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Liu D, Luo C, Dai R, Huang X, Chen X, He L, Mao H, Li J, Zhang L, Yang QY, Mei Z. AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research. Nucleic Acids Res 2024:gkae833. [PMID: 39377391 DOI: 10.1093/nar/gkae833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/28/2024] [Accepted: 09/16/2024] [Indexed: 10/09/2024] Open
Abstract
As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR's capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.
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Affiliation(s)
- Dongxu Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengfang Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyan Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongxia Mao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Linna Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Yong Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572025, China
| | - Zhinan Mei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
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2
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Martirena-Ramírez A, Serrano-Gamboa JG, Pérez-Llano Y, Zenteno-Alegría CO, Iza-Arteaga ML, Del Rayo Sánchez-Carbente M, Fernández-Ocaña AM, Batista-García RA, Folch-Mallol JL. Aspergillus brasiliensis E_15.1: A Novel Thermophilic Endophyte from a Volcanic Crater Unveiled through Comprehensive Genome-Wide, Phenotypic Analysis, and Plant Growth-Promoting Trails. J Fungi (Basel) 2024; 10:517. [PMID: 39194843 DOI: 10.3390/jof10080517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/29/2024] Open
Abstract
Thermophilic fungi have been seldom studied despite the fact that they can contribute to understanding ecological mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano "El Chichonal" in Mexico. This strain was capable of surviving in soil with a temperature of 60 °C and a pH of neutral acidity, which preluded a high thermostability and a potential in industrial application. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in 37 Mb of genomic DNA. We performed a comprehensive phylogenomic analysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasiliensis. Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. A. brasiliensis E_15.1 was found to degrade chitin, chitooligosaccharides, xylan, and cellulose. The genes to biosynthesize clavaric acid (a triterpene with antitumor activity) were found, thus probably having antitumor activity. In addition to the genomic analysis, a set of enzymatic assays confirmed the thermostability of extracellular xylanases and cellulases of A. brasiliensis E_15.1. The enzymatic repertoire of A. brasiliensis E_15.1 suggests that A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.
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Affiliation(s)
- Amanda Martirena-Ramírez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - José Germán Serrano-Gamboa
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Yordanis Pérez-Llano
- Centro de Ciencias Genómicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Claribel Orquídea Zenteno-Alegría
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Mario León Iza-Arteaga
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | | | - Ana María Fernández-Ocaña
- Departamento de Biología Animal, Biología Vegetal y Ecología, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071 Jaén, Spain
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
- Departamento de Biología Animal, Biología Vegetal y Ecología, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071 Jaén, Spain
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
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3
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Huang J, Hu P, Ye L, Shen Z, Chen X, Liu F, Xie Y, Yu J, Fan X, Xiao M, Tsui CKM, Wang W, Li Y, Zhang G, Wong KH, Cai L, Bai FY, Xu Y, Wang L. Pan-drug resistance and hypervirulence in a human fungal pathogen are enabled by mutagenesis induced by mammalian body temperature. Nat Microbiol 2024; 9:1686-1699. [PMID: 38898217 DOI: 10.1038/s41564-024-01720-y] [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: 07/05/2023] [Accepted: 05/02/2024] [Indexed: 06/21/2024]
Abstract
The continuing emergence of invasive fungal pathogens poses an increasing threat to public health. Here, through the China Hospital Invasive Fungal Surveillance Net programme, we identified two independent cases of human infection with a previously undescribed invasive fungal pathogen, Rhodosporidiobolus fluvialis, from a genus in which many species are highly resistant to fluconazole and caspofungin. We demonstrate that R. fluvialis can undergo yeast-to-pseudohyphal transition and that pseudohyphal growth enhances its virulence, revealed by the development of a mouse model. Furthermore, we show that mouse infection or mammalian body temperature induces its mutagenesis, allowing the emergence of hypervirulent mutants favouring pseudohyphal growth. Temperature-induced mutagenesis can also elicit the development of pan-resistance to three of the most commonly used first-line antifungals (fluconazole, caspofungin and amphotericin B) in different Rhodosporidiobolus species. Furthermore, polymyxin B was found to exhibit potent activity against the pan-resistant Rhodosporidiobolus mutants. Collectively, by identifying and characterizing a fungal pathogen in the drug-resistant genus Rhodosporidiobolus, we provide evidence that temperature-dependent mutagenesis can enable the development of pan-drug resistance and hypervirulence in fungi, and support the idea that global warming can promote the evolution of new fungal pathogens.
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Affiliation(s)
- Jingjing Huang
- Department of Clinical Laboratory, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Pengjie Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Leixin Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghao Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinhan Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Clement K M Tsui
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Novena, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Weiping Wang
- Department of Clinical Laboratory, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yingxing Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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4
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Fichant A, Lanceleur R, Hachfi S, Brun-Barale A, Blier AL, Firmesse O, Gallet A, Fessard V, Bonis M. New Approach Methods to Assess the Enteropathogenic Potential of Strains of the Bacillus cereus Group, including Bacillus thuringiensis. Foods 2024; 13:1140. [PMID: 38672813 PMCID: PMC11048917 DOI: 10.3390/foods13081140] [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: 02/14/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Bacillus cereus (Bc) is a wide group of Gram-positive and spore-forming bacteria, known to be the etiological agents of various human infections, primarily food poisoning. The Bc group includes enteropathogenic strains able to germinate in the digestive tract and to produce enterotoxins such as Nhe, Hbl, and CytK. One species of the group, Bacillus thuringiensis (Bt), has the unique feature of producing insecticidal crystals during sporulation, making it an important alternative to chemical pesticides to protect crops from insect pest larvae. Nevertheless, several studies have suggested a link between the ingestion of pesticide strains and human cases of food poisoning, calling their safety into question. Consequently, reliable tools for virulence assessment are worth developing to aid decision making in pesticide regulation. Here, we propose complementary approaches based on two biological models, the human intestinal Caco-2 cell line and the insect Drosophila melanogaster, to assess and rank the enteric virulence potency of Bt strains in comparison with other Bc group members. Using a dataset of 48 Bacillus spp. strains, we showed that some Bc group strains, including Bt, were able to induce cytotoxicity in Caco-2 cells with concomitant release of IL-8 cytokine, a landmark of pro-inflammatory response. In the D. melanogaster model, we were able to sort a panel of 39 strains into four different classes of virulence, ranging from no virulence to strong virulence. Importantly, for the most virulent strains, mortality was associated with a loss of intestinal barrier integrity. Interestingly, although strains can share a common toxinotype, they display different degrees of virulence, suggesting the existence of specific mechanisms of virulence expression in vivo in the intestine.
