1
|
Darcy JL, Amend AS, Swift SOI, Sommers PS, Lozupone CA. specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. ENVIRONMENTAL MICROBIOME 2022; 17:34. [PMID: 35752802 PMCID: PMC9233361 DOI: 10.1186/s40793-022-00426-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables. RESULTS We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well. CONCLUSIONS specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.
Collapse
Affiliation(s)
- John L. Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
| | - Anthony S. Amend
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, HI USA
| | - Sean O. I. Swift
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
| | - Pacifica S. Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO USA
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
| |
Collapse
|
2
|
Cao P, Xu X, Li C, Han L, Mu W, Xiang W, Zhao J, Wang X. Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya. Int J Syst Evol Microbiol 2021; 71. [PMID: 33616515 DOI: 10.1099/ijsem.0.004708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-AAG5T, was isolated from sandy soil collected from Niuwang island in Sanya, Hainan Province, PR China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-AAG5T belongs to the genus Actinomadura and shared highest sequence similarity with Actinomadura macra NBRC 14102T (98.8 %). Strain NEAU-AAG5T grows at 20-40 °C (optimum, 28 °C), pH 6-10 (optimum, pH 7) and has NaCl tolerance of 0-3 %. The menaquinones were identified as MK-9(H4) (4.2 %), MK-9(H6) (49.2 %) and MK-9(H8) (46.5 %). The major fatty acids were C16 : 0 (31.4 %), 10-methyl C18 : 0 (21.3 %) and C18 : 1 ω9c (15.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain NEAU-AAG5T based on whole genome sequences was 72.8 mol%. Digital DNA-DNA hybridization between strain NEAU-AAG5T and its closest phylogenetic neighbour, A. macra NBRC 14102T, resulted in similarity value of 28.0 % (<70 %). Additionally, the average nucleotide identity was 84.2 % for A. macra NBRC 14102T. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-AAG5T can be characterized to represent a novel species of the genus Actinomadura, for which the name Actinomadura litoris sp. nov. is proposed. The type strain is NEAU-AAG5T (=JCM 33456T=CCTCC AA 2019043T).
Collapse
Affiliation(s)
- Peng Cao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Xi Xu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Chenxu Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Liyuan Han
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Wenhao Mu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, PR China
| |
Collapse
|
3
|
Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat S. Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand. J Antibiot (Tokyo) 2021; 74:51-58. [PMID: 32724099 DOI: 10.1038/s41429-020-0353-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 11/08/2022]
Abstract
A novel actinomycete strain CYP1-5T was isolated from the mountain soil sample collected from Chaiyaphum province, Thailand and its taxonomic position was clarified by using a polyphasic taxonomic approach. The chemotaxonomic properties of strain CYP1-5T were consistent within the genus Actinomadura. Cell-wall peptidoglycan of this strain contained meso-diaminopimelic acid. Galactose, madurose, and ribose were presented as the diagnostic sugars in whole-cell hydrolysates. The major menaquinone was MK-9(H6). Major cellular fatty acids were iso-C16:0 and C16:0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside were observed as predominant phospholipids. Based on the results of phylogenetic analyses of 16S rRNA gene sequence, strain CYP1-5T was constituent with the genus Actinomadura and was closely related to Actinomadura syzygii GKU157T (99.5%) and Actinomadura chibensis IFM 10266T (= JCM 14158T) (98.2%). The draft genome size of strain CYP1-5T was 9.30 Mb with 72.2 mol% of G + C content. Strain CYP1-5T showed ANIb values of 94.9% with A. syzygii GKU157T and 93.2% with A. chibensis JCM 14158T. Phenotypic characteristics, phylogenetic analysis and genome data support that strain CYP1-5T could be discriminated from its closest relatives, representing a novel species of the genus Actinomadura, for which the name Actinomadura decatromicini sp. nov. is proposed. The type strain is CYP1-5T (= JCM 16996T = KCTC 19916T = TISTR 2901T).
Collapse
Affiliation(s)
| | - Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
4
|
Benndorf R, Martin K, Küfner M, de Beer ZW, Vollmers J, Kaster AK, Beemelmanns C. Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis. Int J Syst Evol Microbiol 2020; 70:5255-5262. [PMID: 32845828 PMCID: PMC7660899 DOI: 10.1099/ijsem.0.004403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/03/2020] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of two novel aerobic, Gram-positive actinobacteria, designated strains RB29T and RB68T, were determined using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of RB29T were identified as Actinomadura rayongensis DSM 102126T (99.2 % similarity) and Actinomadura atramentaria DSM 43919T (98.7 %), and for strain RB68T was Actinomadura hibisca DSM 44148T (98.3 %). Digital DNA-DNA hybridization (dDDH) between RB29T and its closest phylogenetic neighbours, A. rayongensis DSM 102126T and A. atramentaria DSM 43919T, resulted in similarity values of 53.2 % (50.6-55.9 %) and 26.4 % (24.1-28.9 %), respectively. Additionally, the average nucleotide identity (ANI) was 93.2 % (94.0 %) for A. rayongensis DSM 102126T and 82.3 % (78.9 %) for A. atramentaria DSM 43919T. dDDH analysis between strain RB68T and A. hibisca DSM 44148T gave a similarity value of 24.5 % (22.2-27.0 %). Both strains, RB29T and RB68T, revealed morphological characteristics and chemotaxonomic features typical for the genus Actinomadura, such as the presence of meso-diaminopimelic acid in the cell wall, galactose and glucose as major sugar components within whole-cell hydrolysates and the absence of mycolic acids. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Predominant menaquinones were MK-9(H6) and MK-9(H8) for RB29T and MK-9(H4) and MK-9(H6) for RB68T. The main fatty acids were identified as 10-methyloctadecanoic acid (10-methyl C18:0), 14-methylpentadecanoic acid (iso-C16:0), hexadecanoic acid (C16:0) and cis-9-octadecanoic acid (C18 : 1 ω9c). Here, we propose two novel species of the genus Actinomadura: Actinomadura rubteroloni sp. nov. with the type strain RB29T (=CCUG 72668T=NRRL B-65537T) and Actinomadura macrotermitis sp. nov. with the type strain RB68T (=CCUG 72669T=NRRL B-65538T).
