51
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Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, Carapito C, Van Dorsselaer A, Mahmoud H, Sangal V, Ismail W. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8. Front Microbiol 2020; 11:1417. [PMID: 32733398 PMCID: PMC7358434 DOI: 10.3389/fmicb.2020.01417] [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: 04/19/2020] [Accepted: 06/02/2020] [Indexed: 01/02/2023] Open
Abstract
Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.
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Affiliation(s)
- Dean Thompson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Huda Mahmoud
- Department of Biological Sciences, College of Science, Kuwait University, Safat, Kuwait
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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52
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Shen X, Zhu S, Dong B, Chen Y, Xue Z, Ren N, Chen T, Chen X, Yang J, Chen J. Alteromonas profundi sp. nov., isolated from the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:4531-4536. [PMID: 32614764 DOI: 10.1099/ijsem.0.004308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas, with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).
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Affiliation(s)
- Xudong Shen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Bingxia Dong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- Institute of Respiratory and Disease, Shenzhen People's Hospital, Shenzhen 518020, PR China
| | - Zehao Xue
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Na Ren
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Ting Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xiunuan Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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53
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Streptococcus downii sp. nov., isolated from the oral cavity of a teenager with Down syndrome. Int J Syst Evol Microbiol 2020; 70:4098-4104. [DOI: 10.1099/ijsem.0.004180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A new α-haemolytic streptococcal strain has been isolated from the dental plaque of a teenager with Down syndrome. Genetic and taxonomic analyses place this
Streptococcus
within the oralis group. It is a Gram-stain-positive, non-motile, non-spore-forming spherical alpha-haemolytic coccus arranged in chains, and it ferments a large number of monosaccharides and disaccharides, as well as polymeric carbohydrates. It differs biochemically from closely related species of
Streptococcus
due to its production of α-galactosidase, β-galactosidase and N-acetyl-β-d-glucosaminidase and by the absence of arginine dihydrolase deiminase and IgA1-protease. It grows in a temperature range of 25 to 40 °C (optimal growth temperature at 37 °C) and in a pH range of 4.5 to 8 (optimal pH at 7.0). A phylogenetic analysis based on its 16S and 23S rRNA gene sequences placed it close to
Streptococcus dentisani
CECT 7747T. The ANIb and ANIm values were 93.19 and 93.61 %, respectively, both below the accepted threshold to designate it as a new species of bacteria. A phylogenetic tree based on its core genome placed it close to
Streptococcus oralis
subsp.
dentisani
strain CECT 7747T with a distance in the expanded core phylogeny of 0.1298. The in silico DNA–DNA hybridization value was 52.2 % with respect to the closest species,
S. oralis
subsp.
dentisani
CECT 7747T. Based on these data, a new species of bacteria within the genus
Streptococcus
, family
Streptococcaceae
and order
Lactobacillales
is described, for which the name of Streptococcus downii sp. nov. is proposed (type strain CECT 9732T=CCUG 73139T).
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54
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Xue Z, Zhu S, Chen X, Chen T, Ren N, Chen Y, Dong B, Shen X, Huang Y, Yang J, Chen J. Jiella pacifica sp. nov., isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:4345-4350. [PMID: 32584750 DOI: 10.1099/ijsem.0.004295] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain 40Bstr34T, isolated from a sediment sample from the West Pacific Ocean, was taxonomically characterized by using a polyphasic approach. The strain was phylogenetically close to Jiella aquimaris LZB041T and Jiella endophytica CBS5Q-3T, with 16S rRNA gene sequence similarities of 98.5 and 97.1 %, respectively. The genome of strain 40Bstr34T featured a G+C content of 65.7 % for a 5.8 Mb chromosome. Up-to-date bacterial core gene set analysis revealed that strain 40Bstr34T represents one independent lineage with J.aquimaris LZB041T. In silico DNA-DNA hybridization values between strain 40Bstr34T and its phylogenetic neighbours ranged from 30.3-34.2 %, below the cutoff of 70 %. In addition, the corresponding average nucleotide identity values were between 81.8-83.7 %, which are lower than 95 % threshold. The predominant cellular fatty acids of strain 40Bstr34T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), cyclo-C19 : 0 ω8c and iso-C17 : 0 3-OH, and ubiquinone-10 as the predominant respiratory quinone. The major polar lipids included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Based on the results of phenotypic, chemotaxonomic and genetic analyses, strain 40Bstr34T is identified as representing a novel species of the genus Jiella for which the name Jiella pacifica sp. nov. is proposed. The type strain is 40Bstr34T (=JCM 33903T=MCCC 1K04569T).
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Affiliation(s)
- Zehao Xue
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xiunuan Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Ting Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Na Ren
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- Institute of Respiratory and Disease, Shenzhen People's Hospital, Shenzhen 518020, PR China
| | - Bingxia Dong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xudong Shen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yizhe Huang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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55
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Dai H, Lu B, Li Z, Huang Z, Cai H, Yu K, Wang D. Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O'Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015. BMC Microbiol 2020; 20:152. [PMID: 32522175 PMCID: PMC7288399 DOI: 10.1186/s12866-020-01844-1] [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: 03/05/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. Results Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. Conclusions This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
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Affiliation(s)
- Hang Dai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Zhenpeng Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China
| | - Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Hongyan Cai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China. .,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China.
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56
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de Melo BST, Mendes-Marques CL, Campos TDL, Almeida AMPD, Leal NC, Xavier DE. High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains. FEMS Microbiol Lett 2020; 366:5658690. [PMID: 31804685 DOI: 10.1093/femsle/fnz245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.
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Affiliation(s)
- Beatriz Souza Toscano de Melo
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Carina Lucena Mendes-Marques
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Túlio de Lima Campos
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Alzira Maria Paiva de Almeida
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Nilma Cintra Leal
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
| | - Danilo Elias Xavier
- Departamento de Microbiologia, Instituto Aggeu Magalhães - FIOCRUZ, Av. Prof. Moraes Rego, Cidade Universitária, Recife - PE, 50670-420, Brazil
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57
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Khurana H, Sharma M, Verma H, Lopes BS, Lal R, Negi RK. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191-3200. [PMID: 32512145 DOI: 10.1016/j.ygeno.2020.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Bruno Silvester Lopes
- School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, 0:025 Polwarth Building, Aberdeen AB25 2ZD, UK
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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58
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Muricauda oceani sp. nov., isolated from the East Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:3839-3844. [DOI: 10.1099/ijsem.0.004241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain 501str8T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain 501str8T belonged to the genus
Muricauda
, with closely related type strains
Muricauda aquimarina
SW-63T (98.5 %),
Muricauda lutimaris
SMK-108T (98.3 %) and
Muricauda ruestringensis
B1T (97.9 %). Up-to-date bacterial core gene set analysis revealed that strain 501str8T represented one independent lineage with
M. aquimarina
SW-63T. The average nucleotide identity values of strain 501str8T with
M. aquimarina
SW-63T and
M. lutimaris
SMK-108T were 80.2 and 81.3 %, respectively. In silico DNA–DNA hybridization values between strain 501str8T and
M. aquimarina
SW-63T and
M. lutimaris
SMK-108T were 22.8 and 32.9 %, respectively. The predominant isoprenoid quinone was menaquinone-6, and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G were the dominant cellular fatty acids. The G+C content of the genomic DNA was 42.8 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain 501str8T could be differentiated from closely related species. Therefore, we propose that strain 501str8T represents a novel species of the genus
Muricauda
, for which the name Muricauda oceani sp. nov. is suggested. The type strain is 501str8T (=JCM 33902T=MCCC 1K04567T).
