhoid illness in humans and animals. This problem is further exacerbated by the emergence of antibiotic-resistant strains of Salmonella enterica. Therefore, to meet public health and safety, there is a need for an alternative strategy to tackle antibiotic-resistant bacteria. Bacteriophages or (bacterial viruses), due to their specificity, self-dosing, and antibiofilm activity, serve as a better approach to fighting against drug-resistant bacteria. In the current study, a broad-host range lytic phage phiSalP219 was isolated against multidrug-resistant Salmonella enterica serotypes Paratyphi from a pond water sample. Salmonella phage phiSalP219 was able to lyse 28/30 tested strains of Salmonella enterica. Salmonella phage phiSalP219 exhibits activity in acidic environments (pH3) and high temperatures (70°C). Electron microscopy and genome analysis revealed that phage phiSalP219 is a member of class Caudoviricetes. The genome of Salmonella phage phiSalP219 is 146Kb in size with 44.5% GC content. A total of 250 Coding Sequence (CDS) and 25 tRNAs were predicted in its genome. Predicted open reading frames (ORFs) were divided into five groups based on their annotation results: (1) nucleotide metabolism, (2) DNA replication and transcription, (3) structural proteins, (4) lysis protein, and (5) other proteins. The absence of lysogeny-related genes in their genome indicates that Salmonella phage phiSalP219 is lytic in nature. Phage phiSalP219 was also found to be microbiologically safe (due to the absence of toxin or virulence-related genes) in the control of Salmonella enterica serovar Typhimurium infections in the ready-to-eat meat and also able to eradicate biofilm formed by the same bacterium on the borosilicate glass surface.
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Affiliation(s)
- Anu Bala Jaglan
- ICAR – National Research Centre on Equines, Hisar, India
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Ravikant Verma
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | | | - Nitin Virmani
- ICAR – National Research Centre on Equines, Hisar, India
| | - B. C. Bera
- ICAR – National Research Centre on Equines, Hisar, India
| | - R. K. Vaid
- ICAR – National Research Centre on Equines, Hisar, India
| | - Taruna Anand
- ICAR – National Research Centre on Equines, Hisar, India
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Zhou X, Huang J, Xu S, Cheng H, Liu B, Huang J, Liu J, Pan D, Wu X. Novel Bifunctional Amidase Catalyzing the Degradation of Propanil and Aryloxyphenoxypropionate Herbicides in Rhodococcus sp. C-1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18067-18077. [PMID: 39082634 DOI: 10.1021/acs.jafc.4c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Propanil residues can contaminate habitats where microbial degradation is predominant. In this study, an efficient propanil-degrading strain C-1 was isolated from paddy and identified as Rhodococcus sp. It can completely degrade 10 μg/L-150 mg/L propanil within 0.33-10 h via the hydrolysis of the amide bond, forming 3,4-dichloroaniline. A novel bifunctional amidase, PamC, was identified in strain C-1. PamC can catalyze the hydrolysis of the amide bond of propanil to produce 3,4-dichloroaniline as well as the hydrolysis of the ester bonds of aryloxyphenoxypropionate herbicides (APPHs, clodinafop-propargyl, cyhalofop-butyl, fenoxaprop-p-ethyl, fluazifop-p-butyl, haloxyfop-p-methyl, and quizalofop-p-ethyl) to form aryloxyphenoxypropionic acids. Molecular docking and site-directed mutagenesis confirmed that the catalytic triad Lys82-Ser157-Ser181 was the active center for PamC to hydrolyze propanil and cyhalofop-butyl. This study presents a novel bifunctional amidase with capabilities for both amide and ester bond hydrolysis and enhances our understanding of the molecular mechanisms underlying the degradation of propanil and APPHs.
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Affiliation(s)
- Xiaoyu Zhou
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Jinjin Huang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shiwei Xu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Huan Cheng
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Bin Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Junwei Huang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Junwei Liu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Pan
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
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42
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Heo S, Jung EJ, Park MK, Sung MH, Jeong DW. Evolution and Competitive Struggles of Lactiplantibacillus plantarum under Different Oxygen Contents. Int J Mol Sci 2024; 25:8861. [PMID: 39201547 PMCID: PMC11354895 DOI: 10.3390/ijms25168861] [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: 07/15/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
Lactiplantibacillus (Lb.) plantarum is known as a benign bacterium found in various habitats, including the intestines of animals and fermented foods. Since animal intestines lack oxygen, while fermented foods provide a limited or more oxygen environment, this study aimed to investigate whether there were genetic differences in the growth of Lb. plantarum under aerobic vs. anaerobic conditions. Genomic analysis of Lb. plantarum obtained from five sources-animals, dairy products, fermented meat, fermented vegetables, and humans-was conducted. The analysis included not only an examination of oxygen-utilizing genes but also a comparative pan-genomic analysis to investigate evolutionary relationships between genomes. The ancestral gene analysis of the evolutionary pathway classified Lb. plantarum into groups A and B, with group A further subdivided into A1 and A2. It was confirmed that group A1 does not possess the narGHIJ operon, which is necessary for energy production under limited oxygen conditions. Additionally, it was found that group A1 has experienced more gene acquisition and loss compared to groups A2 and B. Despite an initial assumption that there would be genetic distinctions based on the origin (aerobic or anaerobic conditions), it was observed that such differentiation could not be attributed to the origin. However, the evolutionary process indicated that the loss of genes related to nitrate metabolism was essential in anaerobic or limited oxygen conditions, contrary to the initial hypothesis.
