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You searched for: Journal name Antonie van Leeuwenhoek Remove constraint Journal name: Antonie van Leeuwenhoek Subject term amino acids Remove constraint Subject term: amino acids
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1. Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov

Author:
Sung-Min Kim; Soon Dong Lee; Young Sang Koh; In Seop Kim
Source:
Antonie van Leeuwenhoek 2022 v.115 no.4 pp. 521-532
ISSN:
0003-6072
Subject:
Nocardiaceae; amino acids; chemotaxonomy; genes; new genus; pH; phylogeny; sequence homology; South Korea
Abstract:
... An actinobacterial strain, designated YC3-6ᵀ, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family Nocardiaceae. Levels of 16S rRNA gene similarity indicated that the close relatives are Rhodococcus cavernicola ...
DOI:
10.1007/s10482-022-01718-8

2. Spongiibacter pelagi sp. nov., a marine gammaproteobacterium isolated from coastal seawater

Author:
Jaewoo Yoon
Source:
Antonie van Leeuwenhoek 2022 v.115 no.4 pp. 487-495
ISSN:
0003-6072
Subject:
amino acids; chemotaxonomy; coastal water; coasts; gamma-Proteobacteria; genes; genomics; nucleic acid hybridization; pH; phenotype; phosphatidylethanolamines; phylogeny; quinones; seawater; South Korea
Abstract:
... A novel gammaproteobacterium, designated as KMU-158ᵀ, was isolated from seawater collected on the coastline of Dadaepo in the Republic of Korea, and characterized using a polyphasic taxonomic approach. Strain KMU-158ᵀ was Gram-staining-negative, pale beige-colored, strictly aerobic, rod-shaped, motile, and chemoorganoheterotrophic. The novel isolate was able to grow at 0–3% NaCl concentrations (w/ ...
DOI:
10.1007/s10482-022-01711-1

3. Expression and function of clpS and clpA in Xanthomonas campestris pv. campestris

Author:
Hsueh-Hsia Lo; Hsiao-Ching Chang; Chao-Tsai Liao; Yi-Min Hsiao
Source:
Antonie van Leeuwenhoek 2022 v.115 no.5 pp. 589-607
ISSN:
0003-6072
Subject:
Brassicaceae; Gram-negative bacteria; Xanthomonas campestris pv. campestris; adenosinetriphosphatase; amino acids; heat stress; heat tolerance; host plants; mutants; protein synthesis; proteinases; site-directed mutagenesis; stress tolerance; temperature; transcription (genetics); virulence
Abstract:
... ATP-dependent proteases (FtsH, Lon, and Clp family proteins) are ubiquitous in bacteria and play essential roles in numerous regulatory cell processes. Xanthomonas campestris pv. campestris is a Gram-negative pathogen that can cause black rot diseases in crucifers. The genome of X. campestris pv. campestris has several clp genes, namely, clpS, clpA, clpX, clpP, clpQ, and clpY. Among these genes, o ...
DOI:
10.1007/s10482-022-01725-9

4. Marinifaba aquimaris gen. nov., sp. nov., a novel chitin‐degrading gammaproteobacterium in the family Alteromonadaceae isolated from seawater of the Mariana Trench

Author:
Xin Sui; Xiao-yan He; Ning-hua Liu; Yan-ru Dang; Qian-qian Cha; Mei-ling Sun; Chun-yang Li; Hui-hui Fu; Xiao-yan Song; Qi-long Qin; Xiu-lan Chen; Yu-zhong Zhang; Hai-nan Su; Xi-ying Zhang
Source:
Antonie van Leeuwenhoek 2021 v.114 no.7 pp. 947-955
ISSN:
0003-6072
Subject:
Alteromonadaceae; agar; amino acids; bacteria; casein; chitin; genes; new genus; nitrates; nitrites; phosphatidylethanolamines; phylogeny; seawater; sequence homology; ubiquinones; Pacific Ocean
Abstract:
... A novel Gram-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative bacterium, designated strain SM1970ᵀ, was isolated from a seawater sample collected from the Mariana Trench. Strain SM1970ᵀ grew at 15-37 ᵒC and with 1–5% (w/v) NaCl. It hydrolyzed colloidal chitin, agar and casein but did not reduce nitrate to nitrite. Phylogenetic analysis based on the 16S rRNA gene sequences reve ...
DOI:
10.1007/s10482-021-01568-w

5. Molecular analysis of genes involved in chitin degradation from the chitinolytic bacterium Bacillus velezensis

Author:
Dinh Minh Tran; To Uyen Huynh; Thi Huyen Nguyen; Tu Oanh Do; Quang-Vinh Nguyen; Anh Dzung Nguyen
Source:
Antonie van Leeuwenhoek 2022 v.115 no.2 pp. 215-231
ISSN:
0003-6072
Subject:
Bacillus velezensis; DNA; Escherichia coli; Salvia hispanica; active sites; amino acids; bacteria; biological control agents; black pepper; chitin; chitinase; eggs; fungi; highlands; plant parasitic nematodes; rhizosphere; sequence analysis; signal peptide; spore germination; Vietnam
Abstract:
... Bacillus velezensis RB.IBE29 is a potent biocontrol agent with high chitinase activity isolated from the rhizosphere of black pepper cultivated in the Central Highlands, Vietnam. Genome sequences revealed that this species possesses some GH18 chitinases and AA10 protein(s); however, these enzymes have not been experimentally characterized. In this work, three genes were identified from the genomic ...
DOI:
10.1007/s10482-021-01697-2

6. Streptomyces blattellae, a novel actinomycete isolated from the in vivo of a Blattella germanica

Author:
Gui-Min Liu; Lin-Lin Yuan; Li-Li Zhang; Hong Zeng
Source:
Antonie van Leeuwenhoek 2022 v.115 no.1 pp. 79-87
ISSN:
0003-6072
Subject:
Blattella germanica; Candida albicans; Streptomyces longwoodensis; amino acids; biofilm; cell walls; desert animals; galactose; glucose; hybridization; mannose; menaquinones; multilocus sequence typing; mycelium; nucleotide sequences; pH; phosphatidylcholines; rhamnose; ribose; sequence homology; spores; xylose; China
Abstract:
... During a screening for novel and useful actinobacteria in desert animal, a new actinomycete was isolated and designated strain TRM63209ᵀ. The strain was isolated from in vivo of a Blattella germanica in Tarim University in Alar City, Xinjiang, north-west China. The strain was found to exhibit an inhibitory effect on biofilm formation by Candida albicans ATCC 18,804. The strain was observed to form ...
DOI:
10.1007/s10482-021-01681-w

7. A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades

Author:
Navneet Saini; Radhey S. Gupta
Source:
Antonie van Leeuwenhoek 2021 v.114 no.7 pp. 957-982
ISSN:
0003-6072
Subject:
Coxiella; Legionella; Rickettsiella; amino acids; ancestry; genome; genomics; monophyly; pathogenesis
Abstract:
... The order Legionellales contains several clinically important microorganisms. Although members of this order are well-studied for their pathogenesis, there is a paucity of reliable characteristics distinguishing members of this order and its constituent genera. Genome sequences are now available for 73 Legionellales species encompassing ≈90% of known members from different genera. With the aim of ...
DOI:
10.1007/s10482-021-01569-9

8. Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae, isolated from a surface seawater sample [Erratum: January 2022, v.115(1), p.167]

Author:
Xiao-Mei Zhang; Dao-Feng Zhang; Yuan-Lan Zhang
Source:
Antonie van Leeuwenhoek 2021 v.114 no.5 pp. 497-506
ISSN:
0003-6072
Subject:
Altererythrobacter; amino acids; chemotaxonomy; coenzyme Q10; genomics; isoprenoids; nucleic acid hybridization; nucleotide sequences; pH; phenotype; phylogeny; seawater; sequence homology
Abstract:
... A Gram-stain-negative, light yellow pigmented, non-motile and aerobic bacterial strain, designated HHU E2-1 ᵀ, was isolated from a surface seawater sample. The 16S rRNA gene sequence analysis indicated that HHU E2-1 ᵀ shared the highest sequence similarity to the type strain Qipengyuania gaetbuli DSM 16225 ᵀ (96.90%), which belongs to the family Erythrobacteraceae. Combined phylogeny of 288 single ...
DOI:
10.1007/s10482-021-01531-9

9. Description of Anaerostipes faecalis sp. nov., a new segmented filamentous bacterium isolated from swine faeces

Author:
Seung-Hyeon Choi; Ji Young Choi; Jam-Eon Park; Ji-Sun Kim; Se Won Kang; Jiyoung Lee; Mi-Kyung Lee; Jung-Sook Lee; Ju Huck Lee; Hyunjung Jung; Tai-Young Hur; Hyeun Bum Kim; Ju-Hoon Lee; Jae-Kyung Kim; Yeongjin Hong; Seung-Hwan Park
Source:
Antonie van Leeuwenhoek 2021 v.114 no.11 pp. 1867-1875
ISSN:
0003-6072
Subject:
Lachnospiraceae; acetates; amino acids; arabinose; bacteria; cell walls; chemotaxonomy; feces; genes; genomics; glucose; hybridization; maltose; mannitol; mannose; metabolism; nucleotide sequences; pH; phenotype; phylogeny; sorbitol; swine; xylose
Abstract:
... A novel, strictly anaerobic, gram-negative, segmented filamentous bacterium strain AGMB03513ᵀ, was isolated from the faeces of a 5-month-old pig. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the family Lachnospiraceae, and the closest strain was Anaerostipes butyraticus. Strain AGMB03513ᵀ formed a lineage within the genus Anaerostipes and was closely ...
DOI:
10.1007/s10482-021-01646-z

10. Echinicola salinicaeni sp. nov., a novel bacterium isolated from saltern mud

Author:
Han Zhao; Chun-Yi Song; Rui Yin; Yan-Jun Yi; Shuai-Ting Yun; Ying-Xiu Li; Yan-Xia Zhou
Source:
Antonie van Leeuwenhoek 2021 v.114 no.11 pp. 1915-1924
ISSN:
0003-6072
Subject:
Echinicola; amino acids; bacteria; biosynthesis; carbon; carotenoids; chemotaxonomy; hybridization; menaquinones; nucleotide sequences; pH; phenotype; phosphatidylethanolamines; phylogeny; sequence analysis; silt; temperature; China
Abstract:
... A novel gram-negative, aerobic, pink, motile, gliding, rod-shaped bacterium, designated P51ᵀ, was isolated from saline silt samples in Yantai, China. It was able to grow at 4–42 °C (optimum 33 °C), pH 4.0–9.0 (optimum 7.0), and in 0–11.0% NaCl (optimum 4.0%, w/v). It grew at 4 °C, which was lower than the minimum temperature for related strains. The genome consisted of 4111 genes with a total leng ...
DOI:
10.1007/s10482-021-01650-3

11. Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites

Author:
Hilal Ay
Source:
Antonie van Leeuwenhoek 2021 v.114 no.2 pp. 195-208
ISSN:
0003-6072
Subject:
Actinomadura fibrosa; amino acids; arid soils; biopharmaceutical industry; biosynthesis; galactose; genomics; glucose; menaquinones; metabolites; nucleic acid hybridization; phenotype; phospholipids; phylogeny; ribose; sequence analysis
Abstract:
... Isolation of novel actinobacteria from unexplored habitats as potential sources of novel drug leads has utmost importance. During the course of screening arid soil samples for novel actinobacteria, strain H3C3ᵀ was isolated from Malatya, Turkey and its taxonomic position was revealed by a genome-based polyphasic approach. Pairwise sequence comparison of the 16S rRNA gene showed that the strain is ...
DOI:
10.1007/s10482-020-01511-5