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Affiliation(s)
- Arnaud Fichant
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France; (A.F.); (O.F.)
- Université Côte d’Azur, CNRS, INRAE, ISA, 06903 Sophia-Antipolis, France; (S.H.); (A.B.-B.); (A.G.)
| | - Rachelle Lanceleur
- Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35306 Fougères, France; (R.L.); (A.-L.B.); (V.F.)
| | - Salma Hachfi
- Université Côte d’Azur, CNRS, INRAE, ISA, 06903 Sophia-Antipolis, France; (S.H.); (A.B.-B.); (A.G.)
| | - Alexandra Brun-Barale
- Université Côte d’Azur, CNRS, INRAE, ISA, 06903 Sophia-Antipolis, France; (S.H.); (A.B.-B.); (A.G.)
| | - Anne-Louise Blier
- Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35306 Fougères, France; (R.L.); (A.-L.B.); (V.F.)
| | - Olivier Firmesse
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France; (A.F.); (O.F.)
| | - Armel Gallet
- Université Côte d’Azur, CNRS, INRAE, ISA, 06903 Sophia-Antipolis, France; (S.H.); (A.B.-B.); (A.G.)
| | - Valérie Fessard
- Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35306 Fougères, France; (R.L.); (A.-L.B.); (V.F.)
| | - Mathilde Bonis
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France; (A.F.); (O.F.)
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5
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Folliero V, Ferravante C, Iovane V, Salvati A, Crescenzo L, Perna R, Corvino G, Della Rocca MT, Panetta V, Tranfa A, Greco G, Baldoni T, Pagnini U, Finamore E, Giurato G, Nassa G, Coppola M, Atripaldi L, Greco R, D'Argenio A, Foti MG, Abate R, Del Giudice A, Sarnelli B, Weisz A, Iovane G, Pinto R, Franci G, Galdiero M. Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region. Sci Data 2024; 11:220. [PMID: 38374088 PMCID: PMC10876956 DOI: 10.1038/s41597-024-03032-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018-2021, obtained from the analysis of whole genome sequence. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB, 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB. This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of this disease.
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Affiliation(s)
- Veronica Folliero
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carlo Ferravante
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy
| | - Annamaria Salvati
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Laura Crescenzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Rossella Perna
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Giusy Corvino
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Maria T Della Rocca
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Vittorio Panetta
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Alessandro Tranfa
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Giuseppe Greco
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Teresa Baldoni
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Ugo Pagnini
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Emiliana Finamore
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Giovanni Nassa
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | | | - Luigi Atripaldi
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Rita Greco
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Annamaria D'Argenio
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Maria Grazia Foti
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Rosamaria Abate
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | | | - Bruno Sarnelli
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Renato Pinto
- UOD Prevenzione e Sanità Pubblica Veterinaria, Direzione Generale Tutela della Salute - Regione Campania, Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy.
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy.
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy.
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6
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Ide-Pérez MR, Sánchez-Reyes A, Folch-Mallol JL, Sánchez-Carbente MDR. Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLoS One 2024; 19:e0297232. [PMID: 38354109 PMCID: PMC10866521 DOI: 10.1371/journal.pone.0297232] [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: 08/25/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024] Open
Abstract
Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.
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Affiliation(s)
- Martín R. Ide-Pérez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ayixon Sánchez-Reyes
- Investigador por México-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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7
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Huang Y, Wu Y, Hu H, Tong B, Wang J, Zhang S, Wang Y, Zhang J, Yin Y, Dai S, Zhao W, An B, Pu J, Wang Y, Peng C, Li N, Zhou J, Tan Y, Zhong C. Accelerating the design of pili-enabled living materials using an integrative technological workflow. Nat Chem Biol 2024; 20:201-210. [PMID: 38012344 DOI: 10.1038/s41589-023-01489-x] [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: 09/28/2022] [Accepted: 10/17/2023] [Indexed: 11/29/2023]
Abstract
Bacteria can be programmed to create engineered living materials (ELMs) with self-healing and evolvable functionalities. However, further development of ELMs is greatly hampered by the lack of engineerable nonpathogenic chassis and corresponding programmable endogenous biopolymers. Here, we describe a technological workflow for facilitating ELMs design by rationally integrating bioinformatics, structural biology and synthetic biology technologies. We first develop bioinformatics software, termed Bacteria Biopolymer Sniffer (BBSniffer), that allows fast mining of biopolymers and biopolymer-producing bacteria of interest. As a proof-of-principle study, using existing pathogenic pilus as input, we identify the covalently linked pili (CLP) biosynthetic gene cluster in the industrial workhorse Corynebacterium glutamicum. Genetic manipulation and structural characterization reveal the molecular mechanism of the CLP assembly, ultimately enabling a type of programmable pili for ELM design. Finally, engineering of the CLP-enabled living materials transforms cellulosic biomass into lycopene by coupling the extracellular and intracellular bioconversion ability.
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Affiliation(s)
- Yuanyuan Huang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Yanfei Wu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Han Hu
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, China
| | | | - Jie Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Siyu Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yanyi Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jicong Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Shengkun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wenjuan Zhao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bolin An
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiahua Pu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yaomin Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Nan Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiahai Zhou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Yan Tan
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, China.