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59
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Sisinthy S, Gundlapally SR. Mitsuaria chitinivorans sp. nov. a potential candidate for bioremediation: emended description of the genera Mitsuaria, Roseateles and Pelomonas. Arch Microbiol 2020; 202:1839-1848. [PMID: 32447433 DOI: 10.1007/s00203-020-01905-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/20/2023]
Abstract
As a part of studying the effect of deoxygenation, eutrophication and acidification on bacterial diversity, strain HWN-4T was isolated from tube well water and characterized. The draft genome sequencing of strain HWN-4T revealed a genome size of 5,774,764 bp and the annotation indicated 5102 coding sequences including 66 RNA genes. Strain HWN-4T is Gram negative, rod-shaped, motile in the log phase, catalase and oxidase positive, and the major fatty acids and respiratory quinone present are C10:0 3-OH, C14:0 3OH/C16:1 iso I, C16:1 ω7c/C16:1 ω6c, C16:0 and C17:0 cyclo and ubiquinone-8, respectively. The phylogenetic analyses, based on 16S rRNA gene sequence, indicated that strain HWN-4T is a member of the genus Mitsuaria. The average nucleotide identity (ANI) and genome-to-genome similarity between strain HWN-4T and all other species/strains of the genus Mitsuaria are less than (%) 95.0 and 70.0, respectively. This confirms the status of strain HWN-4T as a novel species. The species status is further confirmed by phenotypic differences exhibited by strain HWN-4T with other members of the same genus. Based on the collective differences exhibited by strain HWN-4T with other members of the genus Mitsuaria, the name Mitsuaria chitinivorans sp. nov. is proposed. Further, the diagnostic signature nucleotides were identified in the 16S rRNA gene sequences of members of the genera Mitsuaria, Pelomonas and Roseateles, that distinctly differentiate them and support an emendation of the genera. Besides, phylogenetic and structural characterization of chitinases from members of the genus Mitsuaria was performed. The type strain of Mitsuaria chitinivorans sp. nov. is HWN-4T = LMG 28685T = KTCC 42483T.
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Affiliation(s)
- Shivaji Sisinthy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
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60
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Walter T, Klim J, Jurkowski M, Gawor J, Köhling I, Słodownik M, Zielenkiewicz U. Plasmidome of an environmental Acinetobacter lwoffii strain originating from a former gold and arsenic mine. Plasmid 2020; 110:102505. [PMID: 32380021 DOI: 10.1016/j.plasmid.2020.102505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/20/2020] [Accepted: 04/12/2020] [Indexed: 02/08/2023]
Abstract
Emerging important Acinetobacter strains commonly accommodate a plethora of mobile elements including plasmids of different size. Plasmids, apart from encoding modules enabling their self-replication and/or transmission, can carry a diverse number of genes, allowing the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. The present study characterizes the plasmidome generated from an arsenic-resistant strain named ZS207, classified as Acinetobacter lwoffii. Sequencing effort revealed the presence of nine plasmids in the size between 4.3 and 38.4 kb as well as one 186.6 kb megaplasmid. All plasmids, except the megaplasmid, do apparently not confer distinguishing phenotypic features. In contrast, the megaplasmid carries arsenic and heavy metals resistance regions similar to those found in permafrost A. lwoffii strains. In-depth in silico analyses have shown a significant similarity between the regions from these plasmids, especially concerning multiple transposable elements, transfer and mobilization genes, and toxin-antitoxin systems. Since ars genes encode proteins of major significance in terms of potential use in bioremediation, arsenic resistance level of ZS207 was determined and the functionality of selected ars genes was examined. Additionally, we checked the functionality of plasmid-encoded toxin-antitoxin systems and their impact on the formation of persister cells.
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Affiliation(s)
- Tomasz Walter
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Joanna Klim
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Marcin Jurkowski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Iwona Köhling
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Małgorzata Słodownik
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland.
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Sarfraz S, Sahi ST, Oulghazi S, Riaz K, Rajput NA, Atiq M, Tufail MR, Hameed A, Faure D. Species Diversity of Dickeya and Pectobacterium Causing Potato Blackleg Disease in Pakistan. PLANT DISEASE 2020; 104:1492-1499. [PMID: 32150503 DOI: 10.1094/pdis-08-19-1743-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Pectobacterium atrosepticum. Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gapA gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (P. atrosepticum), SS28 (Pectobacterium polaris), SS70 (Dickeya dianthicola), SS90 (Pectobacterium parmentieri), SS95 (Pectobacterium punjabense), and SS96 (Pectobacterium versatile) were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA, and rplB). Phylogenetic analysis revealed considerable genetic diversity in the genus Pectobacterium. In silico DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference Pectobacterium and Dickeya strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: P. atrosepticum, P. versatile, P. parmentieri, P. polaris, P. punjabense, and D. dianthicola.
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Affiliation(s)
- Sohaib Sarfraz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Shahbaz Talib Sahi
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Saïd Oulghazi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, Meknes, Morocco
| | - Kashif Riaz
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Nasir Ahmed Rajput
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Atiq
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Rizwan Tufail
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Akhtar Hameed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad 38000, Pakistan
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Pei TT, Li H, Liang X, Wang ZH, Liu G, Wu LL, Kim H, Xie Z, Yu M, Lin S, Xu P, Dong TG. Intramolecular chaperone-mediated secretion of an Rhs effector toxin by a type VI secretion system. Nat Commun 2020; 11:1865. [PMID: 32313027 PMCID: PMC7170923 DOI: 10.1038/s41467-020-15774-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial Rhs proteins containing toxic domains are often secreted by type VI secretion systems (T6SSs) through unclear mechanisms. Here, we show that the T6SS Rhs-family effector TseI of Aeromonas dhakensis is subject to self-cleavage at both the N- and the C-terminus, releasing the middle Rhs core and two VgrG-interacting domains (which we name VIRN and VIRC). VIRC is an endonuclease, and the immunity protein TsiI protects against VIRC toxicity through direct interaction. Proteolytic release of VIRC and VIRN is mediated, respectively, by an internal aspartic protease activity and by two conserved glutamic residues in the Rhs core. Mutations abolishing self-cleavage do not block secretion, but reduce TseI toxicity. Deletion of VIRN or the Rhs core abolishes secretion. TseI homologs from Pseudomonas syringae, P. aeruginosa, and Vibrio parahaemolyticus are also self-cleaved. VIRN and VIRC interact with protein VgrG1, while the Rhs core interacts with protein TecI. We propose that VIRN and the Rhs core act as T6SS intramolecular chaperones to facilitate toxin secretion and function.