12. Halalkalirubrum salinum gen. nov., sp. nov., a halophilic archaeon isolated from a saline lake

Author:
Zhenqiang Zuo; Dahe Zhao; Jian Zhou; Jing Han; Hua Xiang
Source:
Antonie van Leeuwenhoek 2021 v.114 no.1 pp. 83-94
ISSN:
0003-6072
Subject:
amino acids; genes; glycolipids; new genus; nucleic acid hybridization; nucleotide sequences; pH; phosphates; phylogeny; salt lakes; sequence homology; sulfates; China
Abstract:
... A novel extremely halophilic archaeon, strain N1521ᵀ, was isolated from a saline lake in Tibet, China. Cells of the strain were pleomorphic and Gram-stain-negative. It produced red pigments. Growth was observed at 4–42 °C (optimum, 37 °C), pH 7.0–10.5 (optimum, 8.0–9.5), NaCl 11%–25% (optimum, 15%) and in the presence of 0–0.1 M MgCl₂ (optimum, 0.05 M) in aerobic conditions. The minimum NaCl conce ...
DOI:
10.1007/s10482-020-01502-6

13. Halobellus ruber sp. nov., a deep red-pigmented extremely halophilic archaeon isolated from a Korean solar saltern

Author:
Chi Young Hwang; Eui-Sang Cho; Deok Jun Yoon; Myung-Ji Seo
Source:
Antonie van Leeuwenhoek 2021 v.114 no.7 pp. 997-1011
ISSN:
0003-6072
Subject:
amino acids; biosynthesis; carotenoids; chemotaxonomy; computer simulation; genomics; multigene family; nucleic acid hybridization; nucleotide sequences; pH; phenotype; phosphates; phylogeny; secondary metabolites; sulfates; South Korea
Abstract:
... A novel halophilic archaeon, strain MBLA0160ᵀ, was isolated from a solar saltern in Sorae, Republic of Korea. The cells are deep-red pigmented, Gram-negative, rod shaped, motile, and lysed in distilled water. The strain MBLA0160ᵀ grew at 25–45 °C (optimum 37 °C), in 15–30% (w/v) NaCl (optimum 20%) and 0.1–1.0 M MgCl₂ (optimum 0.3–0.5 M) at pH 5.0–9.0 (optimum 7.0). Phylogenetic analysis based on t ...
DOI:
10.1007/s10482-021-01571-1

14. Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment

Author:
Eui-Sang Cho; In-Tae Cha; Seong Woon Roh; Myung-Ji Seo
Source:
Antonie van Leeuwenhoek 2021 v.114 no.12 pp. 2065-2082
ISSN:
0003-6072
Subject:
DNA-directed RNA polymerase; Haloferax; amino acids; computer simulation; genes; metabolism; nucleic acid hybridization; pH; phenotype; phosphates; phylogeny; salt tolerance; seawater; sediments; sequence homology; South Korea
Abstract:
... Three novel halophilic archaea were isolated from seawater and sediment near Yeoungheungdo Island, Republic of Korea. The genome size and G + C content of the isolates MBLA0076ᵀ, MBLA0077ᵀ, and MBLA0078ᵀ were 3.56, 3.48, and 3.48 Mb and 61.7, 60.8, and 61.1 mol%, respectively. The three strains shared 98.5–99.5 % sequence similarity of the 16 S rRNA gene, whereas their sequence similarity to the 1 ...
DOI:
10.1007/s10482-021-01661-0

15. Identification and characterization of a new cry-like gene found in a Bacillus cereus strain

Author:
J. Francisco Castillo-Esparza; Javier Luévano-Borroel; Jorge E. Ibarra
Source:
Antonie van Leeuwenhoek 2021 v.114 no.11 pp. 1759-1770
ISSN:
0003-6072
Subject:
Aedes aegypti; Bacillus cereus; Bacillus thuringiensis; Caenorhabditis elegans; Manduca sexta; Phyllophaga; amino acid sequences; amino acids; genes; insecticides; molecular weight; mutants; plasmids; sporulation; toxicity
Abstract:
... Bacillus thuringiensis is the most successful microbial insecticide against different pests in agriculture and vectors of diseases. Its activity is mostly attributed to the Cry proteins expressed during its sporulation phase. However, these proteins are not exclusive to B. thuringiensis. Some cry genes have been found in other Bacillus species, or even in other genera. In this work, cry genes were ...
DOI:
10.1007/s10482-021-01635-2

16. Identification and classification of Croceivirga thetidis sp. nov., a marine Flavobacteriaceae isolated from the hard coral Acropora

Author:
Jaewoo Yoon; Mina Yasumoto-Hirose; Hiroaki Kasai
Source:
Antonie van Leeuwenhoek 2021 v.114 no.9 pp. 1407-1416
ISSN:
0003-6072
Subject:
Acropora; Flavobacterium; Ryukyu Archipelago; amino acids; corals; genome; nucleic acid hybridization; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; quinones; sequence homology
Abstract:
... A taxonomic investigation using a polyphasic method was conducted to identify a novel marine flavobacterium, designated as DJ-13ᵀ, isolated from the hard coral Acropora sp. collected at Okinawa, Japan. Bacterial cells were Gram-stain-negative, yellow-colored, strictly aerobic, rod-shaped, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate grew at NaCl conce ...
DOI:
10.1007/s10482-021-01611-w

17. Metabacillus elymi sp. nov., isolated from the Rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea

Author:
Soo-Yeong Lee; Jin-Soo Son; Ye-Ji Hwang; Jae-Ho Shin; Sa-Youl Ghim
Source:
Antonie van Leeuwenhoek 2021 v.114 no.10 pp. 1709-1719
ISSN:
0003-6072
Subject:
Bacillaceae; Elymus tsukushiensis; amino acids; computer simulation; flagellum; genes; isoprenoids; menaquinones; nucleic acid hybridization; nucleotide sequences; pH; phylogeny; quinones; rhizosphere; salinity; symbiosis; transmission electron microscopy; wind speed; South Korea
Abstract:
... Dokdo islands in Republic of Korea, is not suited to survive plant because strong wind, low organic content and high salinity. Nevertheless, 64 taxa of plants have a symbiotic relationship with microbe. The Metabacillus elymi KUDC1714ᵀ was isolated from the rhizosphere of Elymus tsukushiensis collected from Dokdo Islands. This bacterial strain was Gram-stain positive, non-motile, non-spore forming ...
DOI:
10.1007/s10482-021-01634-3

18. Planococcus soli sp. nov., isolated from antarctic soil

Author:
Siyue Zhang; Weiwei Ping; Yuhua Xin; Di Xin; Jianli Zhang
Source:
Antonie van Leeuwenhoek 2021 v.114 no.7 pp. 1107-1115
ISSN:
0003-6072
Subject:
agar; alcohols; amino acids; chemotaxonomy; genes; genetic databases; menaquinones; nucleic acid hybridization; pH; phenotype; phylogeny; sequence homology; soil; Antarctic region; Antarctica
Abstract:
... A novel bacterial strain, designated C23ᵀ, was isolated from a soil sample obtained from King George Island, Antarctica. Phenotypic, phylogenetic, chemotaxonomic and molecular analyses were performed on the new isolate. Strain C23ᵀ formed orange colonies on agar plates and was Gram-stain-positive. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain C23ᵀ was a member of the ge ...
DOI:
10.1007/s10482-021-01581-z

19. Rouxiella aceris sp. nov., isolated from tree sap and the emended description of the genus Rouxiella [Erratum: November 2021, Vol.114(11), p.1961-1962]

Author:
Soon Dong Lee; Hong Lim Yang; In Seop Kim
Source:
Antonie van Leeuwenhoek 2021 v.114 no.7 pp. 1013-1024
ISSN:
0003-6072
Subject:
Acer pictum; amino acids; genes; genomics; hybridization; isoprenoids; new species; phenotype; phosphatidylethanolamines; phylogeny; quinones; sap; trees; South Korea
Abstract:
... Polyphasic taxonomic studies were performed for the seven strains, which were isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea. Cells of all the isolates were Gram-reaction-negative, facultatively anaerobic, short rods and contained the major isoprenoid quinone of Q-8, the predominant fatty acids of C₁₆:₀ and C₁₇:₀ cyclo and the major polar lipids including phos ...
DOI:
10.1007/s10482-021-01572-0

20. Schumannella soli sp. nov., a novel actinomycete isolated from mangrove soil by in situ cultivation

Author:
Feina Li; Qinpei Lu; Shuilin Liao; Li Tuo; Shaowei Liu; Qin Yang; Adong Shen; Chenghang Sun
Source:
Antonie van Leeuwenhoek 2021 v.114 no.10 pp. 1657-1667
ISSN:
0003-6072
Subject:
amino acids; biosynthesis; conservation areas; genomics; mangrove soils; monophyly; nucleic acid hybridization; nucleotide sequences; osmotolerance; proteome; secondary metabolites; sequence homology; China
Abstract:
... A novel actinobacterial strain, designated 10F1D-1ᵀ, was isolated from soil sample collected from Futian mangrove nature reserve, China using of the in situ cultivation technique. Preliminary analysis based on the 16S rRNA gene sequence revealed that strain 10F1D-1ᵀ was the member of genus Schumannella with sharing highest sequence similarity (99.7%) to Schumannella luteola DSM 23141ᵀ. Phylogeneti ...
DOI:
10.1007/s10482-021-01631-6

21. Streptomyces polyasparticus sp. nov. isolated from cotton field soil by a medium applied with polyaspartic acid

Author:
Wenlong Liu; Hong Zeng; Zhanfeng Xia; Xiaoxia Luo; Lili Zhang; Chuanxing Wan
Source:
Antonie van Leeuwenhoek 2021 v.114 no.6 pp. 777-786
ISSN:
0003-6072
Subject:
Streptomyces; amino acids; arabinose; carbon; cell walls; cotton; culture media; mannose; menaquinones; multilocus sequence typing; mycelium; nucleic acid hybridization; phosphatidylethanolamines; phylogeny; ribose; soil; spores; China
Abstract:
... A novel Streptomyces strain (TRM66268-LWLᵀ) was isolated from cotton field soil by a medium supplied with polyaspartic acid (PASP) at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. The strain was found to degrade PASP, and grow well on the medium to take PASP as the sole carbon source. The TRM66268-LWLᵀ fermentation broth was applied to the surface of ...
DOI:
10.1007/s10482-021-01557-z

22. Thermaurantiacus tibetensis gen. nov., sp. nov., a novel moderately thermophilic bacterium isolated from hot spring microbial mat in Tibet

Author:
Yu-Zhen Ming; Lan Liu; Ai-Ping Lv; Wen-Dong Xian; Ze-Tao Liu; Meng-Meng Li; Jian-Yu Jiao; Bao-Zhu Fang; Wen-Jun Li
Source:
Antonie van Leeuwenhoek 2021 v.114 no.4 pp. 445-455
ISSN:
0003-6072
Subject:
Sandaracinobacter sibiricus; aerobiosis; amino acids; catalase; genes; glycosphingolipids; hot springs; new genus; pH; phosphatidylethanolamines; phylogeny; temperature; thermophilic bacteria; ubiquinones; China
Abstract:
... Two bacterial strains SYSU G02173ᵀ and SYSU G03142 were isolated from hot springs in Tibet, China. Based on the results of nearly full-length 16S rRNA gene sequences and phylogenetic analyses, strains SYSU G02173ᵀ and SYSU G03142 were assigned to the family Sphingosinicellaceae, and were closest to Sandaracinobacter sibiricus RB16-17 ᵀ (96.04% and 96.12% similarity, respectively). Cells of the bot ...
DOI:
10.1007/s10482-021-01530-w