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Affiliation(s)
- Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea;
| | - Eun Jin Jung
- Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea;
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Moon-Hee Sung
- KookminBio Corporation, Seoul 02826, Republic of Korea;
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea;
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43
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Hirsch AM, Humm E, Rubbi M, del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. Complete genomes of two Variovorax endophytes isolated from surface-sterilized alfalfa nodules. Microbiol Resour Announc 2024; 13:e0033624. [PMID: 38967468 PMCID: PMC11320970 DOI: 10.1128/mra.00336-24] [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: 04/01/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
Variovorax species catabolize a wide range of natural and industrial products and have been shown to be integral rhizosphere inhabitants. Here, we report the complete genomes of V. paradoxus 2u118 and V. sp. SPNA7, which were isolated from alfalfa root nodules and possess plant growth-promoting properties.
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Affiliation(s)
- Ann M. Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Ethan Humm
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Mila Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Giorgia del Vecchio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Sung Min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
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44
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Kim J, Murakami T, Toyoda A, Mori H. Metagenome-assembled genome sequence of Spiroplasma phoeniceum, assembled from the hindgut of Locusta migratoria, a migration grasshopper species. Microbiol Resour Announc 2024; 13:e0035324. [PMID: 39012135 PMCID: PMC11320922 DOI: 10.1128/mra.00353-24] [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: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Spiroplasma phoeniceum is a plant pathogen and a mesophilic microaerophile. Here, we report the metagenome-assembled genome (MAG) sequence of S. phoeniceum binned from hindgut contents of the wild-type male Locusta migratoria, a grasshopper species. The MAG sequence comprises 1,059,205 bp in 91 contigs with a 26.3% of GC content.
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Affiliation(s)
- Jaeha Kim
- Genome Diversity Laboratory, National Institute of Genetics, Mishima-shi, Japan
| | - Takumi Murakami
- School of Life Science and Technology, Tokyo Institute of Technology, Oookayama, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima-shi, Japan
| | - Hiroshi Mori
- Genome Diversity Laboratory, National Institute of Genetics, Mishima-shi, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima-shi, Japan
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45
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Boukeroui Y, González-Siso MI, DeCastro ME, Arab M, Aissaoui N, Nas F, Saibi ANE, Klouche Khelil N. Characterization, whole-genome sequence analysis, and protease production of a new thermophilic Bacillus licheniformis strain isolated from Debagh hot spring, Algeria. Int Microbiol 2024:10.1007/s10123-024-00569-9. [PMID: 39129036 DOI: 10.1007/s10123-024-00569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
A new thermophilic strain, designated as Bacillus sp. LMB3902, was isolated from Hammam Debagh, the hottest spring in Algeria (up to 98 °C). This isolate showed high protease production in skim milk media at 55 °C and exhibited significant specific protease activity by using azocasein as a substrate (157.50 U/mg). Through conventional methods, chemotaxonomic characteristics, 16S rRNA gene sequencing, and comparative genomic analysis with the closely related strain Bacillus licheniformis DSM 13 (ATCC 14580 T), the isolate Bacillus sp. LMB3902 was identified as a potentially new strain of Bacillus licheniformis. In addition, the gene functions of Bacillus sp. LMB3902 strain were predicted using the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups, Non-Redundant Protein Sequence Database, Swiss-Prot, and Pfam databases. The results showed that the genome size of Bacillus sp. LMB3902 was 4.279.557 bp, with an average GC content of 46%. The genome contained 4.760 predicted genes, including 8 rRNAs, 78 tRNAs, and 24 sRNAs. A total of 235 protease genes were annotated including 50 proteases with transmembrane helix structures and eight secreted proteases with signal peptides. Additionally, the majority of secondary metabolites found by antiSMASH platform showed low similarity to identified natural products, such as fengicin (53%), lichenysin (57%), and surfactin (34%), suggesting that this strain may encode for novel uncharacterized natural products which can be useful for biotechnological applications. This study is the first report that describes the complete genome sequence, taxono-genomics, and gene annotation as well as protease production of the Bacillus genus in this hydrothermal vent.