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Affiliation(s)
- Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaoye Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada
| | - Zeng-Hang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201204, Shanghai, China
| | - Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Haeun Kim
- Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Ming Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Tao G Dong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Department of Ecosystem and Public Health, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N4Z6, Canada.
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63
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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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64
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Kämpfer P, Fuglsang-Damgaard D, Overballe-Petersen S, Hasman H, Hammerum AM, Fuursted K, Blom J, Glaeser SP, Hansen F. Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov. Int J Syst Evol Microbiol 2020; 70:1315-1320. [PMID: 31860429 DOI: 10.1099/ijsem.0.003918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of all Pseudocitrobacter species was re-evaluated by comparative genomics based on whole genome sequencing. As a result, it is obvious that Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis. In addition, genome-based analysis of strain CPO20170097T, isolated from a patient in northern Denmark was allocated to the genus Pseudocitrobacter. This strain showed significant genotypic and phenotypic differences from P. faecalis and it is proposed that this strain represents a novel species of the genus, for which the name Pseudocitrobacter vendiensis sp. nov. is proposed with the type strain CPO20170097T (=CCUG 73096T=LMG 31042T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | | | | | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, D-35392, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Frank Hansen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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65
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Fernández-Bravo A, Figueras MJ. An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity. Microorganisms 2020; 8:microorganisms8010129. [PMID: 31963469 PMCID: PMC7022790 DOI: 10.3390/microorganisms8010129] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.
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66
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Roslan NN, Ngalimat MS, Leow ATC, Oslan SN, Baharum SN, Sabri S. Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15. Microbiol Res 2020; 233:126410. [PMID: 31945517 DOI: 10.1016/j.micres.2020.126410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 01/09/2020] [Indexed: 11/18/2022]
Abstract
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
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Affiliation(s)
- Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohamad Syazwan Ngalimat
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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67
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Lin D, Huang Y, Chen Y, Zhu S, Yang J, Chen J. Devosia indica sp. nov., isolated from surface seawater in the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:340-345. [DOI: 10.1099/ijsem.0.003759] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Danqiu Lin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yizhe Huang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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68
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Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. Int J Syst Evol Microbiol 2019; 69:3939-3945. [DOI: 10.1099/ijsem.0.003711] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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69
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da Silva WL, Yang KT, Pettis GS, Soares NR, Giorno R, Clark CA. Flooding-Associated Soft Rot of Sweetpotato Storage Roots Caused by Distinct Clostridium Isolates. PLANT DISEASE 2019; 103:3050-3056. [PMID: 31642734 DOI: 10.1094/pdis-03-19-0548-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flooding of sweetpotatoes in the field leads to development of soft rot on the storage roots while they remain submerged or on subsequent harvest and storage. Incidences of flooding after periods of intense rainy weather are on the rise in the southeastern United States, which is home to the majority of sweetpotato production in the nation. In an effort to characterize the causative agent(s) of this devastating disease, here we describe two distinct bacterial strains isolated from soft-rotted sweetpotato storage roots retrieved from an intentionally flooded field. Both of these anaerobic spore-forming isolates were identified as members of the genus Clostridium based on sequence similarity of multiple housekeeping genes, and both were confirmed to cause soft rot disease on sweetpotato and other vegetable crops. Despite these common features, the isolates were distinguishable by several phenotypic and biochemical properties, and phylogenetic analysis placed them in separate well-supported clades within the genus. Overall, our results demonstrate that multiple plant-pathogenic Clostridium species can cause soft rot disease on sweetpotato and suggest that a variety of other plant hosts may also be susceptible.
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Affiliation(s)
- Washington L da Silva
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06511
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Gregg S Pettis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Natasha R Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Rebecca Giorno
- School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272
| | - Christopher A Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
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Chaudhry V, Patil PB. Evolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches. Genomics 2019; 112:2052-2062. [PMID: 31785311 DOI: 10.1016/j.ygeno.2019.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/16/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022]
Abstract
Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.
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Affiliation(s)
- Vasvi Chaudhry
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India.
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71
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VanMensel D, Chaganti SR, Droppo IG, Weisener CG. Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes. Environ Microbiol 2019; 22:568-583. [PMID: 31736260 DOI: 10.1111/1462-2920.14860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/05/2019] [Accepted: 11/13/2019] [Indexed: 11/28/2022]
Abstract
Pathogenic bacteria associated with freshwater ecosystems can pose significant health risks particularly where recreational water use is popular. Common water quality assessments involve quantifying indicator Escherichia coli within the water column but neglect to consider physical and geochemical factors and contributions from the sediment. In this study, we used high-throughput sequencing to investigate sediment microbial communities at four freshwater public beaches in southern Ontario, Canada and analysed community structure, function, and gene expression with relation to geographical characteristics. Our results indicate that beach sediments at the sediment-water interface could serve as potential sources of bacterial contamination under low-energy environments with tightly packed small sediment particles compared with high-energy environments. Further, the absence of pathogens but expression of pathogenic transcripts suggests occurrence of alternate gene acquisition. Pathogenicity at these locations included expression of Salmonella virulence factors, genes involved in pertussis, and antimicrobial resistance. Finally, we introduce a proposed universal bacterial pathogen model to consider the combined and synergistic processes used by these microbes. To our knowledge, this is the first study of its kind to investigate chemolithotrophic activity related to pathogens within bed sediment at freshwater beaches. This work helps advance current understanding of health risks in these environments.
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Affiliation(s)
- Danielle VanMensel
- Great Lakes Institute for Environmental Research, University of Windsor, Ontario, Canada
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Ontario, Canada.,Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA
| | - Ian G Droppo
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, Ontario, Canada
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72
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Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 T and Zobellia laminariae KMM 3676 T. Mar Drugs 2019; 17:md17120661. [PMID: 31771309 PMCID: PMC6950322 DOI: 10.3390/md17120661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/01/2023] Open
Abstract
We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.