Collapse
Affiliation(s)
- René Benndorf
- Chemical Biology of Microbe–Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Michelle Küfner
- Chemical Biology of Microbe–Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Z. Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe–Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology e. V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| |
Collapse
|
5
|
Zhuang X, Peng C, Wang Z, Zhao J, Shen Y, Liu C, Xiang W. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677-685. [DOI: 10.1007/s10482-019-01380-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/26/2019] [Indexed: 12/20/2022]
|
6
|
Wieme AD, Gosselé F, Snauwaert C, Cleenwerck I, Vandamme P. Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore. Int J Syst Evol Microbiol 2019; 69:3068-3073. [PMID: 31310199 DOI: 10.1099/ijsem.0.003591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The taxonomic position of 'Actinomadura roseorufa' LMG 30035T, a semduramicin-producing mutant of strain ATCC 53666P, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035T was found to be closely related to the type strains of Actinomadura fibrosa ATCC 49459T (98.88 %) and Actinomadura formosensis JCM 7474T (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035T represents a novel Actinomadura species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named Actinomadura species). Analysis of the cell wall revealed the presence of meso-diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H4) and MK-9(H2). The major fatty acids were C16 : 00, 10-methyl C18 : 0, C18 : 1 ω9c and C18 : 00. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035T from validly named species of the genus Actinomadura, and therefore, we propose to classify this strain formally as the novel species Actinomadura roseirufa sp. nov. with LMG 30035T (=CECT 9808T,=ATCC 53664T) as the type strain.
Collapse
Affiliation(s)
- Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Francis Gosselé
- Phibro Animal Health Corporation, Glenpointe Centre East, Frank W. Burr Blvd, Ste 21, Teaneck, NJ 07666, USA
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| |
Collapse
|
7
|
Cao C, Xu T, Liu J, Cai X, Sun Y, Qin S, Jiang J, Huang Y. Actinomadura deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2018; 68:2930-2935. [DOI: 10.1099/ijsem.0.002922] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chengliang Cao
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- 2Jiangsu Yuanyuan Bioengineering Co. Ltd, Xuzhou, Jiangsu, PR China
| | - Tangyu Xu
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jinjuan Liu
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Xiaorui Cai
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Yong Sun
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Sheng Qin
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jihong Jiang
- 1The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Ying Huang
- 3State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| |
Collapse
|
8
|
Rachniyom H, Matsumoto A, Inahashi Y, Take A, Takahashi Y, Thamchaipenet A. Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn. Int J Syst Evol Microbiol 2018. [PMID: 29543147 DOI: 10.1099/ijsem.0.002714] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete strain, designated GKU 128T, isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose. Mycolic acids were absent. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H0) and MK-9(H4). The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The genomic DNA G+C content was 70.5 mol%. Based on 16S rRNA gene sequence analysis, strain GKU 128T was closely related to the type strains of Actinomadura nitritigenes NBRC 15918T (99.2 % sequence similarity) and Actinomadura fibrosa JCM 9371T (98.7 %). The levels of DNA-DNA relatedness between strain GKU 128T and the closely related type species were less than 19 %. On the basis of phenotypic and genotypic characteristics, strain GKU 128T could be distinguished from its closely related type strains and represents a novel species of the genus Actinomadura, for which the name Actinomadura barringtoniae sp. nov. (=TBRC 7225T=NBRC 113074T) is proposed.
Collapse
Affiliation(s)
- Hathairat Rachniyom
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yuki Inahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Akira Take
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Arinthip Thamchaipenet
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| |
Collapse
|
9
|
Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil. Antonie van Leeuwenhoek 2017; 110:787-794. [PMID: 28251351 DOI: 10.1007/s10482-017-0850-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/23/2017] [Indexed: 10/20/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of an Actinomadura strain isolated from the margin of a saline, alkaline lake in Central Anatolia, Turkey. Strain D310ATT was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Actinomadura such as hooked or irregular spiral spore chains, meso-diaminopimelic acid as the major cell wall diaminopimelic acid, and diphosphatidylglycerol and phosphatidylinositol as major polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D310ATT is closely, albeit loosely, associated with Actinomadura darangshiensis DLS-70T with 97.2% sequence similarity, but was readily separated from the latter using diverse phenotypic properties. Consequently, the isolate is considered to represent a new species of Actinomadura for which the name Actinomadura alkaliterrae sp. nov. is proposed, with the type strain D310ATT (=DSM 101185T = KCTC 39657T).
Collapse
|