23. Thermohalobaculum xanthum gen. nov., sp. nov., a moderately thermophilic bacterium isolated from mangrove sediment

Author:
Xinli Pan; Zhe Li; Fei Li; Yuanlin Huang; Qiaozhen Wang; Shushi Huang; Wenjin Hu; Mingguo Jiang
Source:
Antonie van Leeuwenhoek 2021 v.114 no.11 pp. 1819-1828
ISSN:
0003-6072
Subject:
amino acids; chemotaxonomy; chromosomes; mangrove sediments; menaquinones; new genus; nucleic acid hybridization; nucleotide sequences; nutrient utilization; pH; phenotype; phylogeny; sequence homology; stress tolerance; thermophilic bacteria; unsaturated fatty acids; China
Abstract:
... A novel moderately thermophilic and halophilic bacterium, designated strain M0105ᵀ, was isolated from mangrove sediment collected in the Beibu Gulf, south China. The isolate is Gram-negative, non-motile and rod-shaped bacterium with smooth colonies of pale-yellow appearance. Growth occurs at 15–46 °C (optimum 37–40 °C) and pH range of 6.0–10.0 (optimum pH 8.0–9.0). It required 1–7% NaCl (optimum 3 ...
DOI:
10.1007/s10482-021-01641-4

24. Bacillus lacisalsi sp. nov., a moderately haloalkaliphilic bacterium isolated from a saline–alkaline lake

Author:
Luna Dong; Shuangyan Wang; Hao Cao; Baisuo Zhao; Xiaoxia Zhang; Kun Wu; Haisheng Wang
Source:
Antonie van Leeuwenhoek 2020 v.113 no.1 pp. 127-136
ISSN:
0003-6072
Subject:
amino acids; bacteria; chemotaxonomy; endospores; genes; genomics; lakes; menaquinones; nucleic acid hybridization; nucleotide sequences; pH; peptidoglycans; phosphatidylethanolamines; phylogeny; quinones; sequence homology; China
Abstract:
... An alkaliphilic and moderately halophilic strain, designated YSP-3ᵀ, characterised by optimal growth at pH 9.0 and at 8.0% (w/v) NaCl, was isolated from Yangshapao Lake, Jilin Province, China. Cells of this strain is Gram-positive, straight rods and form a central or sub-terminal ellipsoidal endospore. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was grouped in the genu ...
DOI:
10.1007/s10482-019-01322-3

25. Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains

Author:
Arnab Sen; Louis S. Tisa; Maher Gtari; Indrani Sarkar
Source:
Antonie van Leeuwenhoek 2019 v.112 no.1 pp. 115-125
ISSN:
0003-6072
Subject:
Frankia; active sites; amino acids; binding capacity; biosynthesis; carbohydrate binding; cell walls; energy; energy costs; enzymes; genes; genomics; host plants; microorganisms; phylogeny; polysaccharides; proteins
Abstract:
... Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. ...
DOI:
10.1007/s10482-018-1173-y

26. Different roles of two groEL homologues in methylotrophic utiliser of dichloromethane Methylorubrum extorquens DM4

Author:
Yulia E. Firsova; Maria L. Torgonskaya
Source:
Antonie van Leeuwenhoek 2020 v.113 no.1 pp. 101-116
ISSN:
0003-6072
Subject:
amino acids; green fluorescent protein; heat stress; loci; methylene chloride; mutants; operon; reporter genes; toxicity
Abstract:
... The genome of methylotrophic bacteria Methylorubrum extorquens DM4 contains two homologous groESL operons encoding the 60-kDa and 10-kDa subunits of GroE heat shock chaperones with highly similar amino acid sequences. To test a possible functional redundancy of corresponding GroEL proteins we attempted to disrupt the groEL1 and groEL2 genes. Despite the large number of recombinants analysed and th ...
DOI:
10.1007/s10482-019-01320-5

27. Genomic taxonomy of the Mediterranei clade of the genus Vibrio (Gammaproteobacteria)

Author:
Adrián González-Castillo; Julissa Enciso-Ibarra; Bruno Gomez-Gil
Source:
Antonie van Leeuwenhoek 2020 v.113 no.6 pp. 851-859
ISSN:
0003-6072
Subject:
amino acids; computer simulation; genes; genomics; multilocus sequence typing; new species; nucleotide sequences; phenotype; seawater; sequence homology
Abstract:
... The first genomic study of Mediterranei clade using five type strains (V. mediterranei, V. maritimus, V. variabilis, V. thalassae, and V. barjaei) and fourteen reference strains isolated from marine organisms, seawater, water and sediments of the sea was performed. These bacterial strains were characterised by means of a polyphasic approach comprising 16S rRNA gene, multilocus sequence analysis (M ...
DOI:
10.1007/s10482-020-01396-4

28. Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine

Author:
Siqi Sun; Feilong Chen; Yao Xu; Jingwen Liu; Shaoxing Chen
Source:
Antonie van Leeuwenhoek 2019 v.112 no.12 pp. 1849-1861
ISSN:
0003-6072
Subject:
amino acids; chemotaxonomy; genome; lipids; new species; nucleic acid hybridization; nucleotide sequences; phenotype; phylogeny; ribosomal DNA; ribosomal RNA; sequence homology; sulfates; China
Abstract:
... A pleomorphic and non-motile halophilic archaeon forming light-red pigmented colonies, strain ZC67ᵀ, was isolated from the Yuanyongjing Salt Mine, Yunnan, China. Based on similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain ZC67ᵀ belongs to the genus Halorubrum and is closely related to the species of Halorubrum (Hrr.) saccharovorum JCM 8865ᵀ, Hrr. persicum C49ᵀ, Hrr. ...
DOI:
10.1007/s10482-019-01313-4

29. Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil

Author:
Pulak Kumar Maiti; Sukhendu Mandal
Source:
Antonie van Leeuwenhoek 2020 v.113 no.10 pp. 1411-1423
ISSN:
0003-6072
Subject:
Saccharothrix albidocapillata; altitude; amino acids; antimicrobial properties; cell walls; chemotaxonomy; hydrolysates; latitude; longitude; mannose; new species; nucleotide sequences; polyketide synthases; ribose; soil; Himalayan region; India
Abstract:
... A novel actinobacterium, strain PSKA42ᵀ was isolated from a soil sample of Kashmir Himalaya, India (latitude: 34°-01′ N; longitude: 74°-47′ E; altitude: 5328 ft). The morphological, biochemical and molecular characteristics predicted that PSKA42ᵀ belongs to the genera Lentzea. Using the Ezbiocloud server it has also been manifested that the 16S rRNA gene sequence of PSKA42 was 98.4% similar with L ...
DOI:
10.1007/s10482-020-01449-8

30. Streptomyces taklimakanensis sp. nov., an actinomycete isolated from the Taklimakan desert

Author:
Lin-Lin Yuan; Li-Li Zhang; Xiao-Xia Luo; Zhan-Feng Xia; Bei-Bei Sun; Hong Zeng
Source:
Antonie van Leeuwenhoek 2020 v.113 no.7 pp. 1023-1031
ISSN:
0003-6072
Subject:
Candida albicans; Staphylococcus epidermidis; Streptomyces; amino acids; biofilm; cell walls; computer simulation; galactose; glucose; mannose; menaquinones; multilocus sequence typing; mycelium; nucleic acid hybridization; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; ribose; sequence homology; spores; xylose; China
Abstract:
... A novel Streptomyces strain, designated TRM43335ᵀ, was isolated from the Taklimakan desert in Alar City, Xinjiang, north-west China. The strain was found to exhibit an inhibitory effect on biofilm formation by Candida albicans and Staphylococcus epidermidis. A polyphasic approach was used to determine its taxonomic status. The strain was observed to form abundant aerial mycelium, occasionally twis ...
DOI:
10.1007/s10482-020-01416-3

31. Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia

Author:
Ang Liu; Yan-Jiao Zhang; Peng Cheng; Ya-Jie Peng; Jochen Blom; Qing-Jie Xue
Source:
Antonie van Leeuwenhoek 2020 v.113 no.7 pp. 919-931
ISSN:
0003-6072
Subject:
Colwellia; DNA; amino acids; genome; guidelines; new genus; nucleic acid hybridization; phylogeny; sequence analysis
Abstract:
... Microbial taxonomy is the foundation of microbiology and rapid advancements in DNA sequencing technologies are providing new approaches to address prevailing questions in this field. The family Colwelliaceae, which currently comprises four genera, is a diverse and globally abundant group of Gamaproteobacteria. Based on 14 publically available genomes of bacteria strains labeled as members of the f ...
DOI:
10.1007/s10482-020-01405-6

32. Calcite formation induced by Ensifer adhaerens, Microbacterium testaceum, Paeniglutamicibacter kerguelensis, Pseudomonas protegens and Rheinheimera texasensis

Author:
Kouta Hatayama; Katsumi Saito
Source:
Antonie van Leeuwenhoek 2019 v.112 no.5 pp. 711-721
ISSN:
0003-6072
Subject:
Ensifer adhaerens; Microbacterium testaceum; Pseudomonas protegens; Rheinheimera; agar; amino acids; ammonification; bacteria; calcite; calcium carbonate; cellulose acetate; crystals; deamination; pH; porosity; sand
Abstract:
... A wide range of bacterial species are able to induce calcium carbonate precipitation. Using our own laboratory-preserved strains, we have newly discovered that Ensifer sp. MY11e, Microbacterium sp. TMd9a1, Paeniglutamicibacter sp. MSa1a, Pseudomonas sp. GTc3, and Rheinheimera sp. ATWe6 can induce the formation of calcite crystals on an agar medium. Type strains of their closely related species (En ...
DOI:
10.1007/s10482-018-1204-8

33. Comparative transcriptomic analysis identified differentially expressed genes and pathways involved in the interaction between Tremella fuciformis and Annulohypoxylon stygium

Author:
Dongmei Liu; Dwi Pujiana; Yuanyuan Wang; Zhaosong Zhang; Liesheng Zheng; Liguo Chen; Aimin Ma
Source:
Antonie van Leeuwenhoek 2019 v.112 no.11 pp. 1675-1689
ISSN:
0003-6072
Subject:
Tremella fuciformis; amino acids; antibiotics; biosynthesis; databases; gene expression regulation; mushrooms; mycelium; pentoses; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; secondary metabolites; sequence analysis; starch; sucrose; transcriptomics; unigenes
Abstract:
... Tremella fuciformis is an edible and medicinal white jelly mushroom. It has a life cycle that interacts with its companion fungus Annulohypoxylon stygium, both in natural conditions and artificial cultivation. RNA sequencing (RNA-Seq) was used to study the interaction between T. fuciformis and A. stygium by constructing 5 libraries, including the individual T. fuciformis mycelium (1), the T. fucif ...
DOI:
10.1007/s10482-019-01294-4

34. Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil

Author:
Maria S. Nóbrega; Bruno S. Silva; Luciana Leomil; Diogo Antonio Tschoeke; Mariana E. Campeão; Gizele D. Garcia; Graciela A. Dias; Verônica V. Vieira; Cristiane C. Thompson; Fabiano L. Thompson
Source:
Antonie van Leeuwenhoek 2018 v.111 no.7 pp. 1131-1138
ISSN:
0003-6072
Subject:
Alteromonas macleodii; DNA; acetates; aerobes; amino acids; bacteria; beta-glucosidase; carboxylic ester hydrolases; enzyme activity; galactose; glycerol; maltose; mannitol; new species; nucleic acid hybridization; phenotype; ribosomal RNA; seawater; sequence analysis; xylose; Brazil
Abstract:
... Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67Eᵀ and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47ᵀ and Alteromonas macleodii ATCC 27126ᵀ. In silico DNA–DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and averag ...
DOI:
10.1007/s10482-018-1016-x

35. Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family Streptosporangiaceae isolated from the Karakum Desert

Author:
Hayrettin Saygin; Hilal Ay; Kiymet Guven; Demet Cetin; Nevzat Sahin
Source:
Antonie van Leeuwenhoek 2019 v.112 no.3 pp. 409-423
ISSN:
0003-6072
Subject:
Corydalis; Nonomuraea; amino acids; chemotaxonomy; fatty acids; galactose; genes; glucose; glycolipids; menaquinones; mycelium; new genus; new species; nucleotide sequences; phosphatidylethanolamines; phylogeny; quinones; ribose; ribosomal DNA; ribosomal RNA; sequence homology; spores; Turkmenistan
Abstract:
... A novel, Gram-positive, spore-forming actinomycete, designated strain 7K107ᵀ, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. Strain 7K107ᵀ forms extensively branched substrate mycelia and aerial mycelia which differentiate into short chains of spores. The novel strain contains meso-diaminopimelic acid as the diagnostic wall amino acid and glucose, galactose, madur ...
DOI:
10.1007/s10482-018-1169-7

36. Ethanol stress responses of Kluyveromyces marxianus CCT 7735 revealed by proteomic and metabolomic analyses

Author:
Mariana Caroline Tocantins Alvim; Camilo Elber Vital; Edvaldo Barros; Nívea Moreira Vieira; Fernando Augusto da Silveira; Thércia Rocha Balbino; Raphael Hermano Santos Diniz; Amanda Fernandes Brito; Denise Mara Soares Bazzolli; Humberto Josué de Oliveira Ramos; Wendel Batista da Silveira
Source:
Antonie van Leeuwenhoek 2019 v.112 no.6 pp. 827-845
ISSN:
0003-6072
Subject:
Kluyveromyces marxianus; Saccharomyces cerevisiae; amino acids; carbon pathways; ergosterol; ethanol; ethanol production; heat tolerance; lactose; metabolites; metabolomics; oxidative stress; proteins; proteomics; stress response; trehalose
Abstract:
... Kluyveromyces marxianus CCT 7735 offers advantages to ethanol production over Saccharomyces cerevisiae, including thermotolerance and the ability to convert lactose to ethanol. However, its growth is impaired at high ethanol concentrations. Herein we report on the protein and intracellular metabolite profiles of K. marxianus at 1 and 4 h under ethanol exposure. The concentration of some amino acid ...
DOI:
10.1007/s10482-018-01214-y

37. Expression and characterisation of a pH and salt tolerant, thermostable and xylose tolerant recombinant GH43 β-xylosidase from Thermobifida halotolerans YIM 90462T for promoting hemicellulose degradation

Author:
Yi-Rui Yin; Wen-Dong Xian; Ming-Xian Han; En-Min Zhou; Lan Liu; Dalal Hussien M. Alkhalifah; Wael N. Hozzein; Min Xiao; Wen-Jun Li
Source:
Antonie van Leeuwenhoek 2019 v.112 no.3 pp. 339-350
ISSN:
0003-6072
Subject:
Escherichia coli; Thermobifida; amino acids; catalytic activity; gene overexpression; genes; hemicellulose; industrial applications; ionic liquids; molecular weight; open reading frames; pH stability; recombinant proteins; salt tolerance; sodium chloride; thermal stability; xylan 1,4-beta-xylosidase; xylose
Abstract:
... A gene encoding a β-xylosidase (designated as Thxyl43A) was cloned from strain Thermobifida halotolerans YIM 90462ᵀ. The open reading frame of this gene encodes 550 amino acid residues. The gene was over-expressed in Escherichia coli and the recombinant protein was purified. The monomeric Thxyl43A protein presented a molecular mass of 61.5 kDa. When p-nitrophenyl-β-d-xylopyranoside was used as the ...
DOI:
10.1007/s10482-018-1161-2

38. Identification of amino acids negatively affecting Fusarium trichothecene biosynthesis

Author:
Takuya Shiobara; Yuichi Nakajima; Kazuyuki Maeda; Manami Akasaka; Yoshiyuki Kitou; Kyoko Kanamaru; Shuichi Ohsato; Tetsuo Kobayashi; Takumi Nishiuchi; Makoto Kimura
Source:
Antonie van Leeuwenhoek 2019 v.112 no.3 pp. 471-478
ISSN:
0003-6072
Subject:
Fusarium graminearum; amino acids; axenic culture; biosynthesis; culture media; fungi; genes; liquids; monitoring; nitrogen; pH; transcription (genetics); transcription factors; transcriptional activation; trichothecenes
Abstract:
... Nitrogen sources in media have a significant impact on the onset of secondary metabolism in fungi. For transcriptional activation of many nitrogen catabolic genes, an AreA transcription factor is indispensable. This also holds true for Fusarium graminearum that produces trichothecenes, an important group of mycotoxin, in axenic culture. Despite the presence of numerous consensus AreA-binding sites ...
DOI:
10.1007/s10482-018-1172-z

39. A novel pigmented and heavy metal biosorptive bacterium, Leucobacter epilobiisoli sp. nov., isolated from rhizosphere soil of Epilobium hirsutum L.

Author:
Shao-Yang Hou; Fang Wang; Meng-Yue Zhang; Juan Cheng; Yi-Xuan Zhang
Source:
Antonie van Leeuwenhoek 2018 v.111 no.10 pp. 1825-1833
ISSN:
0003-6072
Subject:
Epilobium hirsutum; Leucobacter; amino acids; bacteria; bioremediation; cell walls; chemotaxonomy; fatty acids; glycolipids; heavy metals; menaquinones; new species; nucleic acid hybridization; peptidoglycans; phenotype; phospholipids; phylogeny; rhizosphere; ribosomal RNA; sequence homology; soil; China
Abstract:
... A novel yellow pigmented, Gram-positive, aerobic and heavy metal biosorptive bacterium designated SYP-B2667ᵀ was isolated from rhizosphere soil of Epilobium hirsutum L. in Tongren, Guizhou province, China. Based on 16S rRNA gene sequence analyses, it was shown that strain SYP-B2667ᵀ represents a novel species in the genus Leucobacter, with Leucobacter chromiireducens subsp. solipictus JCM 15573ᵀ a ...
DOI:
10.1007/s10482-018-1071-3

40. Increasing dissolved-oxygen disrupts iron homeostasis in production cultures of Escherichia coli

Author:
Antonino Baez; Joseph Shiloach
Source:
Antonie van Leeuwenhoek 2017 v.110 no.1 pp. 115-124
ISSN:
0003-6072
Subject:
Escherichia coli; NAD (coenzyme); RNA; air; amino acids; bioreactors; biosynthesis; culture media; dissolved oxygen; homeostasis; iron; oxygen; pH; superoxide dismutase; transcription (genetics); transcription factors
Abstract:
... The damaging effect of high oxygen concentration on growth of Escherichia coli is well established. Over-oxygenation increases the intracellular concentration of reactive oxygen species (ROS), causing the destruction of the [4Fe–4S] cluster of dehydratases and limiting the biosynthesis of both branched-chain amino acids and nicotinamide adenine dinucleotide. A key enzyme that reduces the damaging ...
DOI:
10.1007/s10482-016-0781-7

41. Streptomyces sediminis sp. nov. isolated from crater lake sediment

Author:
Hilal Ay; Imen Nouioui; Maria del Carmen Montero-Calasanz; Hans-Peter Klenk; Kamil Isik; Demet Cetin; Nevzat Sahin
Source:
Antonie van Leeuwenhoek 2018 v.111 no.4 pp. 493-500
ISSN:
0003-6072
Subject:
Streptomyces; amino acids; cell walls; chemotaxonomy; fatty acids; glucose; glycolipids; hyphae; lakes; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; ribose; ribosomal RNA; sediments; sequence homology; sodium chloride; spores; temperature; Turkey (country)
Abstract:
... A novel actinobacterial strain, MKSP12ᵀ, was isolated from coastal sediment of a crater lake in central Anatolia, Turkey. The taxonomic position of the strain was clarified using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MKSP12ᵀ is closely related to Streptomyces specialis GW 41-1564ᵀ with 97.1% sequence similarity. The strain produces aerial ...
DOI:
10.1007/s10482-017-0970-z

42. Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile

Author:
Alvaro S. Villalobos; Jutta Wiese; Pablo Aguilar; Cristina Dorador; Johannes F. Imhoff
Source:
Antonie van Leeuwenhoek 2018 v.111 no.6 pp. 955-963
ISSN:
0003-6072
Subject:
Subtercola boreus; Subtercola frigoramans; altitude; amino acids; chemotaxonomy; crosslinking; fatty acid composition; glycolipids; lakes; new species; nucleotide sequences; pH; peptidoglycans; phenotype; phospholipids; phylogeny; quinones; ribosomal DNA; ribosomal RNA; sequence homology; sodium chloride; Chile
Abstract:
... A novel actinobacterium, strain DB165ᵀ, was isolated from cold waters of Llullaillaco Volcano Lake (6170 m asl) in Chile. Phylogenetic analysis based on 16S rRNA gene sequences identified strain DB165ᵀ as belonging to the genus Subtercola in the family Microbacteriaceae, sharing 97.4% of sequence similarity with Subtercola frigoramans DSM 13057ᵀ, 96.7% with Subtercola lobariae DSM 103962ᵀ, and 96. ...
DOI:
10.1007/s10482-017-0994-4
PubMed:
29214367
PubMed Central:
PMC5945732

43. Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean

Author:
Zhao Jiang; Chang-Guo Yuan; Min Xiao; Xin-Peng Tian; Inam-Ullah Khan; Chang-Jin Kim; Xiao-Yang Zhi; Wen-Jun Li
Source:
Antonie van Leeuwenhoek 2016 v.109 no.8 pp. 1153-1160
ISSN:
0003-6072
Subject:
DNA; Macrococcus; amino acids; bacteria; cell walls; chemotaxonomy; fatty acids; galactose; glucose; mannose; marine sediments; menaquinones; new genus; new species; nucleotide sequences; pH; phenotype; phylogeny; rhamnose; ribose; ribosomal RNA; sequence homology; sodium chloride; temperature; xylose; Indian Ocean
Abstract:
... A Gram-stain positive, aerobic, non-motile, asporogenous, coccoid shaped bacterium, designated YIM M12140ᵀ, was isolated from a marine sediment sample collected from the Indian Ocean. Phylogenetic analysis showed that strain YIM M12140ᵀ forms a separate clade within the family Staphylococcaceae. Strain YIM M12140ᵀ shares high 16S rRNA gene sequence similarity with Macrococcus brunensis DSM 19358ᵀ ...
DOI:
10.1007/s10482-016-0717-2

44. Enhancement of the direct antimicrobial activity of Lysep3 against Escherichia coli by inserting cationic peptides into its C terminus