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73
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Smyrli M, Triga A, Dourala N, Varvarigos P, Pavlidis M, Quoc VH, Katharios P. Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea. Microorganisms 2019; 7:microorganisms7110504. [PMID: 31671797 PMCID: PMC6921072 DOI: 10.3390/microorganisms7110504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.
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Affiliation(s)
- Maria Smyrli
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nancy Dourala
- Fish Pathology Department, Selonda Aquaculture, 15125 Athens, Greece.
| | | | - Michael Pavlidis
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
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Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. mSystems 2019; 4:4/5/e00252-19. [PMID: 31641046 PMCID: PMC6811364 DOI: 10.1128/msystems.00252-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.
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75
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Wu H, Gu Q, Xie Y, Lou Z, Xue P, Fang L, Yu C, Jia D, Huang G, Zhu B, Schneider A, Blom J, Lasch P, Borriss R, Gao X. Cold-adapted Bacilli isolated from the Qinghai-Tibetan Plateau are able to promote plant growth in extreme environments. Environ Microbiol 2019; 21:3505-3526. [PMID: 31233661 DOI: 10.1111/1462-2920.14722] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
Abstract
Nearly 1400 Bacillus strains growing in the plant rhizosphere were sampled from different sites on the Qinghai-Tibetan Plateau. Forty-five of the isolates, selected due to their biocontrol activity, were genome-sequenced and their taxonomic identification revealed that they were representatives of the Bacillus subtilis species complex (20) and the Bacillus cereus group (9). Majority of the remaining strains were found closely related to Bacillus pumilus, but their average nucleotide identity based on BLAST and electronic DNA/DNA hybridization values excluded closer taxonomic identification. A total of 45 different gene clusters involved in synthesis of secondary metabolites were detected by mining the genomes of the 45 selected strains. Except eight mesophilic strains, the 37 remaining strains were found either cold-adapted or psychrophilic, able to propagate at 10°C and below (Bacillus wiedmannii NMSL88 and Bacillus sp. RJGP41). Pot experiments performed at 10°C with winter wheat seedlings revealed that cold-adapted representatives of B. pumilus, B. safensis and B. atrophaeus promoted growth of the seedlings under cold conditions, suggesting that these bacilli isolated from a cold environment are promising candidates for developing of bioformulations useful for application in sustainable agriculture under environmental conditions unfavourable for the mesophilic bacteria presently in use.
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Affiliation(s)
- Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Yongli Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Zhiying Lou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Pengqi Xue
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Liu Fang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Chenjie Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Dandan Jia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Guochao Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Bichun Zhu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Rainer Borriss
- Nordreet UG, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
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Tekedar HC, Kumru S, Blom J, Perkins AD, Griffin MJ, Abdelhamed H, Karsi A, Lawrence ML. Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PLoS One 2019; 14:e0221018. [PMID: 31465454 PMCID: PMC6715197 DOI: 10.1371/journal.pone.0221018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Aeromonas veronii is a gram-negative species abundant in aquatic environments that causes disease in humans as well as terrestrial and aquatic animals. In the current study, 41 publicly available A. veronii genomes were compared to investigate distribution of putative virulence genes, global dissemination of pathotypes, and potential mechanisms of virulence. The complete genome of A. veronii strain ML09-123 from an outbreak of motile aeromonas septicemia in farm-raised catfish in the southeastern United States was included. Dissemination of A. veronii strain types was discovered in dispersed geographical locations. Isolate ML09-123 is highly similar to Chinese isolate TH0426, suggesting the two strains have a common origin and may represent a pathotype impacting aquaculture in both countries. Virulence of strain ML09-123 in catfish in a dose-dependent manner was confirmed experimentally. Subsystem category disposition showed the majority of genomes exhibit similar distribution of genomic elements. The type I secretion system (T1SS), type II secretion system (T2SS), type 4 pilus (T4P), and flagellum core elements are conserved in all A. veronii genomes, whereas the type III secretion system (T3SS), type V secretion system (T5SS), type VI secretion system (T6SS), and tight adherence (TAD) system demonstrate variable dispersal. Distribution of mobile elements is dependent on host and geographic origin, suggesting this species has undergone considerable genetic exchange. The data presented here lends insight into the genomic variation of A. veronii and identifies a pathotype impacting aquaculture globally.
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Affiliation(s)
- Hasan C. Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Salih Kumru
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Matt J. Griffin
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, Mississippi State, United States of America
| | - Hossam Abdelhamed
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Mark L. Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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77
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Li FN, Lu Q, Liao SL, Jin T, Li W, Sun CH. Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella. Syst Appl Microbiol 2019; 42:126004. [PMID: 31402073 DOI: 10.1016/j.syapm.2019.126004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 11/17/2022]
Abstract
Two novel strains, designated 11W25H-1T and 8H24J-4-2T, were isolated from surface-sterilized plant tissues collected from the Taklamakan Desert in the Xinjiang Uygur Autonomous Region, China. The strains were characterized by a polyphasic approach in order to clarify their taxonomic positions. They were Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped. The 16S rRNA gene sequences of the strains showed highest similarities with Labedella gwakjiensis KCTC 19176T (99.2% and 98.9%, respectively) and Labedella endophytica CPCC 203961T (98.9% and 99.0%, respectively). The sequence similarity between strains 11W25H-1T and 8H24J-4-2T was 99.4%. Phylogenetic analyses based on 16S rRNA gene sequences and single-copy phylogenetic marker genes (pMGs) showed that the two strains belonged to the genus Labedella and formed a separate cluster from the closest species L. gwakjiensis KCTC 19176T and L. endophytica CPCC 203961T. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly separated the strains from each other and from the other species of the genus Labedella with values below the thresholds for species delineation. The two strains showed chemotaxonomic characteristics and phenotypic properties in agreement with the description of the genus Labedella and also confirmed the differentiation from the closest species. The data demonstrated that strains 11W25H-1T and 8H24J-4-2T represented two novel species of the genus Labedella, for which the names Labedella phragmitis sp. nov. (type strain 11W25H-1T=JCM 33144T=CGMCC 1.16700T) and Labedella populi sp. nov. (type strain 8H24J-4-2T=JCM 33143T=CGMCC 1.16697T) are proposed.
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Affiliation(s)
- Fei-Na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qinpei Lu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shui-Lin Liao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Tao Jin
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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78
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Criscuolo A. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. RESEARCH IDEAS AND OUTCOMES 2019. [DOI: 10.3897/rio.5.e36178] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.