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
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8
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Yang J, Ye Y, Yi R, Bi D, Zhang S, Han S, Kan X. A new perspective on codon usage, selective pressure, and phylogenetic implications of the plastomes in the Telephium clade (Crassulaceae). Gene 2024; 892:147871. [PMID: 37797779 DOI: 10.1016/j.gene.2023.147871] [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: 07/26/2023] [Revised: 09/13/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
The Telephium clade of the Crassulaceae family contains many medicinal, ornamental, and ecologically restorative plants. However, the phylogenetic relationships within the clade remain debated, and comprehensive analyses of codon usage and selection pressure in Telephium plastomes are limited. In this study, we assembled and annotated four plastomes and performed extensive analyses. The plastomes exhibited a typical quadripartite structure and high conservation. The lengths ranged from 151,357 bp to 151,641 bp with 134 genes identified. The GC content was the highest within IR, followed by LSC, and lowest in the SSC region. Meanwhile, a unique inversion was observed within the LSC region of Meterostachys sikokianus. Polymorphisms analysis revealed minimum nucleotide diversity in the IR regions, with over ten highly polymorphic regions identified. Phylogenetically, two subclades formed within the monophyletic Telephium clade, with Umbilicus as the sister group to the remaining Hylotelephium subclade members. Notably, no significant positive selection was found among the 79 plastid genes, which showed varying evolutionary patterns. However, 19 genes contained codons under positive selection. The specific functions of these sites require further investigation. Synonymous codon usage was biased and conserved across the tested plastomes, shaped by natural selection, mutations and other factors of varying influence. We also identified 34 taxon-specific codon aversion motifs from 49 plastid genes. Our plastomic analyses elucidate phylogenetic relationships and evolutionary patterns in this medicinal clade, providing a foundation for further research on these ecologically and pharmaceutically important plants.
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Affiliation(s)
- Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China.
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9
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Crestani C, Arcari G, Landier A, Passet V, Garnier D, Brémont S, Armatys N, Carmi-Leroy A, Toubiana J, Badell E, Brisse S. Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex. Res Microbiol 2023; 174:104113. [PMID: 37572824 DOI: 10.1016/j.resmic.2023.104113] [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: 04/12/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The Corynebacterium diphtheriae species complex comprises seven bacterial species, including Corynebacterium ulcerans, a zoonotic pathogen from multiple animal species. In this work, we characterise phenotypically and genotypically isolates belonging to two C. ulcerans lineages. Results from phylogenetic analyses, in silico DNA-DNA hybridization (DDH) and MALDI-TOF spectra differentiate lineage 2 from C. ulcerans lineage 1, which, together with their distinct transmission dynamics (probable human-to-human vs animal-to-human), indicates that lineage 2 is a separate Corynebacterium species, which we propose to name Corynebacterium ramonii. This species is of particular medical interest considering that its human-to-human transmission is likely, and that some C. ramonii isolates carry the diphtheria toxin gene.
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Affiliation(s)
- Chiara Crestani
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
| | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Dorian Garnier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvie Brémont
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Nathalie Armatys
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Annick Carmi-Leroy
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France; Necker-Enfants Malades University Hospital, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France.
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10
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Lourenço M, Osbelt L, Passet V, Gravey F, Megrian D, Strowig T, Rodrigues C, Brisse S. Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance. Microbiol Spectr 2023; 11:e0481222. [PMID: 37338376 PMCID: PMC10433977 DOI: 10.1128/spectrum.04812-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Klebsiella pneumoniae (Kp), a human gut colonizer and opportunistic pathogen, is a major contributor to the global burden of antimicrobial resistance. Virulent bacteriophages represent promising agents for decolonization and therapy. However, the majority of anti-Kp phages that have been isolated thus far are highly specific to unique capsular types (anti-K phages), which is a major limitation to phage therapy prospects due to the highly polymorphic capsule of Kp. Here, we report on an original anti-Kp phage isolation strategy, using capsule-deficient Kp mutants as hosts (anti-Kd phages). We show that anti-Kd phages have a broad host range, as the majority are able to infect noncapsulated mutants of multiple genetic sublineages and O-types. Additionally, anti-Kd phages induce a lower rate of resistance emergence in vitro and provide increased killing efficiency when in combination with anti-K phages. In vivo, anti-Kd phages are able to replicate in mouse guts colonized with a capsulated Kp strain, suggesting the presence of noncapsulated Kp subpopulations. The original strategy proposed here represents a promising avenue that circumvents the Kp capsule host restriction barrier, offering promise for therapeutic development. IMPORTANCE Klebsiella pneumoniae (Kp) is an ecologically generalist bacterium as well as an opportunistic pathogen that is responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In the last decades, limited advances have been made in the use of virulent phages as alternatives or complements to antibiotics that are used to treat Kp infections. This work demonstrates the potential value of an anti-Klebsiella phage isolation strategy that addresses the issue of the narrow host range of anti-K phages. Anti-Kd phages may be active in infection sites in which capsule expression is intermittent or repressed or in combination with anti-K phages, which often induce the loss of capsule in escape mutants.