Author:
Qiang Ma; Zhimin Guo; Chencheng Gao; Rining Zhu; Shuang Wang; Ling Yu; Wanhai Qin; Xiaojing Xia; Jingmin Gu; Guangmou Yan; Liancheng Lei
Source:
Antonie van Leeuwenhoek 2017 v.110 no.3 pp. 347-355
ISSN:
0003-6072
Subject:
Escherichia coli; Gram-negative bacteria; Gram-positive bacteria; amino acids; anti-infective agents; antibacterial properties; bacterial infections; cell walls; coliphages; genetic engineering; hydrolysis; hydrophobicity; peptidoglycans; polypeptides
Abstract:
... Phage lysins are considered promising antimicrobials against resistant bacterial infections. Some lysins have been reported for the prevention and treatment of Gram-positive bacterial infection. Gram-negative bacterial phage lysins, however, can only destroy the bacterial cell wall from inside because of the obstruction of the bacterial outer membrane that prevents direct hydrolysis of the bacteri ...
DOI:
10.1007/s10482-016-0806-2

45. Lactobacillus kefiri shows inter-strain variations in the amino acid sequence of the S-layer proteins

Author:
Mariano Malamud; Paula Carasi; Sílvia Bronsoms; Sebastián A. Trejo; María de los Angeles Serradell
Source:
Antonie van Leeuwenhoek 2017 v.110 no.4 pp. 515-530
ISSN:
0003-6072
Subject:
Archaea; DNA; Lactobacillus kefiri; amino acids; bacteria; genes; genomics; kefir; phylogeny; probiotics; proteins; proteomics
Abstract:
... The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer p ...
DOI:
10.1007/s10482-016-0820-4

46. Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

Author:
Marike Palmer; Emma T. Steenkamp; Martin P. A. Coetzee; Wai-Yin Chan; Elritha van Zyl; Pieter De Maayer; Teresa A. Coutinho; Jochen Blom; Theo H. M. Smits; Brion Duffy; Stephanus N. Venter
Source:
Antonie van Leeuwenhoek 2017 v.110 no.10 pp. 1287-1309
ISSN:
0003-6072
Subject:
Erwinia; Pantoea; Tatumella; amino acids; bacteria; data collection; genes; lifestyle; multilocus sequence typing; phylogeny; statistical analysis; trees
Abstract:
... Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to reso ...
DOI:
10.1007/s10482-017-0852-4

47. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach

Author:
Luciana R. Appolinario; Diogo A. Tschoeke; Cintia P. J. Rua; Tainá Venas; Mariana E. Campeão; Gilda R. S. Amaral; Luciana Leomil; Louisi de Oliveira; Verônica Viana Vieira; Koko Otsuki; Jean Swings; Fabiano L. Thompson; Cristiane C. Thompson
Source:
Antonie van Leeuwenhoek 2016 v.109 no.3 pp. 431-438
ISSN:
0003-6072
Subject:
DNA; amino acids; beta-N-acetylhexosaminidase; chemotaxonomy; citric acid; esterases; flora; new species; nucleic acid hybridization; nucleotide sequences; phylogeny; ribosomal RNA; sequence analysis; siderophores; uridine; Brazil
Abstract:
... The taxonomic position of strains Ab112ᵀ (CBAS 572ᵀ) and Ab227_MC (CBAS 573) was evaluated by means of genomic taxonomy. These isolates represent the dominant flora cultured from the healthy marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro. Strains CBAS 572ᵀ and CBAS 573 shared >98 % 16S rRNA sequence identity with Endozoicomonas numazuensis and Endozoicomonas montiporae. In silic ...
DOI:
10.1007/s10482-016-0649-x

48. Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov.

Author:
Elena P. Ivanova; Mario López-Pérez; Mila Zabalos; Song Ha Nguyen; Hayden K. Webb; Jason Ryan; Kiril Lagutin; Mikhail Vyssotski; Russell J. Crawford; Francisco Rodriguez-Valera
Source:
Antonie van Leeuwenhoek 2015 v.107 no.1 pp. 119-132
ISSN:
0003-6072
Subject:
Alteromonas macleodii; Gram-negative bacteria; amino acids; chemotaxonomy; ecophysiology; ecotypes; genes; genomics; new species; nucleotide sequences; phylogeny; ribosomal RNA; seawater; sequence analysis; sodium chloride; surface water; Aegean Sea; English Channel; Mediterranean Sea
Abstract:
... Nine non-pigmented, motile, Gram-negative bacteria originally designated as Alteromonas macleodii deep-sea ecotypes, were isolated from seawater samples collected from four separate locations; two deep-sea sites in the Mediterranean Sea and surface water of the Aegean Sea and English Channel. The six strains studied in vitro were found to tolerate up to 20 % NaCl. The DNA–DNA relatedness between t ...
DOI:
10.1007/s10482-014-0309-y
PubMed:
25326795

49. Micromonospora mangrovi sp. nov., isolated from mangrove soil

Author:
Qing-Yi Xie; Jian Ren; Lei Li; Yu Li; Zi-Xin Deng; Kui Hong
Source:
Antonie van Leeuwenhoek 2016 v.109 no.4 pp. 483-491
ISSN:
0003-6072
Subject:
DNA; Micromonospora; amino acids; arabinose; cell walls; fatty acids; galactose; glucose; mangrove soils; mannose; menaquinones; new species; nucleotide sequences; phosphatidylethanolamines; phylogeny; ribosomal RNA; sequence analysis; xylose; China
Abstract:
... A novel actinomycete strain 2803GPT1-18ᵀ was isolated from a composite mangrove soil sample collected from Beihai, Guangxi province, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 2803GPT1-18ᵀ indicated high similarity with ‘Micromonospora harpali’ NEAU-JC6ᵀ (99.2 %), Micromonospora haikouensis 232617ᵀ (99.1 %), Micromonospora wenchangensis 2602GPT1-05ᵀ (99.1 %), Micromonospo ...
DOI:
10.1007/s10482-015-0641-x

50. Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan

Author:
Arshia Amin; Iftikhar Ahmed; Neeli Habib; Saira Abbas; Min Xiao; Wael N. Hozzein; Wen-Jun Li
Source:
Antonie van Leeuwenhoek 2016 v.109 no.8 pp. 1101-1109
ISSN:
0003-6072
Subject:
DNA; Nocardioides jensenii; amino acids; bacteria; catalase; cell walls; chemotaxonomy; fatty acids; glycolipids; hot springs; hydrogen sulfide; menaquinones; new species; nucleotide sequences; pH; peptidoglycans; phosphatidylethanolamines; phylogeny; ribosomal RNA; sequence analysis; sodium chloride; urease; Pakistan
Abstract:
... A Gram-staining positive, non-spore forming, non-pigmented and non-motile bacterium, designated as NCCP-1340ᵀ, was isolated from a hot water spring, Tatta Pani, Pakistan. Cells of strain NCCP-1340ᵀ were observed to be aerobic, rod shaped, catalase and urease positive but H₂S production and oxidase negative. Growth was observed at pH 6.0–8.0 (optimum pH 7.0) and at 20–40 °C (optimum 37 °C). The str ...
DOI:
10.1007/s10482-016-0711-8

51. Ornithinibacillus composti sp. nov., isolated from sludge compost and emended description of the genus Ornithinibacillus

Author:
Qin Lu; Haoran Yuan; Jibing Li; Yong Zhao; Shungui Zhou
Source:
Antonie van Leeuwenhoek 2015 v.107 no.3 pp. 813-819
ISSN:
0003-6072
Subject:
DNA; amino acids; bacteria; chemotaxonomy; composts; fatty acids; new species; nucleotide sequences; pH; peptidoglycans; phospholipids; phylogeny; ribosomal RNA; sequence homology; sludge; sodium chloride
Abstract:
... A Gram-stain positive, aerobic, motile, endospore-forming and rod-shaped bacterium, designated GSS05ᵀ, was isolated from a sludge compost sample and was characterized by means of a polyphasic taxonomic approach. Growth was observed to occur with 0–3 % (w/v) NaCl (optimum 1 %), at pH 5.5–10 (optimum pH 7.5) and at 15–50 °C (optimum 37 °C). According to the results of a phylogenetic analysis, strain ...
DOI:
10.1007/s10482-014-0374-2

52. Photobacterium sanguinicancri sp. nov. isolated from marine animals

Author:
Bruno Gomez-Gil; Ana Roque; Guiomar Rotllant; Jesus L. Romalde; Alejandra Doce; Mieke Eggermont; Tom Defoirdt
Source:
Antonie van Leeuwenhoek 2016 v.109 no.6 pp. 817-825
ISSN:
0003-6072
Subject:
Maja brachydactyla; Mytilus edulis; Photobacterium; amino acids; animals; hemolymph; monophyly; new species; nucleotide sequences; phenotype; ribosomal RNA; Spain
Abstract:
... Six strains were isolated from the hemolymph of the spider crab Maja brachydactyla, captured in Spain, and one from a diseased blue mussel, Mytilus edulis. The 16S rRNA gene sequences showed close similarity to the recently described Photobacterium swingsii (98.1 %) and to a lesser degree to Photobacterium aquimaris (97.8 %). MLSA analyses showed a monophyletic group including P. swingsii that for ...
DOI:
10.1007/s10482-016-0681-x

53. Relationship between honeybee nutrition and their microbial communities

Author:
Miriane Acosta Saraiva; Ana Paula Pegoraro Zemolin; Jeferson Luis Franco; Juliano Tomazzoni Boldo; Valdir Marcos Stefenon; Eric W. Triplett; Flávio Anastácio de Oliveira Camargo; Luiz Fernando Wurdig Roesch
Source:
Antonie van Leeuwenhoek 2015 v.107 no.4 pp. 921-933
ISSN:
0003-6072
Subject:
Neisseriaceae; phylogeny; propolis; genes; pollen; digestive system; Enterobacteriaceae; Flavobacteriaceae; amino acids; Bacillales; Spiroplasmataceae; community structure; microbial communities; lipid metabolism; Lactobacillaceae; bioprocessing; nutrition; Acetobacteraceae; Apoidea; Archaea; biodegradation; Africanized honey bees; bacteria
Abstract:
... The microbiota and the functional genes actively involved in the process of breakdown and utilization of pollen grains in beebread and bee guts are not yet understood. The aim of this work was to assess the diversity and community structure of bacteria and archaea in Africanized honeybee guts and beebread as well as to predict the genes involved in the microbial bioprocessing of pollen using state ...
DOI:
10.1007/s10482-015-0384-8

54. A novel D-amino acid oxidase from a contaminated agricultural soil metagenome and its characterization

Author:
Qian Ou; Yao Liu; Jie Deng; Gao Chen; Ying Yang; Peihong Shen; Bo Wu; Chengjian Jiang
Source:
Antonie van Leeuwenhoek 2015 v.107 no.6 pp. 1615-1623
ISSN:
0003-6072
Subject:
Escherichia coli; agricultural soils; amino acid sequences; amino acids; gene overexpression; genes; genomic libraries; metagenomics; microorganisms; pH; phylogeny; plasmids; recombinant proteins; screening; sequence analysis
Abstract:
... A novel D-amino acid oxidase (DAAO) gene designated as daoE was cloned by the sequence-based screening of a plasmid metagenomic library of uncultured microorganisms from contaminated agricultural soil. The deduced amino acid sequence comparison and phylogenetic analysis indicated that daoE and other putative DAAOs are closely related. The putative DAAO gene was subcloned into a pETBlue-2 vector an ...
DOI:
10.1007/s10482-015-0457-8