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79
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Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP. Identification and characterization of putative Aeromonas spp. T3SS effectors. PLoS One 2019; 14:e0214035. [PMID: 31163020 PMCID: PMC6548356 DOI: 10.1371/journal.pone.0214035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/21/2019] [Indexed: 11/23/2022] Open
Abstract
The genetic determinants of bacterial pathogenicity are highly variable between species and strains. However, a factor that is commonly associated with virulent Gram-negative bacteria, including many Aeromonas spp., is the type 3 secretion system (T3SS), which is used to inject effector proteins into target eukaryotic cells. In this study, we developed a bioinformatics pipeline to identify T3SS effector proteins, applied this approach to the genomes of 105 Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast. The developed pipeline uses a two-step approach, where candidate Aeromonas gene families are initially selected using Hidden Markov Model (HMM) profile searches against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. This approach identified 21 Aeromonas T3SS likely effector families, of which 8 represent known or characterized effectors, while the remaining 13 have not previously been described in Aeromonas. We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic effect in yeast. The results of this study demonstrate the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera.
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Affiliation(s)
- Luiz Thiberio Rangel
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Jeremiah Marden
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - João Carlos Setubal
- Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America
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80
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Khaleque HN, González C, Kaksonen AH, Boxall NJ, Holmes DS, Watkin ELJ. Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (=DSM 14174 =JCM 32253) and 'Acidihalobacter ferrooxidans' V8 (=DSM 14175 =JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively. Int J Syst Evol Microbiol 2019; 69:1557-1565. [DOI: 10.1099/ijsem.0.003313] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Himel N. Khaleque
- 1School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
- 2CSIRO Land and Water, Floreat, Australia
| | - Carolina González
- 3Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | - David S. Holmes
- 3Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Elizabeth L. J. Watkin
- 1School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
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81
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Hayashi Sant’Anna F, Bach E, Porto RZ, Guella F, Hayashi Sant’Anna E, Passaglia LMP. Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy. Crit Rev Microbiol 2019; 45:182-200. [DOI: 10.1080/1040841x.2019.1569587] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando Hayashi Sant’Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Evelise Bach
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renan Z. Porto
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Felipe Guella
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo Hayashi Sant’Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane M. P. Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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83
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Chen Y, Zhu S, Lin D, Wang X, Yang J, Chen J. Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1974-1979. [PMID: 31046895 DOI: 10.1099/ijsem.0.003410] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated CM5-1T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain CM5-1T belongs to the genus Devosia, with closely related type strains Devosia submarina KMM 9415T (98.6 %), Devosia psychrophilaCr7-05T (98.6 %) and Devosia psychrophilaE84T (98.2 %). Up-to-date bacterial core gene set analysis revealed that strain CM5-1T represents one independent lineage with D. submarina KMM 9415T. The average nucleotide identity values of CM5-1T with D. submarina KMM 9415T and D. psychrophila Cr7-05T are 80.1 and 77.9 %, respectively. In silico DNA-DNA hybridization values between strain CM5-1T and D. submarina KMM 9415T and D. psychrophila Cr7-05T are 23.8 and 21.9 %, respectively. Strain CM5-1T contains diphosphatidylglycerol, phosphatidylglycerol and glycolipid as major polar lipids. The sole isoprenoid quinone is ubiquinone-10, and C18 : 1ω7c and 11-methyl C18 : 1ω7c are the dominant cellular fatty acids. The G+C content of the genomic DNA is 61.4 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain CM5-1T could be differentiated from closely related species. Therefore, we propose strain CM5-1T as a novel species of the genus Devosia, for which the name Devosia naphthalenivorans sp. nov. is suggested. The type strain is CM5-1T (=JCM32509T=CGMCC 1.13553T).
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Affiliation(s)
- Yong Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Danqiu Lin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xing Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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Caswell J, Gans JD, Generous N, Hudson CM, Merkley E, Johnson C, Oehmen C, Omberg K, Purvine E, Taylor K, Ting CL, Wolinsky M, Xie G. Defending Our Public Biological Databases as a Global Critical Infrastructure. Front Bioeng Biotechnol 2019; 7:58. [PMID: 31024904 PMCID: PMC6460893 DOI: 10.3389/fbioe.2019.00058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
Progress in modern biology is being driven, in part, by the large amounts of freely available data in public resources such as the International Nucleotide Sequence Database Collaboration (INSDC), the world's primary database of biological sequence (and related) information. INSDC and similar databases have dramatically increased the pace of fundamental biological discovery and enabled a host of innovative therapeutic, diagnostic, and forensic applications. However, as high-value, openly shared resources with a high degree of assumed trust, these repositories share compelling similarities to the early days of the Internet. Consequently, as public biological databases continue to increase in size and importance, we expect that they will face the same threats as undefended cyberspace. There is a unique opportunity, before a significant breach and loss of trust occurs, to ensure they evolve with quality and security as a design philosophy rather than costly "retrofitted" mitigations. This Perspective surveys some potential quality assurance and security weaknesses in existing open genomic and proteomic repositories, describes methods to mitigate the likelihood of both intentional and unintentional errors, and offers recommendations for risk mitigation based on lessons learned from cybersecurity.
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Affiliation(s)
- Jacob Caswell
- Sandia National Laboratories, Albuquerque, NM, United States
| | - Jason D Gans
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States
| | - Nicholas Generous
- Los Alamos National Laboratory, Global Security Directorate, Los Alamos, NM, United States
| | - Corey M Hudson
- Sandia National Laboratories, Livermore, CA, United States
| | - Eric Merkley
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Curtis Johnson
- Sandia National Laboratories, Albuquerque, NM, United States
| | | | - Kristin Omberg
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Emilie Purvine
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karen Taylor
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Murray Wolinsky
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States
| | - Gary Xie
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States
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85
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Gonçalves Pessoa RB, de Oliveira WF, Marques DSC, Dos Santos Correia MT, de Carvalho EVMM, Coelho LCBB. The genus Aeromonas: A general approach. Microb Pathog 2019; 130:81-94. [PMID: 30849490 DOI: 10.1016/j.micpath.2019.02.036] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
The genus Aeromonas comprises more than thirty Gram-negative bacterial species which mostly act as opportunistic microorganisms. These bacteria are distributed naturally in diverse aquatic ecosystems, where they are easily isolated from animals such as fish and crustaceans. A capacity for adaptation also makes Aeromonas able to colonize terrestrial environments and their inhabitants, so these microorganisms can be identified from different sources, such as soils, plants, fruits, vegetables, birds, reptiles, amphibians, among others. Infectious processes usually develop in immunocompromised humans; in fish and other marine animals this process occurs under conditions of stress. Such events are most often associated with incorrect practices in aquaculture. Aeromonas has element diverse ranges, denominated virulence factors, which promote adhesion, colonization and invasion into host cells. These virulence factors, such as membrane components, enzymes and toxins, for example, are differentially expressed among species, making some strains more virulent than others. Due to their diversity, no single virulence factor was considered determinant in the infectious process generated by these microorganisms. Unlike other genera, Aeromonas species are erroneously differentiated by conventional biochemical tests. Therefore, molecular assays are necessary for this purpose. Nevertheless, new means of identification have been considered in order to generate methods that, like molecular tests, can correctly identify these microorganisms. The main objectives of this review are to explain environmental and structural characteristics of the Aeromonas genus and to discuss virulence mechanisms that these bacteria use to infect aquatic organisms and humans, which are important aspects for aquaculture and public health, respectively. In addition, this review aims to clarify new tests for the precise identification of the species of Aeromonas, contributing to the exact and specific diagnosis of infections by these microorganisms and consequently the treatment.
