1
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Pavlović J, Puškárová A, Planý M, Farkas Z, Rusková M, Kvalová K, Kraková L, Bučková M, Pangallo D. Colored stains: Microbial survey of cellulose-based and lignin rich papers. Int J Biol Macromol 2023; 241:124456. [PMID: 37085082 DOI: 10.1016/j.ijbiomac.2023.124456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
During the centuries diverse types of paper were produced and were characterized by a different ratio of natural macromolecules, mainly lignin and cellulose. Handmade paper has a higher content of cellulose respect to the early machine-made paper, where the lignin is the other important component. Microorganisms are able to colonize and deteriorate both types of papers. They can release on their surfaces pigments and colorants which produced anesthetic stains. The microbiota colonising 17 stains on handmade and machine-made paper surfaces together with that in library and archive environments was analyzed. Combination of microbiological and high-throughput sequencing (HTS) approaches were applied. The culture-dependent methodology comprised: isolation, DNA identification, hydrolytic and paper staining assays. The HTS was performed by MinION platform and for the mycobiome a more suitable bioinformatics analysis pipeline, MetONTIIME based on QIIME2 framework, was applied. The paper model staining assay permitted the direct recognition of colorizing isolates which in combination with sequencing data evidenced a complex microbial community able to stain the two types of paper. Staining abilities were confirmed by frequently isolated and detected fungi and also by new ones such as Roussoella euonymi and Achaetomium. We have also evidenced the staining ability of several bacteria.
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Affiliation(s)
- Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Andrea Puškárová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Matej Planý
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Zuzana Farkas
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Magdaléna Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Katarína Kvalová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Lucia Kraková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Mária Bučková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551 Bratislava, Slovakia; Caravella, s.r.o., Tupolevova 2, 85101 Bratislava, Slovakia.
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2
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Zhao F, Wei Z, Zhou G, Kristiansen K, Wang C. Effects of Different Storage Temperatures on Bacterial Communities and Functional Potential in Pork Meat. Foods 2022; 11:foods11152307. [PMID: 35954075 PMCID: PMC9367820 DOI: 10.3390/foods11152307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/06/2023] Open
Abstract
Storage temperature is considered one of the most important factors that affect the microbial spoilage of fresh meat. Chilling and superchilling are the most popular storage techniques on the market, but during transportation, the temperature may reach 10 °C and may even reach room temperature during local retail storage. In the present study, we stored fresh pork meat at different temperatures, −2 °C, 4 °C, 10 °C, and 25 °C. The composition and functional potential of fresh or spoiled meat resident microbes were analyzed based on 16S rRNA gene amplicon sequencing. The microbial composition exhibited high similarity between pork meat stored at −2 °C and 4 °C, with Pseudomonads and Brochothrix being the dominant taxa. Acinetobacter sp., Myroides sp., and Kurthia sp. were markers for spoiled pork meat stored at 25 °C. Both psychrophilic and mesophilic bacteria were observed to grow under a storage temperature of 10 °C, but the overall composition and functional potential based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were found to be similar to that of meat stored at room temperature. Our results broaden the knowledge of possible microbial changes in pork meat during storage, transportation, or retail.
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Affiliation(s)
- Fan Zhao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Zhenqian Wei
- Key Laboratory of Meat Products Processing, Ministry of Agriculture, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Z.W.); (G.Z.)
| | - Guanghong Zhou
- Key Laboratory of Meat Products Processing, Ministry of Agriculture, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Z.W.); (G.Z.)
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
- BGI-Shenzhen, Shenzhen 518083, China
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 166555, China
- Correspondence: (K.K.); (C.W.)
| | - Chong Wang
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
- Key Laboratory of Meat Products Processing, Ministry of Agriculture, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Z.W.); (G.Z.)
- Correspondence: (K.K.); (C.W.)
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3
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Wu S, Zhong L, Liao S, Li T, Zhou Z, Wang G. Sediminibacterium soli sp. nov., isolated from soil. Arch Microbiol 2020; 203:967-973. [PMID: 33104819 DOI: 10.1007/s00203-020-02089-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/25/2022]
Abstract
A Gram-stain-negative, facultative anaerobic strain, designated WSJ-3T, was isolated from soil. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WSJ-3T belongs to genus Sediminibacterium and exhibits the highest sequence similarities to Sediminibacterium roseum SYL130T (97.0%), Sediminibacterium goheungense DSM 28323T (96.9%), Sediminibacterium aquarii AA5T (96.7%), and Sediminibacterium salmoneum NBRC 103935T (95.2%). The average nucleotide identity values of strain WSJ-3T/S. roseum SYL130T and strain WSJ-3T/S. goheungense DSM 28323T are 72.2% and 70.4%, respectively, and digital DNA-DNA hybridization values for these are 19.2% and 19.1%, respectively. Strain WSJ-3T has a genome size of 3.88 Mb, with a DNA G + C content of 50.1 mol% and comprises of 3263 predicted genes. A phylogenetic tree constructed using the genomic core protein coding sequences revealed that strain WSJ-3T clusters with S. roseum SYL130T. Strain WSJ-3T has menaquinone-7 as the only respiratory quinone and phosphatidylethanolamine, three unidentified phospholipids, four unidentified aminophospholipids, two unidentified aminolipids, and three unidentified lipids as the polar lipids. The major fatty acids of strain WSJ-3T are iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. On the basis of the polyphasic results, the isolate represents a novel species of the genus Sediminibacterium, for which the name Sediminibacterium soli sp. nov. is proposed. The type strain is WSJ-3T (= KCTC 72839T = CCTCC AB 2019408T).