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Affiliation(s)
- Yasmina Boukeroui
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro Interdisciplinar de Química E Bioloxía (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 , A Coruña, Spain
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro Interdisciplinar de Química E Bioloxía (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 , A Coruña, Spain
| | - Mounia Arab
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
- Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, 16000, Algiers, Algeria
| | - Nadia Aissaoui
- Laboratory of Sustainable Management of Natural Resources in Arid and Semi Arid Areas (GDRN), Institute of Sciences, University Center of Naâma, 45000, Naâma, Algeria
| | - Fatima Nas
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - Amina Nour Elhouda Saibi
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria
| | - Nihel Klouche Khelil
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE Laboratory), Department of Biology, Faculty of Nature and Life, Earth and Universe Sciences, University of Tlemcen, 13000, Tlemcen, Algeria.
- Laboratory of Experimental Surgery, Dental Surgery Department, Medical Faculty, University of Tlemcen, 13000, Tlemcen, Algeria.
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Almeida GMDF, Ravantti J, Grdzelishvili N, Kakabadze E, Bakuradze N, Javakhishvili E, Megremis S, Chanishvili N, Papadopoulos N, Sundberg LR. Relevance of the bacteriophage adherence to mucus model for Pseudomonas aeruginosa phages. Microbiol Spectr 2024; 12:e0352023. [PMID: 38912817 PMCID: PMC11302309 DOI: 10.1128/spectrum.03520-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Pseudomonas aeruginosa infections are getting increasingly serious as antimicrobial resistance spreads. Phage therapy may be a solution to the problem, especially if improved by current advances on phage-host studies. As a mucosal pathogen, we hypothesize that P. aeruginosa and its phages are linked to the bacteriophage adherence to mucus (BAM) model. This means that phage-host interactions could be influenced by mucin presence, impacting the success of phage infections on the P. aeruginosa host and consequently leading to the protection of the metazoan host. By using a group of four different phages, we tested three important phenotypes associated with the BAM model: phage binding to mucin, phage growth in mucin-exposed hosts, and the influence of mucin on CRISPR immunity of the bacterium. Three of the tested phages significantly bound to mucin, while two had improved growth rates in mucin-exposed hosts. Improved phage growth was likely the result of phage exploitation of mucin-induced physiological changes in the host. We could not detect CRISPR activity in our system but identified two putative anti-CRISPR proteins coded by the phage. Overall, the differential responses seen for the phages tested show that the same bacterial species can be targeted by mucosal-associated phages or by phages not affected by mucus presence. In conclusion, the BAM model is relevant for phage-bacterium interactions in P. aeruginosa, opening new possibilities to improve phage therapy against this important pathogen by considering mucosal interaction dynamics.IMPORTANCESome bacteriophages are involved in a symbiotic relationship with animals, in which phages held in mucosal surfaces protect them from invading bacteria. Pseudomonas aeruginosa is one of the many bacterial pathogens threatening humankind during the current antimicrobial resistance crisis. Here, we have tested whether P. aeruginosa and its phages are affected by mucosal conditions. We discovered by using a collection of four phages that, indeed, mucosal interaction dynamics can be seen in this model. Three of the tested phages significantly bound to mucin, while two had improved growth rates in mucin-exposed hosts. These results link P. aeruginosa and its phages to the bacteriophage adherence to the mucus model and open opportunities to explore this to improve phage therapy, be it by exploiting the phenotypes detected or by actively selecting mucosal-adapted phages for treatment.