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Affiliation(s)
- Rafael Bastos Gonçalves Pessoa
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Weslley Felix de Oliveira
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Diego Santa Clara Marques
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Maria Tereza Dos Santos Correia
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Elba Verônica Matoso Maciel de Carvalho
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil
| | - Luana Cassandra Breitenbach Barroso Coelho
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, s/n, Cidade Universitária, CEP: 50670-420, Recife, Pernambuco, Brazil.
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86
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Prabha R, Singh DP. Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders. 3 Biotech 2019; 9:87. [PMID: 30800598 DOI: 10.1007/s13205-019-1635-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Phylogenetic studies based on a definite set of marker genes usually reconstruct evolutionary relationships among the prokaryotic species. Based on specific target sequences, such studies represent variations and allow identification of similarities or dissimilarities in organisms. With the advent of completely sequenced genomes and accumulation of information on whole prokaryotic genomes, phylogenetic reconstructions should be considered more reliable if they are ideally based on entire genomes to resolve phylogenetic interest. We applied phylogenomics approaches taking into account completely sequenced cyanobacterial genomes to reconstruct underlying species that represented major taxonomic classes and belonged to distinctly different habitats (freshwater, marine, soils, and rocks). We did not rely on describing phylogeny of all representative class of cyanobacterial species on the basis of only ribosomal gene, 16S rDNA gene. In contrast, we analyzed combined molecular marker and phylogenomics approaches (genome alignment, gene content and gene order, composition vector and protein domain content) for accurately inferring phylogenetic relationship of species. We have shown that this approach reflects the impact of evolution on the organisms and considers connects with the ecological adaptation in cyanobacteria in different habitats. Analysis revealed that the members from marine habitat occupy different profile than those from freshwater. Impact of GC content and genomic repetitiveness over the diversification of cyanobacterial species and their possible role in adaptation was also reflected. Members occupying similar habitats cover more evolutionary distance together and also evolve various strategies for adaptation and survival either through genomic repetitiveness or preferences for genes of particular functions or modified GC content. Genomes undergo different changes for their adaptation in diverse habitats.
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Affiliation(s)
- Ratna Prabha
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, 275101 India
- 2Department of Biotechnology, Mewar University, Gangrar, Chittorgarh, Rajasthan India
| | - Dhananjaya P Singh
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, 275101 India
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87
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Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine. J Microbiol 2019; 57:381-387. [PMID: 30796749 DOI: 10.1007/s12275-019-8631-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022]
Abstract
A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102T was most closely related to Kandleria vitulina DSM 20405T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053T (91.1%), Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis DSM 5348T (89.6%). The average nucleotide identity values between strain SG0102T and related species, K. vitulina DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G + C content of the strain SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2ω9/12c. The cell wall peptidoglycan of strain SG0102T contained the meso-diaminopimelic acid. The strain SG0102T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102T (= KCTC 15725T = NBRC 113396T).
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88
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Genome Analysis of the Marine Bacterium Labrenzia sp. Strain 011, a Potential Protective Agent of Mollusks. DATA 2019. [DOI: 10.3390/data4010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The marine bacterium Labrenzia sp. strain 011 was isolated from the coastal sediment of Kronsgaard, Germany. The Labrenzia species are suggested to be protective agents of mollusks. Labrenzia sp. strain 011 produces specialized metabolites, which showed activity against a range of microorganisms, thereunder strong inhibitory effects against Pseudoroseovarius crassostreae DSM 16,950 (genus Roseovarius), the causative agent of oyster disease. The genome of Labrenzia sp. strain 011 was sequenced and assembled into 65 contigs, has a size of 5.1 Mbp, and a G+C content of 61.6%. A comparative genome analysis defined Labrenzia sp. strain 011 as a distinct new species within the genus Labrenzia, whereby 44% of the genome was contributed to the Labrenzia core genome. The genomic data provided here is expected to contribute to a deeper understanding of the mollusk-protective role of Labrenzia spp.
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89
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Tekedar HC, Abdelhamed H, Kumru S, Blom J, Karsi A, Lawrence ML. Comparative Genomics of Aeromonas hydrophila Secretion Systems and Mutational Analysis of hcp1 and vgrG1 Genes From T6SS. Front Microbiol 2019; 9:3216. [PMID: 30687246 PMCID: PMC6333679 DOI: 10.3389/fmicb.2018.03216] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022] Open
Abstract
Virulent Aeromonas hydrophila causes severe motile Aeromonas septicemia in warmwater fishes. In recent years, channel catfish farming in the U.S.A. and carp farming in China have been affected by virulent A. hydrophila, and genome comparisons revealed that these virulent A. hydrophila strains belong to the same clonal group. Bacterial secretion systems are often important virulence factors; in the current study, we investigated whether secretion systems contribute to the virulent phenotype of these strains. Thus, we conducted comparative secretion system analysis using 55 A. hydrophila genomes, including virulent A. hydrophila strains from U.S.A. and China. Interestingly, tight adherence (TaD) system is consistently encoded in all the vAh strains. The majority of U.S.A. isolates do not possess a complete type VI secretion system, but three core elements [tssD (hcp), tssH, and tssI (vgrG)] are encoded. On the other hand, Chinese isolates have a complete type VI secretion system operon. None of the virulent A. hydrophila isolates have a type III secretion system. Deletion of two genes encoding type VI secretion system proteins (hcp1 and vgrG1) from virulent A. hydrophila isolate ML09-119 reduced virulence 2.24-fold in catfish fingerlings compared to the parent strain ML09-119. By determining the distribution of genes encoding secretion systems in A. hydrophila strains, our study clarifies which systems may contribute to core A. hydrophila functions and which may contribute to more specialized adaptations such as virulence. Our study also clarifies the role of type VI secretion system in A. hydrophila virulence.