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Affiliation(s)
- Shijuan Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Limin Zhong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Shuijiao Liao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Tengfei Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Zijie Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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4
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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5
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Duan S, Zhou X, Xiao H, Miao J, Zhao L. Characterization of Bacterial Microbiota in Tilapia Fillets Under Different Storage Temperatures. J Food Sci 2019; 84:1487-1493. [PMID: 31066925 DOI: 10.1111/1750-3841.14630] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
This paper investigates the bacterial microbiota in tilapia fillets under cold (4 °C), iced (0 °C), and superchilled (-3 °C) storage conditions. At 4 °C, at least seven species/strains of Pseudomonas were detected in the fillets, five of which were dominant either at a certain stage or throughout the entire storage period. Shewanella was less dominant than Pseudomonas at 4 °C, while Serratia became dominant after 6 days storage at 4 °C. The microbiota in fillets stored at 0 and -3 °C were very similar and rarely changed during storage, yet differed greatly from the microbiota at 4 °C. Only two Pseudomonas species/strains grew at 0 and -3 °C, one of which was the most dominant. A Vibrionimonas sp. not found at 4 °C was found to be the second most dominant species at 0 and -3 °C. Shewanella and Psychrobacter were also present at 0 and -3 °C but were the minor genera. The most dominant strains at -3, 0, and 4 °C were separately isolated and subjected to full length 16S rDNA sequencing, which demonstrated that they were identical and were Pseudomonas fluorescens. The changes of the total bacterial count and TVBN value of the fillets inoculated with the isolated P. fluorescens were very similar to those of fillets with natural microbiota. This implies that P. fluorescens is the most important spoiler of tilapia fillets at -3, 0, or 4 °C. PRACTICAL APPLICATION: This research shows that fewer species of bacteria survive at 0 and -3 °C than those at 4 °C, while among these bacteria, the most important spoiler is P. fluorescens. This may provide some clues to extend the shelf life of tilapia fillets by taking some inhibitory measures targeted at P. fluorescens in the future.
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Affiliation(s)
- Shan Duan
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
| | - Xingzhi Zhou
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,CapitalBio Genomics Co., Ltd. Building 11, Dongguan-Taiwan Bio-Tech Collaboration Incubation Center, Dongguan, 523808, China
| | - Hang Xiao
- Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
| | - Jianyin Miao
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China
| | - Lei Zhao
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
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6
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Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium. Microbiol Resour Announc 2019; 8:8/14/e01701-18. [PMID: 30948472 PMCID: PMC6449563 DOI: 10.1128/mra.01701-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.
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7
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Albert RA, McGuine M, Pavlons SC, Roecker J, Bruess J, Mossman S, Sun S, King M, Hong S, Farrance CE, Danner J, Joung Y, Shapiro N, Whitman WB, Busse HJ. Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2019; 69:1376-1383. [PMID: 30882299 DOI: 10.1099/ijsem.0.003319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367T, Bosea lathyri LMG 26379T, Bosea lupini LMG 26383T, Bosea eneae CCUG 43111T, Bosea vestrisii CCUG 43114T and Boseamassiliensis CCUG 43117T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131T and Bosea vaviloviae Vaf-18T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5-35 °C, pH values of pH 5.5-8.0, a salt tolerance range of 0.0-1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131T (NRRL B-65405=LMG 30034).
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Affiliation(s)
- Richard A Albert
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA.,2Water Quality Center, Marquette University, Civil and Environmental Engineering, P.O. Box 1881 Milwaukee, WI, USA
| | - Molly McGuine
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C Pavlons
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jon Roecker
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jennifer Bruess
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shane Mossman
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Sona Sun
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Mike King
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Sunhee Hong
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | | | - Joseph Danner
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | - Yochan Joung
- 5Department of Biological Sciences, College of Natural Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Nicole Shapiro
- 6DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - William B Whitman
- 7Microbiology Department, Univeristy of Georgia, Athens, GA 30602, USA
| | - Hans-Jürgen Busse
- 8Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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8
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Choi J, Cha S, Chhetri G, Yang D, Seo T. Edaphocola aurantiacus gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from wetland soil in South Korea. Antonie van Leeuwenhoek 2018; 112:687-694. [PMID: 30474773 DOI: 10.1007/s10482-018-1199-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/10/2018] [Indexed: 11/28/2022]
Abstract
A short rod-shaped, yellow-orange pigmented, strictly aerobic bacterium, designated as strain H2T, was isolated from the wetland soil of Halla Mountain, Jeju-island, South Korea. Growth was observed at temperatures of 10-30 °C (optimum at 25-30 °C), pH of 6-8 (optimum at pH 7), and salt concentrations of 0-1% (w/v) NaCl (optimum at 0%). The strain H2T was found to be a catalase and oxidase-positive, non-motile, Gram-negative bacterium. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, strain H2T was found to be related to the members of the Chitinophagaceae family, being closely related to Taibaiella chishuiensis AY17T (94.3% sequence similarity). The major polar lipids are phosphatidylethanolamine and glycolipid. Strain H2T contained MK-7 as the only menaquinone as well as iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major fatty acids (> 15%). The DNA G+C content of strain H2T was determined to be 48.3 mol%. Based on the phylogenetic, phenotypic characteristics and chemotaxonomic analysis data, strain H2T (= KCTC 62115T = JCM 32353T) should be classified as representative of a novel species of a novel genus within the family Chitinophagaceae, for which the name Edaphocola aurantiacus gen. nov., sp. nov., is proposed.