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Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - François Gravey
- Dynamycure Inserm UM1311 Normandie Univ, UNICAEN, UNIROUEN, Caen, France
| | - Daniela Megrian
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Carla Rodrigues
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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11
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Yadav IS, Rawat N, Chhuneja P, Kaur S, Uauy C, Lazo G, Gu YQ, Doležel J, Tiwari VK. Comparative genomic analysis of 5M g chromosome of Aegilops geniculata and 5U u chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1144000. [PMID: 37521926 PMCID: PMC10373596 DOI: 10.3389/fpls.2023.1144000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Wheat is one of the most important cereal crops for the global food security. Due to its narrow genetic base, modern bread wheat cultivars face challenges from increasing abiotic and biotic stresses. Since genetic improvement is the most sustainable approach, finding novel genes and alleles is critical for enhancing the genetic diversity of wheat. The tertiary gene pool of wheat is considered a gold mine for genetic diversity as novel genes and alleles can be identified and transferred to wheat cultivars. Aegilops geniculata and Ae. umbellulata are the key members of the tertiary gene pool of wheat and harbor important genes against abiotic and biotic stresses. Homoeologous-group five chromosomes (5Uu and 5Mg) have been extensively studied from Ae. geniculata and Ae. umbellulata as they harbor several important genes including Lr57, Lr76, Yr40, Yr70, Sr53 and chromosomal pairing loci. In the present study, using chromosome DNA sequencing and RNAseq datasets, we performed comparative analysis to study homoeologous gene evolution in 5Mg, 5Uu, and group 5 wheat chromosomes. Our findings highlight the diversity of transcription factors and resistance genes, resulting from the differential expansion of the gene families. Both the chromosomes were found to be enriched with the "response to stimulus" category of genes providing resistance against biotic and abiotic stress. Phylogenetic study positioned the M genome closer to the D genome, with higher proximity to the A genome than the B genome. Over 4000 genes were impacted by SNPs on 5D, with 4-5% of those genes displaying non-disruptive variations that affect gene function.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Gerard Lazo
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Yong Q. Gu
- Agricultural Research Service, United States Department of Agriculture (USDA), Albany, CA, United States
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Olomouc, Czechia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
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12
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Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01852-x. [PMID: 37338631 PMCID: PMC10371898 DOI: 10.1007/s10482-023-01852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, IFB-Core, UMS 3601, Institut Français de Bioinformatique, Evry, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, CIP - Collection of Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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13
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Permana B, Harris PNA, Runnegar N, Lindsay M, Henderson BC, Playford EG, Paterson DL, Beatson SA, Forde BM. Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland. Microbiol Spectr 2023; 11:e0420422. [PMID: 37191518 PMCID: PMC10269735 DOI: 10.1128/spectrum.04204-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome single nucleotide polymorphism (SNP) distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events. In silico genotyping confirmed that all study isolates were vanB-type VREfm carrying virulence characteristics of the hospital-associated E. faecium. Phylogenetic analysis identified two distinct phylogenetic clades, only one of which was responsible for a hospital outbreak. Four outbreak subtypes could be defined with examples of recent transmissions. Inference on transmission trees suggested complex transmission routes with unknown environmental reservoirs mediating the outbreak. WGS-based cluster analysis with publicly available genomes identified closely related Australian ST78 and ST203 isolates, highlighting the capacity for WGS to resolve complex clonal relationships between the VREfm lineages. Whole genome-based analysis has provided a high-resolution description of an outbreak of vanB-type VREfm ST78 in a Queensland hospital. Combined routine genomic surveillance and epidemiological analysis have facilitated better understanding of the local epidemiology of this endemic strain, providing valuable insight for better targeted control of VREfm. IMPORTANCE Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of health care-associated infections (HAIs) globally. In Australia, the spread of hospital-adapted VREfm is largely driven by a single clonal group (clonal complex [CC]), CC17, to which the lineage ST78 belongs. While implementing a genomic surveillance program in Queensland, we observed increased incidence of ST78 colonizations and infections among patients. Here, we demonstrate the use of real-time genomic surveillance as a tool to support and enhance infection control (IC) practices. Our results show that real-time whole-genome sequencing (WGS) can efficiently disrupt outbreaks by identifying transmission routes that in turn can be targeted using resource-limited interventions. Additionally, we demonstrate that by placing local outbreaks in a global context, high-risk clones can be identified and targeted prior to them becoming established within clinical environments. Finally, the persistence of these organism within the hospital highlights the need for routine genomic surveillance as a management tool to control VRE transmission.
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Affiliation(s)
- Budi Permana
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Herston Infectious Diseases Institute, Metro North Health, Brisbane, Australia
| | - Patrick N. A. Harris
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Pathology Queensland, Central Laboratory, Brisbane, Australia
| | - Naomi Runnegar
- Princess Alexandra–Southside Clinical School, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Margaret Lindsay
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | | | - E. G. Playford
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - David L. Paterson
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
| | - Brian M. Forde
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
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14
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Wilson D, Rogers JD. Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. J Comput Biol 2023; 30:250-260. [PMID: 36848254 DOI: 10.1089/cmb.2022.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.
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Affiliation(s)
- Deangelo Wilson
- School of Computing, DePaul University, Chicago, Illinois, USA
| | - John D Rogers
- School of Computing, DePaul University, Chicago, Illinois, USA
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15
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Requena E, Alonso-Guirado L, Veloso J, Villarino M, Melgarejo P, Espeso EA, Larena I. Comparative analysis of Penicillium genomes reveals the absence of a specific genetic basis for biocontrol in Penicillium rubens strain 212. Front Microbiol 2023; 13:1075327. [PMID: 36713150 PMCID: PMC9880469 DOI: 10.3389/fmicb.2022.1075327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
Penicillium rubens strain 212 (PO212) is a filamentous fungus belonging to the division Ascomycete. PO212 acts as an effective biocontrol agent against several pathogens in a variety of horticultural crops including Fusarium oxysporum f.sp. lycopersici, causing vascular wilt disease in tomato plants. We assembled draft genomes of two P. rubens strains, the biocontrol agent PO212 and the soil isolate S27, which lacks biocontrol activity. We also performed comparative analyses of the genomic sequence of PO212 with that of the other P. rubens and P. chrysogenum strains. This is the first Penicillium strain with biocontrol activity whose genome has been sequenced and compared. PO212 genome size is 2,982 Mb, which is currently organized into 65 scaffolds and a total of 10,164 predicted Open Reading Frames (ORFs). Sequencing confirmed that PO212 belongs to P. rubens clade. The comparative analysis of the PO212 genome with the genomes of other P. rubens and Penicillium chrysogenum strains available in databases showed strong conservation among genomes, but a correlation was not found between these genomic data and the biocontrol phenotype displayed by PO212. Finally, the comparative analysis between PO212 and S27 genomes showed high sequence conservation and a low number of variations mainly located in ORF regions. These differences found in coding regions between PO212 and S27 genomes can explain neither the biocontrol activity of PO212 nor the absence of such activity in S27, opening a possible avenue toward transcriptomic and epigenetic studies that may shed light on this mechanism for fighting plant diseases caused by fungal pathogens. The genome sequences described in this study provide a useful novel resource for future research into the biology, ecology, and evolution of biological control agents.