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Affiliation(s)
- Hasan C Tekedar
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Hossam Abdelhamed
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Salih Kumru
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Mark L Lawrence
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
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90
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Goldstein S, Beka L, Graf J, Klassen JL. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. BMC Genomics 2019; 20:23. [PMID: 30626323 PMCID: PMC6325685 DOI: 10.1186/s12864-018-5381-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/16/2018] [Indexed: 11/23/2022] Open
Abstract
Background Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have extreme %GC content remains challenging. Long-read, single-molecule sequencing technologies such as the Oxford Nanopore MinION have the potential to overcome these difficulties, although the best approach for harnessing their potential remains poorly evaluated. Results We sequenced nine bacterial genomes spanning a wide range of GC contents using Illumina MiSeq and Oxford Nanopore MinION sequencing technologies to determine the advantages of each approach, both individually and combined. Assemblies using only MiSeq reads were highly accurate but lacked contiguity, a deficiency that was partially overcome by adding MinION reads to these assemblies. Even more contiguous genome assemblies were generated by using MinION reads for initial assembly, but these assemblies were more error-prone and required further polishing. This was especially pronounced when Illumina libraries were biased, as was the case for our strains with both high and low GC content. Increased genome contiguity dramatically improved the annotation of insertion sequences and secondary metabolite biosynthetic gene clusters, likely because long-reads can disambiguate these highly repetitive but biologically important genomic regions. Conclusions Genome assembly using short-reads is challenged by repetitive sequences and extreme GC contents. Our results indicate that these difficulties can be largely overcome by using single-molecule, long-read sequencing technologies such as the Oxford Nanopore MinION. Using MinION reads for assembly followed by polishing with Illumina reads generated the most contiguous genomes with sufficient accuracy to enable the accurate annotation of important but difficult to sequence genomic features such as insertion sequences and secondary metabolite biosynthetic gene clusters. The combination of Oxford Nanopore and Illumina sequencing can therefore cost-effectively advance studies of microbial evolution and genome-driven drug discovery. Electronic supplementary material The online version of this article (10.1186/s12864-018-5381-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Goldstein
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Lidia Beka
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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91
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Kim JS, Lee KC, Suh MK, Han KI, Eom MK, Lee JH, Park SH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS. Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces. J Microbiol 2018; 57:38-44. [PMID: 30594982 DOI: 10.1007/s12275-019-8550-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
A Gram-stain-positive, obligately anaerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung Yeob Yu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | | | | | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea. .,University of Science and Technology, Daejeon, 34113, Republic of Korea.
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92
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Lin D, Chen Y, Zhu S, Yang J, Chen J. Alteromonas indica sp. nov., isolated from surface seawater from the Indian Ocean. Int J Syst Evol Microbiol 2018; 68:3881-3885. [DOI: 10.1099/ijsem.0.003078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Danqiu Lin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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93
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Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, Poehlein A, Ziemert N, König GM, Schäberle TF. Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Sci Rep 2018; 8:16600. [PMID: 30413766 PMCID: PMC6226438 DOI: 10.1038/s41598-018-34954-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6-11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13-16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.
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Affiliation(s)
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Mohammad Alanjary
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Henrik Harms
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Poehlein
- Department of Genomics and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August-University Göttingen, Göttingen, Germany
| | - Nadine Ziemert
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
| | - Till F Schäberle
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany. .,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany. .,Department of Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.
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94
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Liu Y, Lai Q, Shao Z. Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae. Front Microbiol 2018; 9:2453. [PMID: 30364313 PMCID: PMC6193092 DOI: 10.3389/fmicb.2018.02453] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/25/2018] [Indexed: 12/30/2022] Open
Abstract
Idiomarinaceae is a family of Gram-stain negative, mesophilic euryhalophiles. To provide a robust framework for the evolutionary and taxonomic relationships of bacteria of this family, we compared herein the genomes of 36 type strains and 43 non-type strains using 16S rRNA gene sequences, core genome based 78 single-copy orthologous proteins, digital DNA-DNA hybridization and average nucleotide identity (ANI) estimation. The 79 bacteria of this family were consistently divided into taxon I, taxon II, and taxon III corresponding to the three genera Idiomarina, Pseudidiomarina, and Aliidiomarina, which contained 13 putative new genospecies in addition to 35 well-defined species represented by each type strain. Furthermore, genetic diversity of this family was evident at the genus- and species levels, and exceeded that which is defined currently by the named species. In view of multiple genotypic characteristics clearly distinct from the other two genera, we propose reinstating the genus Pseudidiomarina as a monophyletic taxon. Taken together, this is the first genome-based study of the taxonomy and diversity of bacteria within the family Idiomarinaceae, and will contribute to further insights into microbial evolution and adaptation to saline environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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95
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Comparative Genomics of the First and Complete Genome of " Actinobacillus porcitonsillarum" Supports the Novel Species Hypothesis. Int J Genomics 2018; 2018:5261719. [PMID: 30363939 PMCID: PMC6186353 DOI: 10.1155/2018/5261719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/12/2018] [Indexed: 11/25/2022] Open
Abstract
“Actinobacillus porcitonsillarum” is considered a nonpathogenic member of the Pasteurellaceae family, which phenotypically resembles the pathogen Actinobacillus pleuropneumoniae. Previous studies suggested that “A. porcitonsillarum” may represent a new species closely related to Actinobacillus minor, yet no full genome has been sequenced so far. We implemented the Oxford Nanopore and Illumina sequencing technologies to obtain the highly accurate and complete genome sequence of the “A. porcitonsillarum” strain 9953L55. After validating our de novo assembly strategy by comparing the A. pleuropneumoniae S4074T genome sequence obtained by Oxford Nanopore Technology combined with Illumina reads with a PacBio-sequenced S4074T genome from the NCBI database, we performed comparative analyses of the 9953L55 genome with the A. minor type strain NM305T, A. minor strain 202, and A. pleuropneumoniae S4074T. The 2,263,191 bp circular genome of 9953L55 consisted of 2168 and 2033 predicted genes and proteins, respectively. The lipopolysaccharide cluster resembled the genetic organization of A. pleuropneumoniae serotypes 1, 9, and 11, possibly explaining the positive reactions observed previously in serotyping tests. In contrast to NM305T, we confirmed the presence of a complete apxIICABD operon in 9953L55 and 202 accounting for their hemolytic phenotype and Christie-Atkins-Munch-Petersen (CAMP) reaction positivity. Orthologous gene cluster analysis provided insight into the differential ability of strains of the A. minor/“porcitonsillarum” complex and A. pleuropneumoniae to ferment lactose, raffinose, trehalose, and mannitol. The four strains showed distinct and shared transposable elements, CRISPR/Cas systems, and integrated prophages. Genome comparisons based on average nucleotide identity and in silico DNA-DNA hybridization confirmed the close relationship among strains belonging to the A. minor/“porcitonsillarum” complex compared to other Actinobacillus spp., but also suggested that 9953L55 and 202 belong to the same novel species closely related to A. minor, namely, “A. porcitonsillarum.” Recognition of the taxon as a separate species would improve diagnostics and control strategies of pig pleuropneumonia.