55. A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

Author:
Radhey S. Gupta; Sohail Naushad; Chirayu Chokshi; Emma Griffiths; Mobolaji Adeolu
Source:
Antonie van Leeuwenhoek 2015 v.108 no.3 pp. 765-781
ISSN:
0003-6072
Subject:
Chlamydia; Chlamydophila; Parachlamydiaceae; Simkaniaceae; Waddliaceae; amino acids; genetic distance; genetic markers; genome; nucleotide sequences; phylogeny; proteins; ribosomal RNA; sequence analysis
Abstract:
... The phylum Chlamydiae contains nine ecologically and genetically diverse families all placed within a single order. In this work, we have completed a comprehensive comparative analysis of 36 sequenced Chlamydiae genomes in order to identify shared molecular characteristics, namely conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can serve as distinguis ...
DOI:
10.1007/s10482-015-0532-1

56. Characterization of an extracellularly derived α-mannosidase from the liquid exudate of the sclerotia of Sclerotinia sclerotiorum (Lib.) de Bary

Author:
Zhengli Liu; Ran Wei; Wen He; Ying Ruan; Chunlin Liu
Source:
Antonie van Leeuwenhoek 2015 v.108 no.1 pp. 107-115
ISSN:
0003-6072
Subject:
Sclerotinia sclerotiorum; alpha-mannosidase; amino acids; cluster analysis; droplets; glycoproteins; glycosides; hydrolysis; matrix-assisted laser desorption-ionization mass spectrometry; open reading frames; sclerotia; signal peptide
Abstract:
... Class I α-mannosidases play an important role in co- and post-translational N-glycosylation modification of proteins, and also in glycoprotein glycan hydrolysis. Herein, we investigated a protein named Man-41, from liquid exudate droplets secreted on the surface of developing sclerotia by Sclerotinia sclerotiorum. The protein was identified by MALDI-TOF mass spectrometry to be a α-mannosidase. The ...
DOI:
10.1007/s10482-015-0468-5

57. Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated from an oil-contaminated site

Author:
Heeji Hong; So-Jeong Kim; Ui-Gi Min; Yong-Jae Lee; Song-Gun Kim; Man-Young Jung; Yong-Seok Seo; Sung-Keun Rhee
Source:
Antonie van Leeuwenhoek 2015 v.107 no.4 pp. 971-977
ISSN:
0003-6072
Subject:
Clostridiaceae; DNA; amino acids; bacteria; chemotaxonomy; fatty acids; fructose; glucose; iron; mannitol; menaquinones; new species; nucleotide sequences; pH; phosphatidylethanolamines; phylogeny; polluted soils; ribosomal RNA; sequence homology; sodium chloride; sulfur; temperature; South Korea
Abstract:
... In this study, an alkaliphilic and heterotrophic iron-reducing bacterial strain, IRF9ᵀ, was isolated from an oil-contaminated soil in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IRF9ᵀbelongs to the genus Geosporobacter in the family Clostridiaceae and is most closely related to Geosporobacter subterraneus VNs68ᵀ(96.9 % sequence similarity). Cell ...
DOI:
10.1007/s10482-015-0389-3

58. Isolation and characterization of a proteinaceous α-amylase inhibitor AAI-CC5 from Streptomyces sp. CC5, and its gene cloning and expression

Author:
Zhibin Sun; Weihao Lu; Pingping Liu; Hui Wang; Yan Huang; Yuguo Zhao; Yi Kong; Zhongli Cui
Source:
Antonie van Leeuwenhoek 2015 v.107 no.2 pp. 345-356
ISSN:
0003-6072
Subject:
Escherichia coli; Streptomyces; affinity chromatography; alpha-amylase; amino acids; diabetes; heat stability; mammals; molecular cloning; molecular weight; obesity; soil; therapeutics; trypsin
Abstract:
... An α-amylase inhibitor producing Streptomyces sp. strain CC5 was isolated from soil. A proteinaceous α-amylase inhibitor AAI-CC5 was purified from strain CC5. AAI-CC5 specifically inhibited mammalian α-amylases. The molecular weight of the inhibitor was determined to be 8,212 Da by MALDI-TOF Mass Spectrum. The N-terminal 15 amino acid residues of the purified AAI-CC5 were DTGSPAPECVEYFQS, which is ...
DOI:
10.1007/s10482-014-0333-y
PubMed:
25411086

59. Oenococcus alcoholitolerans sp. nov., a lactic acid bacteria isolated from cachaça and ethanol fermentation processes

Author:
Fernanda Badotti; Ana Paula B. Moreira; Luciane A. Chimetto Tonon; Brígida T. Luckwu de Lucena; Fátima de Cássia O. Gomes; Ricardo Kruger; Cristiane C. Thompson; Marcos Antonio de Morais Jr.; Carlos A. Rosa; Fabiano L. Thompson
Source:
Antonie van Leeuwenhoek 2014 v.106 no.6 pp. 1259-1267
ISSN:
0003-6072
Subject:
Oenococcus oeni; amino acids; ethanol fermentation; genome; lactic acid bacteria; new species; nucleotide sequences; phylogeny; ribosomal RNA; sequence homology; sucrose; tanks; trehalose; Brazil
Abstract:
... Four strains of lactic acid bacteria isolated from cachaça and alcohol fermentation vats in Brazil were characterised in order to determine their taxonomic position. Phylogenetic analysis revealed that they belong to the genus Oenococcus and should be distinguished from their closest neighbours. The 16S rRNA gene sequence similarity against the type strains of the other two species of the genus wa ...
DOI:
10.1007/s10482-014-0296-z
PubMed:
25315101

60. Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea

Author:
Teresa Lucena; María A. Ruvira; M. Carmen Macián; María J. Pujalte; David R. Arahal
Source:
Antonie van Leeuwenhoek 2014 v.105 no.4 pp. 671-678
ISSN:
0003-6072
Subject:
DNA; Roseobacter; Roseovarius; acid phosphatase; alkaline phosphatase; amino acids; bacteria; calcium; carbohydrates; carbon; enzyme activity; fatty acids; magnesium; nitrates; nucleotide sequences; phylogeny; ribosomal RNA; seawater; sequence homology; sodium; Mediterranean Sea
Abstract:
... Strain 4SM10ᵀ, an aerobic marine, Gram-negative, heterotrophic and non pigmented bacterium isolated from seawater from Vinaroz in Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence placed the strain within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analyses also showed that strain 4SM10ᵀforms a stable clade with species o ...
DOI:
10.1007/s10482-014-0121-8
PubMed:
24488274

61. Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production

Author:
P. Hemarajata; J. K. Spinler; M. A. Balderas; J. Versalovic
Source:
Antonie van Leeuwenhoek 2014 v.105 no.3 pp. 579-592
ISSN:
0003-6072
Subject:
Lactobacillus reuteri; amino acids; antiporters; bacteria; chloride channels; decarboxylation; digestive system; gene expression regulation; genes; histamine; histidine decarboxylase; humans; immunomodulation; microbial genetics; mutagenesis; necrosis; protons; transposons; tumor necrosis factors
Abstract:
... The gut microbiome may modulate intestinal immunity by luminal conversion of dietary amino acids to biologically active signals. The model probiotic organism Lactobacillus reuteri ATCC PTA 6475 is indigenous to the human microbiome, and converts the amino acid L-histidine to the biogenic amine, histamine. Histamine suppresses tumor necrosis factor (TNF) production by human myeloid cells and is a p ...
DOI:
10.1007/s10482-014-0113-8
PubMed:
24488273
PubMed Central:
PMC4011013

62. Microlunatus cavernae sp. nov., a novel actinobacterium isolated from Alu ancient cave, Yunnan, south-west China

Author:
Juan Cheng; Wei Chen; Bing Huo-Zhang; Salam Nimaichand; En-Min Zhou; Xin-Hua Lu; Hans-Peter Klenk; Wen-Jun Li
Source:
Antonie van Leeuwenhoek 2013 v.104 no.1 pp. 95-101
ISSN:
0003-6072
Subject:
DNA; Microlunatus; amino acids; caves; cell walls; fatty acids; galactose; glucose; hydrolysates; nucleic acid hybridization; nucleotide sequences; ribosomal RNA; sequence analysis; soil sampling; China
Abstract:
... A Gram-positive, coccoid, non-endospore-forming actinobacterium, designated YIM C01117(T), was isolated from a soil sample collected from Alu ancient cave, Yunnan province, south-west China. Based on the 16S rRNA gene sequence analysis, strain YIM C01117(T) was shown to belong to the genus Microlunatus, with highest sequence similarity of 97.4 % to Microlunatus soli DSM 21800(T). The whole genomic ...
DOI:
10.1007/s10482-013-9929-x
PubMed:
23653120

63. Sinomonas notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng

Author:
Meng-Yue Zhang; Jun Xie; Tian-Yuan Zhang; Huan Xu; Juan Cheng; Shan-Hui Li; Wen-Jun Li; Yi-Xuan Zhang
Source:
Antonie van Leeuwenhoek 2014 v.106 no.4 pp. 827-835
ISSN:
0003-6072
Subject:
DNA; Panax notoginseng; amino acids; color; fatty acids; galactose; glucose; glycolipids; hydrogen; mannose; nucleotide sequences; pH; phylogeny; rhamnose; rhizosphere; ribose; ribosomal RNA; sodium chloride; soil
Abstract:
... A Gram-positive, aerobic, non-motile and pale yellow colour actinobacterial strain, designated SYP-B575ᵀ, was isolated from rhizosphere soil of Panax notoginseng. The optimal growth of the strain was found to occur at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis indicated that strain SYP-B575ᵀ clearly belongs to the genus Sinomonas and should be considered as a candidate of novel species ...
DOI:
10.1007/s10482-014-0252-y
PubMed:
25103948

64. Utilization of 15N-labelled yeast hydrolysate in Lactococcus lactis IL1403 culture indicates co-consumption of peptide-bound and free amino acids with simultaneous efflux of free amino acids

Author:
Kaspar Kevvai; Mary-Liis Kütt; Ildar Nisamedtinov; Toomas Paalme
Source:
Antonie van Leeuwenhoek 2014 v.105 no.3 pp. 511-522
ISSN:
0003-6072
Subject:
Lactococcus lactis subsp. lactis; amino acids; biomass; fermentation; free amino acids; hydrolysates; mathematical models; peptides; yeasts
Abstract:
... Lactococcus lactis subsp. lactis IL1403 was grown in medium containing unlabelled free amino acids and¹⁵N-labelled yeast hydrolysate to gain insight into the role of peptides as a source of amino acids under conditions where free amino acids are abundant. A mathematical model was composed to estimate the fluxes of free and peptide-derived amino acids into and out of the intracellular amino acid po ...
DOI:
10.1007/s10482-013-0103-2

65. Isolation and characterization of novel ginsenoside-hydrolyzing glycosidase from Microbacterium esteraromaticum that transforms ginsenoside Rb2 to rare ginsenoside 20(S)-Rg3

Author:
Lin-Hu Quan; Chao Wang; Yan Jin; Ting-Rui Wang; Yeon-Ju Kim; Deok Chun Yang
Source:
Antonie van Leeuwenhoek 2013 v.104 no.1 pp. 129-137
ISSN:
0003-6072
Subject:
Microbacterium esteraromaticum; amino acids; biotransformation; buffers; enzymes; genes; molecular weight; pH; polyacrylamide gel electrophoresis; proteins; sodium phosphate
Abstract:
... Ginsenoside Rb2 was transformed by recombinant glycosidase (Bgp2) into ginsenosides Rd and 20(S)-Rg3. The bgp2 gene consists of 2,430 bp that encode 809 amino acids, and this gene has homology to the glycosyl hydrolase family 2 protein domain. SDS-PAGE was used to determine that the molecular mass of purified Bgp2 was 87 kDa. Using 0.1 mg ml(-1) of enzyme in 20 mM sodium phosphate buffer at 40 °C ...
DOI:
10.1007/s10482-013-9933-1
PubMed:
23670791

66. Physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability

Author:
Will de Barros Pita; Denise Castro Silva; Diogo Ardaillon Simões; Volkmar Passoth; Marcos Antonio de Morais Jr.
Source:
Antonie van Leeuwenhoek 2013 v.104 no.5 pp. 855-868
ISSN:
0003-6072
Subject:
Saccharomyces cerevisiae; amino acids; biosynthesis; carbon; ethanol; ethanol production; fermentation; gene expression; genes; glucose; glutamate dehydrogenase; glutamates; nitrates; nitrogen; nitrogen compounds; nitrogen metabolism; sugarcane
Abstract:
... The assimilation of nitrate, a nitrogenous compound, was previously described as an important factor favoring Dekkera bruxellensis in the competition with Saccharomyces cerevisiae for the industrial sugarcane substrate. In this substrate, nitrogen sources are limited and diverse, and a recent report showed that amino acids enable D. bruxellensis to grow anaerobically. Thus, understanding the regul ...
DOI:
10.1007/s10482-013-9998-x
PubMed:
23959165

67. Salinicoccus halitifaciens sp. nov., a novel bacterium participating in halite formation

Author:
Chintalapati Venkata Ramana; Are Srinivas; Yadav Subhash; Lodha Tushar; Tapas Mukherjee; Pemmaraju Usha Kiran; Chintalapati Sasikala
Source:
Antonie van Leeuwenhoek 2013 v.103 no.4 pp. 885-898
ISSN:
0003-6072
Subject:
DNA; Salinicoccus; amino acids; bacteria; ethanolamine; fatty acids; isoprenoids; lakes; nucleic acid hybridization; nucleotide sequences; pH; ribosomal RNA; India
Abstract:
... Strain JC90ᵀ was isolated from a soda lake in Lonar, India. Strain JC90ᵀ maintains its external pH to 8.5 and participates in halite formation. Based on 16S rRNA gene sequence similarity studies, strain JC90ᵀ was found to belong to the genus Salinicoccus and is most closely related to “Salinicoccus kekensis” K164ᵀ (99.3 %), Salinicoccus alkaliphilus T8ᵀ (98.4 %) and other members of the genus Sali ...
DOI:
10.1007/s10482-012-9870-4
PubMed:
23307136

68. The effect of hexose ratios on metabolite production in Saccharomyces cerevisiae strains obtained from the spontaneous fermentation of mezcal

Author:
Amanda A. Oliva Hernández; Patricia Taillandier; Diana Reséndez Pérez; José A. Narváez Zapata; Claudia Patricia Larralde Corona
Source:
Antonie van Leeuwenhoek 2013 v.103 no.4 pp. 833-843
ISSN:
0003-6072
Subject:
Agave; Saccharomyces cerevisiae; acetic acid; alcoholic fermentation; amino acids; ethanol; fructose; glucose; glycerol; sugar content; transporters; wine industry
Abstract:
... Mezcal from Tamaulipas (México) is produced by spontaneous alcoholic fermentation using Agave spp. musts, which are rich in fructose. In this study eight Saccharomyces cerevisiae isolates obtained at the final stage of fermentation from a traditional mezcal winery were analysed in three semi-synthetic media. Medium M1 had a sugar content of 100 g l⁻¹ and a glucose/fructose (G/F) of 9:1. Medium M2 ...
DOI:
10.1007/s10482-012-9865-1
PubMed:
23271642

69. Molecular and enzymatic characterization of a subfamily I.4 lipase from an edible oil-degrader Bacillus sp. HH-01

Author:
Kamijo, Takashi; Saito, Akihiro; Ema, Sadaharu; Yoh, Inchi; Hayashi, Hiroko; Nagata, Ryo; Nagata, Yoshiho; Ando, Akikazu
Source:
Antonie van Leeuwenhoek 2011 v.99 no.2 pp. 179-187
ISSN:
0003-6072
Subject:
Bacillus subtilis; Escherichia coli; amino acid sequences; amino acids; carboxylic ester hydrolases; cooking fats and oils; genes; hydrolysis; nucleotide sequences; pH; plant fats and oils; ribosomal RNA; sequence analysis; temperature
Abstract:
... An edible-oil degrading bacterial strain HH-01 was isolated from oil plant gummy matter and was classified as a member of the genus Bacillus on the basis of the nucleotide sequence of the 16S rRNA gene. A putative lipase gene and its flanking regions were cloned from the strain based on its similarity to lipase genes from other Bacillus spp. The deduced product was composed of 214 amino acids and ...
DOI:
10.1007/s10482-010-9474-9

70. The unusual cell biology of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis

Author:
Harald Huber; Ulf Küper; Stefanie Daxer; Reinhard Rachel
Source:
Antonie van Leeuwenhoek 2012 v.102 no.2 pp. 203-219
ISSN:
0003-6072
Subject:
Archaea; DNA; H-transporting ATP synthase; acetate-CoA ligase; adenosine triphosphate; amino acids; appendages; biocenosis; carbon dioxide; coculture; electrons; energy conservation; hosts; hydrogen; lipids; plasma membrane; prokaryotic cells; protein synthesis; proteins; ribosomes; sulfur
Abstract:
... The Crenarchaeon Ignicoccus hospitalis is an anaerobic, obligate chemolithoautotrophic hyperthermophile, growing by reduction of elemental sulfur using molecular hydrogen as electron donor. Together with Nanoarchaeum equitans it forms a unique, archaeal biocoenosis, in which I. hospitalis serves as host for N. equitans. Both organisms can be cultivated in a stable coculture which is mandatory for ...
DOI:
10.1007/s10482-012-9748-5
PubMed:
22653377

71. Verminephrobacter aporrectodeae sp. nov. subsp. tuberculatae and subsp. caliginosae, the specific nephridial symbionts of the earthworms Aporrectodea tuberculata and A. caliginosa

Author:
Marie B. Lund; Sarah Schätzle; Andreas Schramm; Kasper U. Kjeldsen
Source:
Antonie van Leeuwenhoek 2012 v.101 no.3 pp. 507-514
ISSN:
0003-6072
Subject:
Aporrectodea caliginosa; Eisenia fetida; amino acids; bacteria; clones; earthworms; fatty acids; genes; glucose; host specificity; nucleic acid hybridization; nucleotide sequences; oxygen; pH; phenotype; ribosomal RNA; sequence analysis; symbionts; temperature
Abstract:
... Clone library-based studies have shown that almost all lumbricid earthworm species harbour host-specific symbiotic bacteria belonging to the novel genus Verminephrobacter in their nephridia (excretory organs). To date the only described representative from this genus is Verminephrobacter eiseniae, the specific symbiont of the earthworm Eisenia fetida. In this study two novel rod-shaped, non-endosp ...
DOI:
10.1007/s10482-011-9659-x
PubMed:
22041977

72. A new β-glucosidase gene from the zygomycete fungus Rhizomucor miehei

Author:
Takó, Miklós; Tóth, Adél; Nagy, László G.; Krisch, Judit; Vágvölgyi, Csaba; Papp, Tamás
Source:
Antonie van Leeuwenhoek 2010 v.97 no.1 pp. 1-10
ISSN:
0003-6072
Subject:
Mucor; proteins; Rhizomucor miehei; plasmids; amino acids; active sites; introns; sequence homology; beta-glucosidase; fungi
Abstract:
... In this study, a β-glucosidase coding gene (bgl) of the zygomycete fungus Rhizomucor miehei has been cloned and characterized. The gene comprises a total of 2,826 bp including the coding sequence of a 717 amino acids length putative protein and 10 introns dispersed in the whole coding region. The putative N-and C-terminal catalytic domains (aa 68 to aa 274 and aa 358-601, respectively) were identi ...
DOI:
10.1007/s10482-009-9382-z

73. Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru

Author:
Finster, Kai W.; Kjeldsen, Kasper U.
Source:
Antonie van Leeuwenhoek 2010 v.97 no.3 pp. 221-229
ISSN:
0003-6072
Subject:
DNA; Desulfovibrio acrylicus; acetates; amino acids; coasts; electrons; fatty acids; glycerol; hydrogen; new subspecies; nucleic acid hybridization; nucleotide sequences; oxygen; pH; phylogeny; ribosomal RNA; sequence analysis; sodium chloride; sulfate-reducing bacteria; sulfates; surface water level; Peru
Abstract:
... Two deltaproteobacterial sulfate reducers, designated strain I.8.1T and I.9.1T, were isolated from the oxygen minimum zone water column off the coast of Peru at 400 and 500 m water depth. The strains were Gram-negative, vibrio-shaped and motile. Both strains were psychrotolerant, grew optimally at 20°C at pH 7.0-8.0 and at 2.5-3.5% NaCl (w/v). The strains grew by utilizing hydrogen/acetate, C₃₋₄ f ...
DOI:
10.1007/s10482-009-9403-y
PubMed:
20012196

74. Microbial engineering of dehydro-amino acids and lanthionines in non-lantibiotic peptides

Author:
Moll, Gert N.; Kuipers, Anneke; Rink, Rick
Source:
Antonie van Leeuwenhoek 2010 v.97 no.4 pp. 319-333
ISSN:
0003-6072
Subject:
acids; amino acids; bacteria; bacteriocins; bioengineering; couplings; enzymes; peptides; signal peptide
Abstract:
... This minireview focusses on the use of bacteria to introduce dehydroresidues and (methyl)lanthionines in (poly)peptides. It mainly describes the broad exploitation of bacteria containing lantibiotic enzymes for the engineering of these residues in a wide variety of peptides in particular in peptides unrelated to lantibiotics. Lantibiotic dehydratases dehydrate serines and threonines present in pep ...
DOI:
10.1007/s10482-010-9418-4
PubMed:
20140513

75. Inactivation and sub-lethal injury of Escherichia coli in a copper water storage vessel: effect of inorganic and organic constituents

Author:
Sharan, Riti; Chhibber, Sanjay; Attri, Savita; Reed, Robert H.
Source:
Antonie van Leeuwenhoek 2010 v.98 no.1 pp. 103-115
ISSN:
0003-6072
Subject:
Escherichia coli; absorption; additives; aerobic conditions; agar; amino acids; anaerobic conditions; bacteria; copper; glucose; humic acids; inorganic ions; lactose; proteins; pyruvic acid; sodium; sodium chloride; starch; water quality; water treatment
Abstract:
... This study provides information on the effects of inorganic and organic constituents on inactivation and sub-lethal injury of Escherichia coli in water stored in a copper vessel. E. coli suspensions were stored for up to 24 h in copper vessels containing one of the following dissolved constituents at 1 g/l: salts of inorganic ions, carbohydrates, proteins and complex natural organic mixtures. Samp ...
DOI:
10.1007/s10482-010-9435-3
PubMed:
20358286

76. Biochemical characterization and sequence analysis of a xylanase produced by an exo-symbiotic bacterium of Gryllotalpa orientalis, Cellulosimicrobium sp. HY-12