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Affiliation(s)
- Elena Requena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Lola Alonso-Guirado
- Grupo de Epidemiología Genética y Molecular, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Javier Veloso
- Departamento de Biología Funcional, Escuela Politécnica Superior de Ingeniería, Universidad de Santiago de Compostela, Lugo, Spain
| | - María Villarino
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Paloma Melgarejo
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Eduardo Antonio Espeso
- Laboratorio de Biología Celular de Aspergillus, Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas Margarita Salas, CSIC (CIB-CSIC), Madrid, Spain
| | - Inmaculada Larena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
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16
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Rachtman E, Sarmashghi S, Bafna V, Mirarab S. Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Syst 2022; 13:817-829.e3. [PMID: 36265468 PMCID: PMC9589918 DOI: 10.1016/j.cels.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/14/2022] [Accepted: 06/28/2022] [Indexed: 01/26/2023]
Abstract
Computing distance between two genomes without alignments or even access to assemblies has many downstream analyses. However, alignment-free methods, including in the fast-growing field of genome skimming, are hampered by a significant methodological gap. While accurate methods (many k-mer-based) for assembly-free distance calculation exist, measuring the uncertainty of estimated distances has not been sufficiently studied. In this paper, we show that bootstrapping, the standard non-parametric method of measuring estimator uncertainty, is not accurate for k-mer-based methods that rely on k-mer frequency profiles. Instead, we propose using subsampling (with no replacement) in combination with a correction step to reduce the variance of the inferred distribution. We show that the distribution of distances using our procedure matches the true uncertainty of the estimator. The resulting phylogenetic support values effectively differentiate between correct and incorrect branches and identify controversial branches that change across alignment-free and alignment-based phylogenies reported in the literature.
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Affiliation(s)
- Eleonora Rachtman
- Bioinformatics and Systems Biology Graduate Program, UC San Diego, San Diego, CA 92093, USA
| | - Shahab Sarmashghi
- Department of Electrical and Computer Engineering, UC San Diego, San Diego, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, UC San Diego, San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC San Diego, San Diego, CA 92093, USA.
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17
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Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root. Arch Microbiol 2022; 204:630. [PMID: 36115912 PMCID: PMC9482572 DOI: 10.1007/s00203-022-03225-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022]
Abstract
A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA−DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, Institut Français de Bioinformatique, IFB-Core, UMS 3601, Evry, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP-Collection of Institut Pasteur, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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18
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Balaban M, Bristy NA, Faisal A, Bayzid MS, Mirarab S. Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model. BIOINFORMATICS ADVANCES 2022; 2:vbac055. [PMID: 35992043 PMCID: PMC9383262 DOI: 10.1093/bioadv/vbac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
While alignment has been the dominant approach for determining homology prior to phylogenetic inference, alignment-free methods can simplify the analysis, especially when analyzing genome-wide data. Furthermore, alignment-free methods present the only option for emerging forms of data, such as genome skims, which do not permit assembly. Despite the appeal, alignment-free methods have not been competitive with alignment-based methods in terms of accuracy. One limitation of alignment-free methods is their reliance on simplified models of sequence evolution such as Jukes-Cantor. If we can estimate frequencies of base substitutions in an alignment-free setting, we can compute pairwise distances under more complex models. However, since the strand of DNA sequences is unknown for many forms of genome-wide data, which arguably present the best use case for alignment-free methods, the most complex models that one can use are the so-called no strand-bias models. We show how to calculate distances under a four-parameter no strand-bias model called TK4 without relying on alignments or assemblies. The main idea is to replace letters in the input sequences and recompute Jaccard indices between k-mer sets. However, on larger genomes, we also need to compute the number of k-mer mismatches after replacement due to random chance as opposed to homology. We show in simulation that alignment-free distances can be highly accurate when genomes evolve under the assumed models and study the accuracy on assembled and unassembled biological data. Availability and implementation Our software is available open source at https://github.com/nishatbristy007/NSB. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Ahnaf Faisal
- Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1205, Bangladesh
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Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Mol Biol Evol 2022; 39:6608353. [PMID: 35700230 PMCID: PMC9254007 DOI: 10.1093/molbev/msac135] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.
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Affiliation(s)
- Melanie Hennart
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Julien Guglielmini
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Sébastien Bridel
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alexis Criscuolo
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
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20
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Kämpfer P, McInroy JA, Clermont D, Neumann-Schaal M, Criscuolo A, Busse HJ, Glaeser SP. Leucobacter soli sp. nov., from soil amended with humic acid. Int J Syst Evol Microbiol 2021; 71. [PMID: 34904944 DOI: 10.1099/ijsem.0.005156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, AL 36849, USA
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP-Collection de l´Institut Pasteur, F-75015 Paris, France
| | - Meina Neumann-Schaal
- Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015 Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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21
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Kämpfer P, Busse HJ, Clermont D, Criscuolo A, Glaeser SP. Devosia equisanguinis sp. nov., isolated from horse blood. Int J Syst Evol Microbiol 2021; 71. [PMID: 34788212 DOI: 10.1099/ijsem.0.005090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25-37 °C (range: 10-36 °C), at a pH range of pH 6.5-10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia. Major fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia, for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien, Austria
| | - Dominique Clermont
- CIP - Collection of Institut Pasteur, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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22
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Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S. Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. J Clin Microbiol 2021; 59:e0158121. [PMID: 34524891 PMCID: PMC8601238 DOI: 10.1128/jcm.01581-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST gene diversity among 602 isolates from sporadic clinical cases, small clusters, or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed a short-timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500-cgMLST-mismatch threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible (https://bigsdb.pasteur.fr/diphtheria). Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies of ecology, evolution, and virulence heterogeneity among C. diphtheriae sublineages.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris, France
| | - Melanie Hennart
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
- Université de Paris, Service de Pédiatrie Générale et Maladies Infectieuses, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
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23
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Kämpfer P, Busse HJ, McInroy JA, Clermont D, Criscuolo A, Glaeser SP. Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672916 DOI: 10.1099/ijsem.0.005051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA-DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK-6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien A-1210, Austria
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
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24
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Danès L, Tchitchek N, Bécavin C. Bacnet: a user-friendly platform for building multi-omics websites. Bioinformatics 2021; 37:1335-1336. [PMID: 32966562 DOI: 10.1093/bioinformatics/btaa828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 09/09/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY To face up to the exponential growth of heterogeneous datasets of various organisms, we developed a user-friendly platform for building multi-omics websites, which is named Bacnet. This platform helps bioinformaticians to construct four key web interfaces: (i) an interactive genome viewer; (ii) an expression and protein atlas; (iii) an interface for analysis of co-expression network; (iv) an interface for exploring homolog presence. We believe our platform will help the bioinformaticians to construct personalized user interfaces dedicated to biologists studying non-reference organisms. AVAILABILITY AND IMPLEMENTATION https://github.com/becavin-lab/bacnet; Java; Eclipse RAP; Eclipse RCP.