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Torres Manno M, Zuljan F, Alarcón S, Esteban L, Blancato V, Espariz M, Magni C. Genetic and phenotypic features defining industrial relevant Lactococcus lactis, L. cremoris and L. lactis biovar. diacetylactis strains. J Biotechnol 2018; 282:25-31. [DOI: 10.1016/j.jbiotec.2018.06.345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 12/11/2022]
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97
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Talagrand-Reboul E, Latif-Eugenín F, Beaz-Hidalgo R, Colston S, Figueras MJ, Graf J, Jumas-Bilak E, Lamy B. Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads. PLoS One 2018; 13:e0201428. [PMID: 30110345 PMCID: PMC6093642 DOI: 10.1371/journal.pone.0201428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Many virulence factors have been described for opportunistic pathogens within the genus Aeromonas. Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, Strasbourg, France
- * E-mail: (BL); (ETR)
| | - Fadua Latif-Eugenín
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Roxana Beaz-Hidalgo
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Sophie Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Maria-Jose Figueras
- Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département d’Hygiène Hospitalière, CHRU de Montpellier, Montpellier, France
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département de Bactériologie, CHU de Nice, Nice, France
- * E-mail: (BL); (ETR)
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98
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Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J. Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients. mBio 2018; 9:e01328-18. [PMID: 30042201 PMCID: PMC6058295 DOI: 10.1128/mbio.01328-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Fluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiont Aeromonas, a puzzling rise in Cp-resistant (Cpr) Aeromonas infections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonas isolates to exposure of the leech microbiota to very low levels of Cp (0.01 to 0.04 µg/ml), <1/100 of the clinical resistance breakpoint for Aeromonas Using competition experiments and comparative genomics of 37 strains, we determined the mechanisms of resistance in clinical and leech-derived Aeromonas isolates, traced their origin, and determined that the presence of merely 0.01 µg/ml Cp provides a strong competitive advantage for Cpr strains. Deep-sequencing the Cpr-conferring region of gyrA enabled tracing of the mutation-harboring Aeromonas population in archived gut samples, and an increase in the frequency of the Cpr-conferring mutation in 2011 coincides with the initial reports of CprAeromonas infections in patients receiving leech therapy.IMPORTANCE The role of subtherapeutic antimicrobial contamination in selecting for resistant strains has received increasing attention and is an important clinical matter. This study describes the relationship of resistant bacteria from the medicinal leech, Hirudo verbana, with patient infections following leech therapy. While our results highlight the need for alternative antibiotic therapies, the rise of Cpr bacteria demonstrates the importance of restricting the exposure of animals to antibiotics approved for veterinary use. The shift to a more resistant community and the dispersion of Cpr-conferring mechanisms via mobile elements occurred in a natural setting due to the presence of very low levels of fluoroquinolones, revealing the challenges of controlling the spread of antibiotic-resistant bacteria and highlighting the importance of a holistic approach in the management of antibiotic use.
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Affiliation(s)
- Lidia Beka
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Matthew S Fullmer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sophie M Colston
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Michael C Nelson
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Département d'Hygiène Hospitalière, CHRU de Montpellier, Montpellier, France
| | - Paul Walker
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Bradley Ford
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Iain S Whitaker
- Institute of Life Sciences, Swansea University College of Medicine, Swansea, Wales, United Kingdom
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, CHRU de Montpellier, Montpellier, France
- INSERM U1065, C3M, Team 6, Nice, France
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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99
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Puah SM, Khor WC, Kee BP, Tan JAMA, Puthucheary SD, Chua KH. Development of a species-specific PCR-RFLP targeting rpoD gene fragment for discrimination of Aeromonas species. J Med Microbiol 2018; 67:1271-1278. [PMID: 30024365 DOI: 10.1099/jmm.0.000796] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE The taxonomy of Aeromonas keeps expanding and their identification remains problematic due to their phenotypic and genotypic heterogeneity. In this study, we aimed to develop a rapid and reliable polymerase chain reaction-restriction fragment length polymorphism assay targeting the rpoD gene to enable the differentiation of aeromonads into 27 distinct species using microfluidic capillary electrophoresis. METHODOLOGY A pair of degenerate primers (Aero F: 5'-YGARATCGAYATCGCCAARCGB-3' and Aero R: 5'-GRCCDATGCTCATRCGRCGGTT-3') was designed that amplified the rpoD gene of 27 Aeromonas species. Subsequently, in silico analysis enabled the differentiation of 25 species using the single restriction endonuclease AluI, while 2 species, A. sanarelli and A. taiwanensis, required an additional restriction endonuclease, HpyCH4IV. Twelve type strains (A. hydrophila ATCC7966T, A. caviae ATCC15468T, A. veronii ATCC9071T, A. media DSM4881T, A. allosaccharophila DSM11576T, A. dhakensis DSM17689T, A. enteropelogens DSM7312T, A. jandaei DSM7311T, A. rivuli DSM22539T, A. salmonicida ATCC33658T, A. taiwanensis DSM24096T and A. sanarelli DSM24094T) were randomly selected from the 27 Aeromonas species for experimental validation.Results/key findings. The twelve type strains demonstrated distinctive RFLP patterns and supported the in silico digestion. Subsequently, 60 clinical and environmental strains from our collection, comprising nine Aeromonas species, were used for screening examinations, and the results were in agreement. CONCLUSION This method provides an alternative method for laboratory identification, surveillance and epidemiological investigations of clinical and environmental specimens.
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Affiliation(s)
- Suat Moi Puah
- 1Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wei Ching Khor
- 1Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Boon Pin Kee
- 1Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Kek Heng Chua
- 1Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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100
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Navarro A, Martínez-Murcia A. Phylogenetic analyses of the genusAeromonasbased on housekeeping gene sequencing and its influence on systematics. J Appl Microbiol 2018; 125:622-631. [DOI: 10.1111/jam.13887] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/14/2018] [Accepted: 04/11/2018] [Indexed: 11/27/2022]
Affiliation(s)
- A. Navarro
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
| | - A. Martínez-Murcia
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
- Area de Microbiología; EPSO; Universidad Miguel Hernández; Orihuela, Alicante Spain
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