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Affiliation(s)
- Jiwon Choi
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Seho Cha
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Dahye Yang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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9
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Zhang L, Chen XL, Hu Q, Chen K, Yan X, Li SP, Freilich S, Jiang JD. Haoranjiania flava gen. nov., sp. nov., a new member of the family Chitinophagaceae, isolated from activated sludge. Int J Syst Evol Microbiol 2016; 66:4686-4691. [DOI: 10.1099/ijsem.0.001411] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiao-Long Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shun-Peng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shiri Freilich
- Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, PO Box 1021, Ramat Yishay 30095, Israel
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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10
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Kim Y, Kim B, Kang K, Ahn TY. Sediminibacterium aquarii sp. nov., isolated from sediment in a fishbowl. Int J Syst Evol Microbiol 2016; 66:4501-4505. [DOI: 10.1099/ijsem.0.001380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yonghoon Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Bobae Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
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11
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Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rosselló-Mora R, Busse HJ. Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas. Int J Syst Evol Microbiol 2016; 66:4027-4032. [DOI: 10.1099/ijsem.0.001305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Richard A. Albert
- Water Quality Center, Marquette University, Civil & Environmental Engineering, P.O. Box 1881, Milwaukee, WI, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nancy E. Waas
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C. Pavlons
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jamie L. Pearson
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jon Roecker
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nikklas Tewalt
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Natalie Cleeve
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Ramon Rosselló-Mora
- Grup de Microbiologia Marina, Institut Mediterrani d'Estudis Avançats, E-07190 Esporles, Mallorca, Spain
| | - Hans-Jürgen Busse
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Hungary
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12
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Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016; 66:4039-4045. [DOI: 10.1099/ijsem.0.001307] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Siddiqi Muhammad Shafi
- Chemical Research Department, Green Planet Co. Ltd, Okayama ken, tsushima nishizaka2 chome 5-41-203, Okayama, Japan
| | - Kang Duk Choi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
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Siddiqi MZ, Im WT. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449-3455. [DOI: 10.1099/ijsem.0.001216] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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14
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Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost. Int J Syst Evol Microbiol 2016; 66:3681-3687. [PMID: 27335062 DOI: 10.1099/ijsem.0.001252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated strain BS27T, was isolated from mushroom compost and subjected to a taxonomic study using a polyphasic approach. Colonies of BS27T were milky-white, circular with regular fringes and opaque. Cells were short rods, 0.3-0.5 µm wide and 1.2-2.0 µm long. Phylogenetic study based on the 16S rRNA gene sequence placed BS27T in a distinct lineage in the family Chitinophagaceae, sharing 90.1-90.9 % sequence similarity with members of the closely related genera Chitinophaga, Flavitalea, Flavihumibacter, Lacibacter and Flavisolibacter. The novel isolate showed the highest sequence similarities with the members of the genus Chitinophaga. BS27T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1I and/or anteiso-C17 : 1B (summed feature 4) as major fatty acids. The DNA G+C content was 53.0 mol%. The major polar lipids of BS27T were phosphatidylethanolamine (PE) and five unidentified polar lipids (L1, L2, L5, L6 and L7). The results of physiological and biochemical tests allowed phenotypic differentiation of BS27T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate BS27T represents a novel genus and species in the family Chitinophagaceae for which the name Compostibacter hankyongensisgen. nov., sp. nov. is proposed. The type strain is BS27T (=KACC 18745T=JCM 17664T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | | | - Kang Duk Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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15
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Lv YY, Wang J, Chen MH, You J, Qiu LH. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:1785-1791. [DOI: 10.1099/ijsem.0.000940] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ying-Ying Lv
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PRChina
| | - Jia Wang
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PRChina
| | - Mei-Hong Chen
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PRChina
| | - Jia You
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PRChina
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PRChina
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Kang H, Kim H, Joung Y, Joh K. Parasediminibacterium paludis gen. nov., sp. nov., isolated from wetland. Int J Syst Evol Microbiol 2016; 66:326-331. [DOI: 10.1099/ijsem.0.000719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 449-791, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 449-791, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 449-791, Republic of Korea
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