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Affiliation(s)
- Gabriel Magno de Freitas Almeida
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Janne Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Nino Grdzelishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
- Faculty of Natural Science and Medicine, Ilia State University, Tbilisi, Georgia
| | - Elene Kakabadze
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | - Nata Bakuradze
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | - Elene Javakhishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | | | - Nina Chanishvili
- George Eliava Institute of Bacteriophages, Microbiology & Virology, Tbilisi, Georgia
| | | | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Centre, University of Jyväskylä, Jyväskylä, Finland
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Manzoor S, Abbas S, Zulfiqar S, Wang HC, Xiao M, Li WJ, Arshad M, Ahmed I. Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602 T isolated from tannery effluent in Pakistan. Antonie Van Leeuwenhoek 2024; 117:111. [PMID: 39103503 DOI: 10.1007/s10482-024-02006-3] [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: 05/26/2024] [Accepted: 07/27/2024] [Indexed: 08/07/2024]
Abstract
The strain designated NCCP-602T was isolated from tannery effluent, and displayed aerobic, gram-positive, rod-shaped cells that were characterized by oxidase negative, catalase positive, and non-motile features. The most favourable growth conditions were observed at a temperature of 30°C, pH 7.0, and NaCl concentration of 1% (w/v). It tolerated heavy metals at high concentrations of chromium (3600 ppm), copper (3300 ppm), cadmium (3000 ppm), arsenic (1200 ppm) and lead (1500 ppm). The results of phylogenetic analysis, derived from sequences of the 16S rRNA gene, indicated the position of strain NCCP-602T within genus Brevibacterium and showed that it was closely related to Brevibacterium ammoniilyticum JCM 17537T. Strain NCCP-602 T formed a robust branch that was clearly separate from closely related taxa. A comparison of 16S rRNA gene sequence similarity and dDDH values between the closely related type strains and strain NCCP-602T provided additional evidence supporting the classification of strain NCCP-602T as a distinct novel genospecies. The polar lipid profile included diphosphatidylglycerol, glycolipid, phospholipids and amino lipids. MK-7 and MK-8 were found as the respiratory quinones, while anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0, and anteiso-C17:0 were identified as the predominant cellular fatty acids (> 10%). Considering the convergence of phylogenetic, phenotypic, chemotaxonomic, and genotypic traits, it is suggested that strain NCCP-602 T be classified as a distinct species Brevibacterium metallidurans sp. nov. within genus Brevibacterium with type strain NCCP-602T (JCM 18882T = CGMCC1.62055T).
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Affiliation(s)
- Sadia Manzoor
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Saira Abbas
- Department of Zoology, University of Science and Technology, Bannu, Pakistan
| | - Sobia Zulfiqar
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Hong-Chuan Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan.
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Golubev S, Rasterkovskaya M, Sungurtseva I, Burov A, Muratova A. Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L. Microorganisms 2024; 12:1586. [PMID: 39203428 PMCID: PMC11356111 DOI: 10.3390/microorganisms12081586] [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: 07/06/2024] [Revised: 07/24/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH-heavy-metal contamination.
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Affiliation(s)
| | | | | | | | - Anna Muratova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia; (S.G.); (M.R.); (I.S.); (A.B.)
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49
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Tan S, Liu L, Jiao JY, Li MM, Hu CJ, Lv AP, Qi YL, Li YX, Rao YZ, Qu YN, Jiang HC, Soo RM, Evans PN, Hua ZS, Li WJ. Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota. Mol Biol Evol 2024; 41:msae151. [PMID: 39041196 PMCID: PMC11304991 DOI: 10.1093/molbev/msae151] [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: 01/29/2024] [Revised: 06/16/2024] [Accepted: 07/17/2024] [Indexed: 07/24/2024] Open
Abstract
Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chao-Jian Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Rochelle M Soo
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD 4072, Australia
| | - Paul N Evans
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD 4072, Australia
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Guangdong Provincial Key Laboratory of Plant Stress Biology, Sun Yat-Sen University, Guangzhou 510275, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, PR 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, PR China
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50
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Long PL, Wang YF, Fu L, Xiao Y, Tang SG, Gao J. Reclassification of Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 as a Later Heterotypic Synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953 using a Polyphasic Approach. Curr Microbiol 2024; 81:292. [PMID: 39090417 DOI: 10.1007/s00284-024-03820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
The taxonomic relationship between Streptomyces violarus and Streptomyces violaceus was reevaluated using a polyphasic taxonomic approach in this work. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Streptomyces violarus JCM 4534 T was closely related to Streptomyces arenae ISP 5293 T. However, phylogenetic analysis based on five house-keeping gene (atpD, gyrB, recA, rpoB and trpB) showed that the evolutionary neighbor of Streptomyces violarus JCM 4534 T was Streptomyces violaceus CGMCC 4.1456 T, suggesting that there was a close genetic relationship between these two strains. The average nucleotide identity and digital DNA-DNA hybridization values between them were 97.0 and 72.9%, respectively, greater than the 96.7 and 70% cut-off points recommended for delineating a Streptomyces species. This result indicated that they belonged to the same genomic species which was also verified by a comprehensive comparison of phenotypic and chemotaxonomic characteristics between Streptomyces violarus JCM 4534 T and Streptomyces violaceus CGMCC 4.1456 T. According to all these data and the rule of priority in nomenclature, it is proposed the Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 is a later heterotypic synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953. In addition, based on dDDH, Streptomyces violaceus and Streptomyces violarus are simultaneously designated as two different subspecies, i.e., Streptomyces violaceus subsp. violaceus and Streptomyces violaceus subsp. violarus.
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Affiliation(s)
- Pei-Lan Long
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yin-Feng Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Li Fu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yan Xiao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China
| | | | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, 411201, China.
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan, 411201, China.
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