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Pan Z, Wang W, Chen J, Chen Z, Avellán-Llaguno RD, Xu W, Duan Y, Liu B, Huang Q. Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168728. [PMID: 37992830 DOI: 10.1016/j.scitotenv.2023.168728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.
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Affiliation(s)
- Zhizhen Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Weiyi Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Institute of Life Sciences and Green Development, College of Life Sciences, Hebei University, Hebei 071002, China
| | - Jingyu Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zheng Chen
- Institue of Plant Protection, Fujian Academy of Agriculture Sciences, Fuzhou 350003, China
| | - Ricardo David Avellán-Llaguno
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wenjuan Xu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yifang Duan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bo Liu
- Fujian Academy of Agriculture Sciences, Fuzhou 350003, China
| | - Qiansheng Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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2
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Chhetri G, Kim I, Park S, Jung Y, Seo T. Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant. Arch Microbiol 2023; 205:324. [PMID: 37656250 DOI: 10.1007/s00203-023-03657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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3
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Zhang L, Huang W, Ning W, Song B, Osman G, Zhu J, Wang W. Radiobacillus kanasensis sp. nov., a halotolerant bacterium isolated from woodland soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36821360 DOI: 10.1099/ijsem.0.005718] [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: 02/24/2023] Open
Abstract
A novel Gram-positive, aerobic, rod-shaped, non-motile, endospore-forming salt-tolerant bacterium strain (80T), was isolated from woodland soil collected near Kanas lake in the Altay region of Xinjiang, PR China. The strain grew at 15-45 °C, pH6.0-9.0 and with 0-14 % (w/v) NaCl. The complete genome size of the novel strain was 4 031 766 bp including a circle chromosome and a circle plasmid. The genomic DNA G+C content was 38.99 mol %. Phylogenetic analysis based on 16S rRNA gene sequence and genome showed that strain 80T has the highest similarity to Radiobacillus deserti TKL69T. However, the novel strain showed an average nucleotide identity value of 78.65 % (lower than 95 %) and a digital DNA-DNA hybridization value of 22.30 % with R. deserti TKL69T based on the genome sequences. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17:0 and C16 : 1 ω7c alcohol. The only respiratory quinone was MK-7. The cell wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified glycolipids were identified as the major polar lipids. The phylogenetic, phenotypic and chemotaxonomic analyses showed that strain 80T represents a novel species of the genus Radiobacillus and the name Radiobacillus kanasensis sp. nov. is proposed. The type strain is 80T (=GDMCC 1.2844T=JCM 35077T).
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Affiliation(s)
- Lijuan Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wei Huang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wang Ning
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Bo Song
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Ghenijan Osman
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Jing Zhu
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wei Wang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
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4
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Li J, Zhang B, Liu G, Liu Y, Yang H, Yang R, Huang Y, Li S, Chen T, Zhang W, Zhang G. Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:6338-6347. [PMID: 33118923 DOI: 10.1099/ijsem.0.004536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, endospore-forming and UV-resistant bacterial strain, designated strain TKL69T, was isolated from sandy soil sampled in the Taklimakan Desert. The strain grew at 20-50 °C, pH 6-9 and with 0-12 % (w/v) NaCl. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The only respiratory quinone was MK-7. The cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidyl glycerol, two unidentified aminophospholipids and one unidentified phospholipid were identified as the major polar lipids. Genomic DNA analysis revealed a G+C content of 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TKL69T has the highest similarity to Salinibacillus xinjiangensis CGMCC 1.12331T (96.9 %) but belongs to an independent taxon separated from other genera of the family Bacillaceae. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain TKL69T represents a novel species of a new genus, for which the name Radiobacillus gen. nov., sp. nov. is proposed, with the type strain being Radiobacillus deserti TKL69T (=JCM 33497T=CICC 24779T).
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Affiliation(s)
- Juan Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Yang Liu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploition and Application, Gansu Province, Lanzhou 730000, PR China
| | - Ruiqi Yang
- School of Geography and Environmental Engineering, Lanzhou City University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yixuan Huang
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Shiweng Li
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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5
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Zhang W, Bahadur A, Zhang G, Zhang B, Wu X, Chen T, Liu G. Diverse Bacterial Communities From Qaidam Basin of the Qinghai-Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions. Front Microbiol 2020; 11:554105. [PMID: 33042062 PMCID: PMC7530167 DOI: 10.3389/fmicb.2020.554105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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6
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Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME, Holmes B, Steigerwalt AG, Villarma A, Sheth M, Batra D, Rowe LA, Burroughs M, Pryor JC, Bernardet JF, Hugo C, Kämpfer P, Newman JD, McQuiston JR. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432-4450. [PMID: 32735208 PMCID: PMC7660247 DOI: 10.1099/ijsem.0.003935] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/28/2019] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
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Affiliation(s)
- Ainsley C. Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A. Gulvik
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M. Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W. Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Melissa E. Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Barry Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - Arnie G. Steigerwalt
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Aaron Villarma
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Lori A. Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mark Burroughs
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jessica C. Pryor
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jean-François Bernardet
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Domaine de Vilvert, Jouy-en-Josas, France
| | - Celia Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Jeffrey D. Newman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Biology Department, Lycoming College, Williamsport PA 17701, USA
| | - John R. McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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7
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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8
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Siddaramappa S, Narjala A, Viswanathan V, Maliye C, Lakshminarayanan R. Phylogenetic insights into the diversity of Chryseobacterium species. Access Microbiol 2019; 1:e000019. [PMID: 32974515 PMCID: PMC7471780 DOI: 10.1099/acmi.0.000019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/03/2019] [Indexed: 01/28/2023] Open
Abstract
The genus Chryseobacterium was formally established in 1994 and contains 112 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin-type pigment. The genomes of 83 of these 112 species have been sequenced in view of their importance in clinical microbiology and potential applications in biotechnology. The National Center for Biotechnology Information taxonomy browser lists 1415 strains as members of the genus Chryseobacterium, of which the genomes of 94 strains have been sequenced. In this study, by comparing the 16S rDNA and the deduced proteome sequences, at least 20 of these strains have been proposed to represent novel species of the genus Chryseobacterium. Furthermore, a yellow-coloured bacterium isolated from dry soil in the USA (and identified as Flavobacterium sp. strain B-14859) has also been reconciled as a novel member of the genus Chryseobacterium based on the analysis of 16S rDNA sequences and the presence of flexirubin. Yet another bacterium (isolated from a water sample collected in the Western Ghats of India and identified as Chryseobacterium sp. strain WG4) was also found to represent a novel species. These proposals need to be validated using polyphasic taxonomic approaches.