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Affiliation(s)
- Loane Danès
- Hub de Bioinformatique et Biostatistique - Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR 3756 Institut Pasteur, Paris F-75015, France
| | - Nicolas Tchitchek
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris F-75005, France
| | - Christophe Bécavin
- Hub de Bioinformatique et Biostatistique - Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR 3756 Institut Pasteur, Paris F-75015, France.,Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
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25
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Eger E, Heiden SE, Korolew K, Bayingana C, Ndoli JM, Sendegeya A, Gahutu JB, Kurz MSE, Mockenhaupt FP, Müller J, Simm S, Schaufler K. Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda. Front Microbiol 2021; 12:662575. [PMID: 34054764 PMCID: PMC8160302 DOI: 10.3389/fmicb.2021.662575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes blaCTX–M–15, tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.
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Affiliation(s)
- Elias Eger
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Stefan E Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Katja Korolew
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Claude Bayingana
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Jules M Ndoli
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Augustin Sendegeya
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Jean Bosco Gahutu
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Mathis S E Kurz
- Institute of Tropical Medicine and International Health, Charité Medical University of Berlin, Berlin, Germany
| | - Frank P Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité Medical University of Berlin, Berlin, Germany
| | - Julia Müller
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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Mietchen D, Penev L, Georgiev T, Ovcharova B, Kostadinova I. Open science in practice: 300 published research ideas and outcomes illustrate how RIO Journal facilitates engagement with the research process. RESEARCH IDEAS AND OUTCOMES 2021. [DOI: 10.3897/rio.7.e68595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Since Research Ideas and Outcomes was launched in late 2015, it has stimulated experimentation around the publication of and engagement with research processes, especially those with a strong open science component. Here, we zoom in on the first 300 RIO articles that have been published and elucidate how they relate to the different stages and variants of the research cycle, how they help address societal challenges and what forms of engagement have evolved around these resources, most of which have a nature and scope that would prevent them from entering the scholarly record via more traditional journals. Building on these observations, we describe some changes we recently introduced in the policies and peer review process at RIO to further facilitate engagement with the research process, including the establishment of an article collections feature that allows us to bring together research ideas and outcomes from within one research cycle or across multiple ones, irrespective of where they have been published.
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Kämpfer P, Glaeser SP, McInroy JA, Clermont D, Criscuolo A, Busse HJ. Pseudomonas carbonaria sp. nov., isolated from charcoal. Int J Syst Evol Microbiol 2021; 71. [PMID: 33835910 DOI: 10.1099/ijsem.0.004750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
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Levin D, Raab N, Pinto Y, Rothschild D, Zanir G, Godneva A, Mellul N, Futorian D, Gal D, Leviatan S, Zeevi D, Bachelet I, Segal E. Diversity and functional landscapes in the microbiota of animals in the wild. Science 2021; 372:science.abb5352. [PMID: 33766942 DOI: 10.1126/science.abb5352] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.
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Affiliation(s)
| | | | | | - Daphna Rothschild
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | | | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel.,Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10065, USA
| | - Ido Bachelet
- Wild Biotech, Rehovot, Israel.,Augmanity, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001 Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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Kämpfer P, Busse HJ, Glaeser SP, Clermont D, Criscuolo A, Mietke H. Jeotgalicoccus meleagridis sp. nov. isolated from bioaerosol from emissions of a turkey fattening plant and reclassification of Jeotgalicoccus halophilus Liu et al. 2011 as a later heterotypic synonym of Jeotgalicoccus aerolatus Martin et al. 2011. Int J Syst Evol Microbiol 2021; 71. [PMID: 33724175 DOI: 10.1099/ijsem.0.004745] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile, non-spore-forming, coccus (strain Do 184T) was isolated from exhaust air of a turkey fattening plant on mannitol salt agar. The strain shared high 16S rRNA gene sequence similarity to the type strains of Jeotgalicoccus aerolatus (98.0%) followed by Jeotgalicoccus marinus (97.2%) and Jeotgalicoccus huakuii (97.1%). All other 16S rRNA gene sequence similarities to species of the genus Jeotgalicoccus were below 97%. The average nucleotide identities (ANI) between the Do 184T genome assembly and the ones of type strains of species of the genus Jeotgalicoccus were far below the 95% species delineation cutoff value, ranging from 79.47% (J. marinus DSM 19772T) to 75.30% (J. pinnipedialis CIP 107946T). The quinone system of Do 184T, the polar lipid profile, the polyamine pattern and the fatty acid profile were in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of Do 184T to this genus. Do 184T represents a novel species, for which the name Jeotgalicoccus meleagridis sp. nov. is proposed, with the type strain Do 184T (=LMG 31100T=CCM 8918T=CIP 111649T). In addition, data on genome sequences of Jeotgalicoccus halophilus C1-52T =CGMCC 1.8911T=NBRC 105788T and Jeotgalicoccus aerolatus MPA-33T=CCM 7679T=CCUG 57953T=DSM 22420T=CIP 111750T indicate that both isolates represent the same species. Pairwise ANI between the genomes of these two strains lead to similarities of 98.98-99.05 %. These results indicate that these strains represent members of the same species. Due to priority of publication it is proposed that Jeotgalicoccus halophilus is reclassified as Jeotgalicoccus aerolatus.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique ‒ Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Henriette Mietke
- Staatliche Betriebsgesellschaft für Umwelt und Landwirtschaft, D-01683 Nossen, Germany
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30
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Song Y, Menezes da Silva N, Vicente VA, Quan Y, Teixeira M, Gong J, de Hoog S, Li R. Comparative genomics of opportunistic Phialophora species involved in divergent disease types. Mycoses 2021; 64:555-568. [PMID: 33455056 DOI: 10.1111/myc.13244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Black opportunists Phialophora verrucosa complex species can cause different disease types in competent and in immunocompromised individuals, but are remarkably overrepresented in CARD9-related infections. OBJECTIVES To better understand the ecology and potential pathogenicity of opportunistic Phialophora species and reveal eventual genetic parameters associated with the behaviour in vivo and genetic profiles in patients with CARD9 immunodeficiency. METHODS Genomes of 26 strains belonging to six species of the Phialophora verrucosa complex were sequenced. Using multilocus analysis, all environmental and clinical strains were identified correctly. We compared the genomes of agents from different disease types among each other including CARD9 immunodeficiency. RESULTS We obtained genome sizes of the 26 Phialophora strains ranged between 32 and 37 MB. Some species showed considerable intraspecific genomic variation. P americana showed the highest degree of variability. P verrucosa was variable in CAZy enzymes, whereas P americana varied in PKS-related genes. Phialophora species, particularly P verrucosa, are relatively frequent in patients with CARD9-related immunodeficiency. Different mutations in the CARD9 gene seem to increase susceptibility for infection by different groups of species, that is either Candida, dermatophytes or black fungi. A number of patients with chromoblastomycosis revealed an as yet unknown CARD9 mutation. TNFα impairment was prevalent in patients with CARD9 infections, while CBM patients were invariably IFNγ. CONCLUSIONS From genomic investigations, the known virulence factors between clinical and environmental strains did not reveal any significant difference. Phialophora complex has an equal chance to cause infection in humans, either healthy or CARD9-impaired.