Author:
Oh, Hyun-Woo; Heo, Sun-Yeon; Kim, Do Young; Park, Doo-Sang; Bae, Kyung Sook; Park, Ho-Yong
Source:
Antonie van Leeuwenhoek 2008 v.93 no.4 pp. 437-442
ISSN:
0003-6072
Subject:
Cellulosimicrobium; Gryllotalpa; amino acids; bacteria; carboxymethylcellulose; genes; molecular weight; open reading frames; pH; sequence analysis; xylan; xylanases
Abstract:
... An exo-symbiotic bacterium capable of hydrolyzing xylan was isolated from the gut of the mole cricket, Gryllotalpa orientalis, and identified as Cellulosimicrobium sp. HY-12. The xylanase (XylA CspHY₋₁₂) of this organism bound tightly to both DEAE and mono Q resins, and its molecular mass (M r) was about 39.0 kDa. The highest xylanase activity was observed at pH 6.0 and 60°C. The enzyme was greatl ...
DOI:
10.1007/s10482-007-9210-2
PubMed:
18027102

77. Characterization of a novel 3-hydroxybutyrate dehydrogenase from Ralstonia pickettii T1

Author:
Takanashi, Masahiko; Shiraki, Mari; Saito, Terumi
Source:
Antonie van Leeuwenhoek 2009 v.95 no.3 pp. 249-262
ISSN:
0003-6072
Subject:
Ralstonia pickettii; Western blotting; amino acids; carbon; cell culture; citrates; enzymes; genes; knockout mutants; oxidation; oxidative stress; succinic acid; sugars
Abstract:
... We previously reported that the activities of two 3-hydroxybutyrate dehydrogenases (BDH1 and BDH2) were greatly influenced by culture conditions when Ralstonia pickettii T1, a strain growing on extracellular poly-3-hydroxybutyrate (PHB), was grown on different carbon sources such as 3HB and succinate. In this study, knockout mutants of bdh1 or bdh2 were constructed and characterized under differen ...
DOI:
10.1007/s10482-009-9308-9

78. Cloning, characterization and expression of the extracellular lipase gene from Aureobasidium pullulans HN2-3 isolated from sea saltern

Author:
Liu, Zhiqiang; Li, Xiaoyu; Chi, Zhenming; Wang, Lin; Li, Jing; Wang, Xianghong
Source:
Antonie van Leeuwenhoek 2008 v.94 no.2 pp. 245-255
ISSN:
0003-6072
Subject:
Aspergillus fumigatus; Aureobasidium pullulans; Escherichia coli; Neosartorya; Western blotting; amino acids; clones; complementary DNA; consensus sequence; enzyme activity; molecular weight; open reading frames; peanut oil; phylogeny; plasmids; polyacrylamide gel electrophoresis; rapid amplification of cDNA ends; recombinant proteins; signal peptide; structural genes; triacylglycerol lipase
Abstract:
... The extracellular lipase structural gene was isolated from cDNA of Aureobasidium pullulans HN2-3 by using SMARTTM RACE cDNA amplification kit. The gene had an open reading frame of 1245 bp long encoding a lipase. The coding region of the gene was interrupted by only one intron (55 bp). It encodes 414 amino acid residues of a protein with a putative signal peptide of 26 amino acids. The protein seq ...
DOI:
10.1007/s10482-008-9237-z
PubMed:
18340544

79. Identification and characterisation of ssrA in members of the Helicobacter genus

Author:
Dong, Quanjiang; Zhang, Li; Goh, Khean-lee; Forman, David; O'Rourke, Jani; Harris, Andrew; Mitchell, Hazel
Source:
Antonie van Leeuwenhoek 2007 v.92 no.3 pp. 301-307
ISSN:
0003-6072
Subject:
Helicobacter; amino acids; messenger RNA; phylogeny; ribosomes; transfer RNA
Abstract:
... Bacterial ssrA encodes tmRNA that functions both as a tRNA and an mRNA to rescue the stalled ribosome on defective mRNAs. In this study, ssrA was identified in four gastric species of Helicobacters and four enterohepatic species of Helicobacters. The tag peptide of 14 amino acids encoded by ssrA showed a pattern of Val¹Ala¹³ in gastric species, a pattern of Ala¹Val¹³ in enterohepatic species, in c ...
DOI:
10.1007/s10482-007-9152-8
PubMed:
17372848

80. Sequences downstream of the start codon and their relations to G + C content and optimal growth temperature in prokaryotic genomes

Author:
Li, Wencheng; Zou, Huan; Tao, Meifeng
Source:
Antonie van Leeuwenhoek 2007 v.92 no.4 pp. 417-427
ISSN:
0003-6072
Subject:
correlation; messenger RNA; proteins; open reading frames; amino acids; start codon; temperature; bacteria
Abstract:
... The mechanism of translation initiation is responsible for shaping the mRNA sequences downstream of the start codon. However, this region has not been systematically analyzed in prokaryotes. We used sequence logos and statistic methods to analyze the patterns of overrepresented sequences in this region for 125 species of bacteria and 23 species of archaea. The specific positions are compared to th ...
DOI:
10.1007/s10482-007-9170-6
PubMed:
17562217

81. The isoepoxydon dehydrogenase gene of the patulin metabolic pathway differs for Penicillium griseofulvum and Penicillium expansum

Author:
Mary Ann Dombrink-Kurtzman
Source:
Antonie van Leeuwenhoek 2006 v.89 no.1 pp. 1-8
ISSN:
0003-6072
Subject:
DNA; Penicillium expansum; Penicillium griseofulvum; amino acid sequences; amino acids; biochemical pathways; genes; nucleotide sequences; patulin; sequence analysis
Abstract:
... Purified DNA from isolates of Penicillium griseofulvum and P. expansum was used as a template to amplify a 600-bp fragment of the isoepoxydon dehydrogenase (idh) gene of the patulin biosynthetic pathway. Primer pairs designed from the P. griseofulvum gene (GenBank accession AF006680) to amplify specific regions of the idh gene yielded similar-sized bands for all strains. Asymmetrical amplification ...
Handle:
10113/287
DOI:
10.1007/s10482-005-9002-5
PubMed:
16328863

82. The nature of the nitrogen source added to nitrogen depleted vinifications conducted by a Saccharomyces cerevisiae strain in synthetic must affects gene expression and the levels of several volatile compounds

Author:
Jiménez-Martí, Elena; Aranda, Agustín; Mendes-Ferreira, Alexandra; Mendes-Faia, Arlete; del Olmo, Marcel lí
Source:
Antonie van Leeuwenhoek 2007 v.92 no.1 pp. 61-75
ISSN:
0003-6072
Subject:
Saccharomyces cerevisiae; amino acids; ammonia; ammonium salts; fermentation; gene expression; genes; grape juice; microbial contamination; nitrogen; nitrogen metabolism; risk; starvation; stress response; sugars; volatile compounds; wine yeasts; winemaking; wines
Abstract:
... Nitrogen starvation may lead to stuck and sluggish fermentations. These undesirable situations result in wines with high residual sugar, longer vinification times, and risks of microbial contamination. The typical oenological method to prevent these problems is the early addition of ammonium salts to the grape juice, although excessive levels of these compounds may lead to negative consequences fo ...
DOI:
10.1007/s10482-006-9135-1
PubMed:
17252314

83. A newly constructed primer pair for the PCR amplification, cloningand sequencing of the flagellin (flaA) gene from isolatesof urease-negative Campylobacter lari

Author:
Tsuyoshi Sekizuka; Taeko Yokoi; Ohoshi Murayama; B. Cherie Millar; JohnE. Moore; Motoo Matsuda
Source:
Antonie van Leeuwenhoek 2005 v.88 no.2 pp. 113-120
ISSN:
0003-6072
Subject:
Campylobacter coli; Campylobacter jejuni; Campylobacter lari; amino acid sequences; amino acids; flagellin; food animals; genes; humans; molecular weight; mussels; open reading frames; phenotypic variation; polymerase chain reaction; sequence homology; Japan; Northern Ireland
Abstract:
... A newly constructed primer pair (lari-Af/lari-Ar) designed to generate a product of the flagellin (flaA) gene for urease-negative Campylobacter lari produced a PCR amplicon of about 1700 bp for 16 isolates from 7 seagulls, 5 humans, 3 food animals and one mussel in Japan and Northern Ireland. Nucleotide sequencing and alignments of the flaA amplicons from these isolates demonstrated that the deduc ...
DOI:
10.1007/s10482-005-2386-4

84. Oxidative stress and heat-shock responses in Desulfovibrio vulgaris bygenome-wide transcriptomic analysis

Author:
Weiwen Zhang; David E. Culley; Mike Hogan; Luigi Vitiritti; Fred J. Brockman
Source:
Antonie van Leeuwenhoek 2006 v.90 no.1 pp. 41-55
ISSN:
0003-6072
Subject:
Desulfovibrio vulgaris; amino acids; biochemical pathways; biosynthesis; fatty acid metabolism; gene expression regulation; genes; heat stress; oxidative stress; proteins; stress response; sulfate-reducing bacteria; superoxide dismutase; transcriptomics
Abstract:
... Sulfate-reducing bacteria such as Desulfovibrio vulgaris have developed a set of responses that allow them to survive in hostile environments. To obtain further knowledge of the protective mechanisms employed by D.␣vulgaris in response to oxidative stress and heat shock, we performed a genome-wide transcriptomic analysis to determine the cellular responses to both stimuli. The results showed that ...
DOI:
10.1007/s10482-006-9059-9
PubMed:
16680520

85. Purification and characterization of curvaticin L442, a bacteriocin produced by Lactobacillus curvatus L442

Author:
Nia Xiraphi; Marina Georgalaki; Gonzalez Van Driessche; Bart Devreese; Jozef Van Beeumen; Effie Tsakalidou; John Metaxopoulos; Eleftherios H. Drosinos
Source:
Antonie van Leeuwenhoek 2006 v.89 no.1 pp. 19-26
ISSN:
0003-6072
Subject:
sequence analysis; Lactobacillus curvatus; proteolysis; cation exchange; amino acid sequences; triacylglycerol lipase; amino acids; gel chromatography; pH; Listeria monocytogenes; ammonium sulfate; pathogens; sausages
Abstract:
... Lactobacillus curvatus L442, isolated from Greek traditional fermented sausage prepared without the addition of starters, produces a bacteriocin, curvaticin L442, which is active against the pathogen Listeria monocytogenes. The bacteriocin was purified by 50% ammonium sulphate precipitation, cation exchange, reverse phase and gel filtration chromatography. Partial N-terminal sequence analysis usin ...
DOI:
10.1007/s10482-005-9004-3
PubMed:
16244793

86. Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens

Author:
Hirasawa, Kazumichi; Uchimura, Kohsuke; Kashiwa, Masami; Grant, William D.; Ito, Susumu; Kobayashi, Tohru; Horikoshi, Koki
Source:
Antonie van Leeuwenhoek 2006 v.89 no.2 pp. 211-219
ISSN:
0003-6072
Subject:
Bacillus agaradhaerens; enzyme stability; sequence analysis; thermal stability; buffers; molecular weight; surfactants; amino acids; seawater; pH; potassium chloride; sodium chloride; temperature; endo-1,4-beta-glucanase; metal ions; enzyme activity
Abstract:
... An endoglucanase was purified to homogeneity from an alkaline culture broth of a strain isolated from seawater and identified here as Bacillus agaradhaerens JAM-KU023. The molecular mass was around 38-kDa and the N-terminal 19 amino acids of the purified enzyme exhibited 100% sequence identity to Cel5A of B. agaradhaerens DSM8721T. The enzyme activity increased around 4-fold by the addition of 0.2 ...
DOI:
10.1007/s10482-005-9023-0
PubMed:
16710633