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Affiliation(s)
- Shivakumara Siddaramappa
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Anushree Narjala
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Vandana Viswanathan
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Chaitra Maliye
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Raghavendran Lakshminarayanan
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
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Kim T, Kim M, Kang O, Jiang F, Chang X, Liu P, Zhang Y, Da X, Zheng C, Fang C, Peng F. Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense. Int J Syst Evol Microbiol 2015; 66:609-615. [PMID: 26558703 DOI: 10.1099/ijsem.0.000761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow, Gram-reaction-negative, non-motile, aerobic bacterium, designated D07T, was isolated from a tundra soil near Ny-Ålesund, Svalbard archipelago, Norway (78° N). Growth occurred at 4-37 °C (optimum 28-30 °C) and at pH 6.0-9.0 (optimum pH 7.0-8.0). The strain produced flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D07T belonged to the genus Chryseobacterium in the family Flavobacteriaceae. The 16S rRNA gene sequence of this strain showed 93.83 and 93.31 % sequence similarity, respectively, to those of Chryseobacterium contaminans C26T and Chryseobacterium taklimakanense X-65T. Strain D07T contained anteiso-C15 : 0 (25.91 %), iso-C15 : 0 (16.05 %), iso-C16 : 0 3-OH (9.64 %), iso-C16 : 0 (9.42 %) and iso-C14 : 0 (7.36 %) as the predominant cellular fatty acids, MK-6 as the major respiratory quinone and phosphatidylethanolamine, five unknown aminolipids and three unknown lipids as the main polar lipids. The DNA G+C content was 49.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D07T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium frigidum sp. nov. is proposed. The type strain is D07T ( = CCTCC AB 2011160T = KCTC 42897T). Emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense are also provided.
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Affiliation(s)
- TongRyul Kim
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China.,College of Life Sciences, Kim Il Sung University, Pyongyang, DPR Korea
| | - MyongChol Kim
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China.,College of Life Sciences, Kim Il Sung University, Pyongyang, DPR Korea
| | - OkChol Kang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China.,College of Life Sciences, Kim Il Sung University, Pyongyang, DPR Korea
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Ping Liu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xuyang Da
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Congyi Zheng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Song J, Choi A, Im M, Joung Y, Yoshizawa S, Cho JC, Kogure K. Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2015; 65:4850-4856. [PMID: 26443199 DOI: 10.1099/ijsem.0.000662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, proteorhodopsin-containing, orange, rod-shaped bacterium, designated SAORIC-234T, was isolated from deep seawater in the Pacific Ocean. 16S rRNA gene sequence analysis revealed that the strain could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and shared less than 94.6 % similarity with other species of the family with validly published names. The phenotypic characteristics of this novel isolate, such as growth properties and enzyme activities, could be differentiated from those of other species. The strain was non-motile, oxidase-positive and catalase-negative. The G+C content of the genomic DNA was determined to be 34.8 mol% and menaquinone-6 (MK-6) was the predominant isoprenoid quinone. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids comprised phosphatidylethanolamine, three unknown aminolipids and three unknown lipids. On the basis of the taxonomic data collected in this study, it was concluded that strain SAORIC-234T represents a novel genus and species in the family Flavobacteriaceae, for which the name Aurantivirga profunda gen. nov., sp. nov. is proposed. The type strain of the type species, Aurantivirga profunda sp. nov., is SAORIC-234T ( = NBRC 110606T = KACC 18400T).
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Affiliation(s)
- Jaeho Song
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Ahyoung Choi
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Mihye Im
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kazuhiro Kogure
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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Holmes B, Steigerwalt AG, Nicholson AC. DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. Int J Syst Evol Microbiol 2013; 63:4639-4662. [PMID: 23934253 DOI: 10.1099/ijs.0.054353-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.
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Affiliation(s)
- B Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - A G Steigerwalt
- Special Bacteriology Reference Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - A C Nicholson
- Special Bacteriology Reference Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Spongiimonas flava gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from an unidentified marine sponge. Antonie van Leeuwenhoek 2012; 103:625-33. [DOI: 10.1007/s10482-012-9846-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/31/2012] [Indexed: 01/19/2023]
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