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Affiliation(s)
- Yinggai Song
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | - Nickolas Menezes da Silva
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Vania A Vicente
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Yu Quan
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Marcus Teixeira
- Núcleo de Medicina Tropical, University of Brasília, Brasília, Brazil.,Applied Research & Development Building, Northern Arizona University, Flagstaff, AZ, USA
| | - Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil.,Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Ruoyu Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China.,Research Center for Medical Mycology, Peking University, Beijing, China.,National Clinical Research Center for Skin and Immune Diseases, Beijing, China
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Heiden SE, Hübner NO, Bohnert JA, Heidecke CD, Kramer A, Balau V, Gierer W, Schaefer S, Eckmanns T, Gatermann S, Eger E, Guenther S, Becker K, Schaufler K. A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition. Genome Med 2020; 12:113. [PMID: 33298160 PMCID: PMC7724794 DOI: 10.1186/s13073-020-00814-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several different parts of the world after first being described in Europe in 2008. From June to October 2019, we recorded an outbreak of an extensively drug-resistant ST307 lineage in four medical facilities in north-eastern Germany. METHODS Here, we investigated these isolates and those from subsequent cases in the same facilities. We performed whole-genome sequencing to study phylogenetics, microevolution, and plasmid transmission, as well as phenotypic experiments including growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance for an in-depth characterization of this outbreak clone. RESULTS Phylogenetics suggest a homogenous phylogram with several sub-clades containing either isolates from only one patient or isolates originating from different patients, suggesting inter-patient transmission. We identified three large resistance plasmids, carrying either NDM-1, CTX-M-15, or OXA-48, which K. pneumoniae ST307 likely donated to other K. pneumoniae isolates of different STs and even other bacterial species (e.g., Enterobacter cloacae) within the clinical settings. Several chromosomally and plasmid-encoded, hypervirulence-associated virulence factors (e.g., yersiniabactin, metabolite transporter, aerobactin, and heavy metal resistance genes) were identified in addition. While growth, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance were comparable to several control strains, results from siderophore secretion and hypermucoviscosity experiments revealed superiority of the ST307 clone, similar to an archetypical, hypervirulent K. pneumoniae strain (hvKP1). CONCLUSIONS The combination of extensive drug resistance and virulence, partly conferred through a "mosaic" plasmid carrying both antibiotic resistance and hypervirulence-associated features, demonstrates serious public health implications.
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Affiliation(s)
- Stefan E Heiden
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Jürgen A Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Claus-Dieter Heidecke
- Department of General, Visceral, Thoracic and Vascular Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Axel Kramer
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Veronika Balau
- IMD Laboratory Greifswald, Institute of Medical Diagnostics, Greifswald, Germany
| | | | | | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Ruhr University Bochum, Bochum, Germany
| | - Elias Eger
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany.
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Mühle E, Abry C, Leclerc P, Goly GM, Criscuolo A, Busse HJ, Kämpfer P, Bernardet JF, Clermont D, Chesneau O. Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s. Int J Syst Evol Microbiol 2020; 71. [PMID: 33253083 DOI: 10.1099/ijsem.0.004576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l'Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium. Both strains, CIP 105534T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH (shown as summed feature 3), C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum. All average nucleotide identity (ANI) and digital DNA-DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium, for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534T (=LMG 1342T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.
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Affiliation(s)
- Estelle Mühle
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Chloé Abry
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Priscilla Leclerc
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Gogoa-Marthe Goly
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du docteur Roux, 75015 Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, Heinrich-Buff-Ring 26 (IFZ), 35392 Giessen, Germany
| | - Jean-François Bernardet
- Unité de Virologie et Immunologie Moléculaires, Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE), 4 avenue Jean Jaurès, 78350 Jouy-en-Josas, France
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
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Criscuolo A. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Res 2020; 9:1309. [PMID: 33335719 PMCID: PMC7713896 DOI: 10.12688/f1000research.26930.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/29/2022] Open
Abstract
Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.
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Affiliation(s)
- Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756, CNRS, 75015 Paris, France
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34
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Kämpfer P, Glaeser SP, McInroy JA, Xu J, Busse HJ, Clermont D, Criscuolo A. Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum. Int J Syst Evol Microbiol 2020; 70:5824-5831. [PMID: 33034547 DOI: 10.1099/ijsem.0.004482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A Gram-staining-negative non endospore-forming strain, PXU-55T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium. The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the PXU-55T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% (Flavobacterium defluvii), and 86.1 and 29.9% (Flavobacterium johnsoniae). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C16:0 3-OH, C16:0 3-OH and C15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium. Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55T (=CIP 111646T=CCM 8914T) represents a novel species with the name Flavobacterium panici sp. nov.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Jia Xu
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
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Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar R. Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. Front Microbiol 2020; 11:1725. [PMID: 33013721 PMCID: PMC7500135 DOI: 10.3389/fmicb.2020.01725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 11/28/2022] Open
Abstract
The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.
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Affiliation(s)
- Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India.,P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, India
| | | | - Madhuri Gupta
- Department of Zoology, University of Delhi, Delhi, India
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India.,Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, India.,P.G. Department of Zoology, Magadh University, Bodh Gaya, India
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Draft Genome Sequences of 13 Plant-Associated Actinobacteria of the Family Microbacteriaceae. Microbiol Resour Announc 2020; 9:9/38/e00795-20. [PMID: 32943566 PMCID: PMC7498432 DOI: 10.1128/mra.00795-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Draft genome sequences of 13 bacterial strains from the family Microbacteriaceae were generated using Illumina technology. The genome sizes varied from 3.0 to 4.8 Mb, and the DNA G+C content was 68.1 to 72.5%. The sequences obtained will contribute to the development of genome-based taxonomy and understanding of molecular interactions between bacteria and plants.
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Complete and Draft Genome Sequences of 12 Plant-Associated Rathayibacter Strains of Known and Putative New Species. Microbiol Resour Announc 2020; 9:9/22/e00316-20. [PMID: 32467269 PMCID: PMC7256256 DOI: 10.1128/mra.00316-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter. Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter.
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Gujarati S, Chaudhari D, Hagir A, Khairnar M, Shouche Y, Rahi P. Klebsiella indica sp. nov., isolated from the surface of a tomato. Int J Syst Evol Microbiol 2020; 70:3278-3286. [DOI: 10.1099/ijsem.0.004168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A novel bacterial strain, designated TOUT106T, was isolated from the surface of a tomato. The cells were rod-shaped, Gram-negative, encapsulated and non-motile. Strain TOUT106T grows best at 28 °C and pH 7.0 and can tolerate up to 2 % (w/v) NaCl. Based on 16S rRNA gene phylogeny, strain TOUT106T was placed close to the
Salmonella
clade, with close similarity to
Salmonella enterica
subsp.
arizonae
strain NCTC 8297T (98.42 %). Results of genome-based phylogenetic analysis revealed that strain TOUT106T is placed well in the Klebsiella–Raoultella clade, by forming a distinct branch with
Klebsiella michiganensis
DSM25444T,
Klebsiella oxytoca
NCTC132727T,
Klebsiella grimontii
06D021T and
Klebsiella pasteurii
SB6412T. The genomic DNA G+C content of strain TOUT106T is 53.53 mol%. The average nucleotide identity values of TOUT106T were less than 86.5 % with closely related members of the family
Enterobacteriaceae
. The major fatty acids of strain TOUT106T were C16 : 0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14 : 0, C19:0 cyclo ω8c, C18:1 ω6c/C18:1 ω7c, C12 : 0 and C16:1 ω7c/C16:1 ω6c. Strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS compared to its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain TOUT106T could be distinguished from the recognized species of the genus
Klebsiella
. It is suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T=KACC 21384T=JCM 33718T).
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Affiliation(s)
- Sukriti Gujarati
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Diptaraj Chaudhari
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Ashwini Hagir
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India
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Abstract
Background Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. Results We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods. Yet, despite the potential limitation, our study shows that GTM has excellent accuracy, generally matching or improving on two previous DTMs, and is much faster than both. Conclusions The proposed GTM approach to the DTM problem is a useful new tool for large-scale phylogenomic analysis, and shows the surprising potential for unblended DTM methods.
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Affiliation(s)
- Vladimir Smirnov
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 N Goodwin Ave, Urbana, 61801, IL, US
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 N Goodwin Ave, Urbana, 61801, IL, US.
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The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples. Appl Environ Microbiol 2020; 86:AEM.02711-19. [PMID: 32005732 PMCID: PMC7082575 DOI: 10.1128/aem.02711-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources. Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10−1 CFU g−1 after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 103 to 1.5 × 104 CFU g−1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates. IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.
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41
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Tarlachkov SV, Shevchuk TV, Montero-Calasanz MDC, Starodumova IP. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. Bioinformatics 2020; 36:1668-1672. [PMID: 31711117 DOI: 10.1093/bioinformatics/btz840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/30/2019] [Accepted: 11/10/2019] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions. RESULTS This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sergey V Tarlachkov
- All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research.,Department of Plant Molecular Biology and Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Taras V Shevchuk
- Department of Plant Molecular Biology and Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Maria Del Carmen Montero-Calasanz
- Plant and Microbial Biology Research Group, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Irina P Starodumova
- All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research
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Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Médigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC, Vallenet D. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol 2020; 16:e1007732. [PMID: 32191703 PMCID: PMC7108747 DOI: 10.1371/journal.pcbi.1007732] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/31/2020] [Accepted: 02/12/2020] [Indexed: 12/21/2022] Open
Abstract
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.
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Affiliation(s)
- Guillaume Gautreau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Adelme Bazin
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Mathieu Gachet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Rémi Planel
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Laura Burlot
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Mathieu Dubois
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Amandine Perrin
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Stéphane Cruveiller
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Catherine Matias
- Laboratoire de Probabilités, Statistique et Modélisation, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, Paris, France
| | - Christophe Ambroise
- Laboratoire de Mathématiques et Modélisation d’Evry, UMR CNRS 8071, Université d’Evry Val d’Essonne, Evry, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
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Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex. Res Microbiol 2020; 171:122-127. [PMID: 32119905 DOI: 10.1016/j.resmic.2020.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Abstract
A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF mass spectrometry. The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190T) are clearly demarcated from C. diphtheriae, Corynebacterium belfantii, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. The average nucleotide identity of FRC0190T with C. diphtheriae NCTC11397T was 92.6%, and was 91.8% with C. belfantii FRC0043T. C. diphtheriae subsp. lausannense strain CHUV2995T appeared to be a later heterotypic synonym of C. belfantii (ANI, 99.3%). Phenotyping data revealed an atypical negative or heterogeneous intermediate maltose fermentation reaction for the six isolates. MALDI-TOF mass spectrometry differentiated the new group from the other Corynebacterium taxa by the presence of specific spectral peaks. rpoB sequences showed identity to atypical, maltose-negative C. diphtheriae biovar Belfanti isolates previously described from two cats in the USA. We propose the name Corynebacterium rouxii sp. nov. for the novel group, with FRC0190T (= CIP 111752T = DSM 110354T) as type strain.
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