Journal of Microbiology

Journal Articles

Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces: Yuyuan Huang , Lingzhi Dong , Jian Gong , Jing Yang , Shan Lu , Xin-He Lai , Dong Jin , Qianni Huang , Ji Pu , Liyun Liu , Jianguo Xu; J. Microbiol. 2022;60(10):977-985. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2134-8

507 View
1 Download
4 Web of Science
5 Crossref

Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20􍿁54􍿂N, 106°49􍿁20􍿂E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09􍿁10􍿂N, 102°04􍿁39􍿂E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5– 1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170T contained MK-8(H2), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170T. Anteiso-C15:0 and anteiso-C17:0 were the major fatty acids (> 10%) of strains HY170T and HY001, with anteiso-C17:1A predominant in strain HY170T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170T = CGMCC 1.18600T = JCM 34230T).

Citations

Citations to this article as recorded by

Comparative metagenomics of wild and cultivated Fragaria chiloensis reveals major rhizosphere microbiome shifts linked to stress adaptation
Carlos Farkas, Matías Guerra, Adan Andreu Heredia, Jean Franco Castro
Current Research in Microbial Sciences.2025; 9: 100460. CrossRef
Antagonistic Behavior of Streptomyces chartreuse against Pathogenic Bacteria in Ricinus communis L.
Bhoomi N. Patel, Priti Patel, Gayatri Patel
Biosciences Biotechnology Research Asia.2024; 21(1): 185. CrossRef
Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan
Sadia Manzoor, Saira Abbas, Sobia Zulfiqar, Hong-Chuan Wang, Min Xiao, Wen-Jun Li, Muhammad Arshad, Iftikhar Ahmed
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing β-cryptoxanthin Isolated from the Tongtian River Sediments
Yuyuan Huang, Yifan Jiao, Sihui Zhang, Yuanmeihui Tao, Suping Zhang, Dong Jin, Ji Pu, Liyun Liu, Jing Yang, Shan Lu
Journal of Microbiology.2023; 61(4): 379. CrossRef
Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)
Yuyuan Huang, Suping Zhang, Yuanmeihui Tao, Jing Yang, Shan Lu, Dong Jin, Ji Pu, Wenbo Luo, Han Zheng, Liyun Liu, Jia-fu Jiang, Jianguo Xu
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Comparative analysis of type 2 diabetes-associated gut microbiota between Han and Mongolian people: Shu-chun Li , Yao Xiao , Ri-tu Wu , Dan Xie , Huan-hu Zhao , Gang-yi Shen , En-qi Wu; J. Microbiol. 2021;59(7):693-701. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0454-8

504 View
1 Download
21 Web of Science
18 Crossref

Abstract PDF

Due to the different rates of diabetes in different ethnic groups and the structural differences in intestinal microbiota, this study evaluated the changes in diabetes-related intestinal microbiota in two ethnic groups. Fifty-six stool samples were collected from subjects from the Han and Mongolian ethnic groups in China, including participants without diabetes (non-diabetic, ND) and with type 2 diabetes (T2D). The 16S rDNA gene V3 + V4 area was extracted from microbiota, amplified by PCR, and used to perform high-throughput sequencing and screen differential microbiota associated with ethnicity. The results showed that there were 44 T2D-related bacterial markers in the Han subjects, of which Flavonifractor, Alistipes, Prevotella, Oscillibacter, Clostridium XlVa, and Lachnospiracea_incertae_sedis were most closely related to diabetes. There were 20 T2D-related bacterial markers in the Mongolian subjects, of which Fastidiosipila and Barnesiella were most closely related to diabetes. The common markers of T2D bacteria in the two ethnic groups were Papillibacter and Bifidobacterium. There were 17 metabolic pathways with significant differences between the ND and T2D groups in the Han group, and 29 metabolic pathways in the Mongolian group. The glutamatergic metabolic pathway was the only common metabolic pathway in two ethnic groups. The composition and function of diabetes-related bacteria were significantly different among the different ethnic groups, which suggested that the influence of ethnic differences should be fully considered when studying the association between diabetes and bacteria. In addition, the common bacterial markers found in diabetic patients of different ethnic groups in this study can be used as potential targets to study the pathogenesis and treatment of diabetes.

Citations

Citations to this article as recorded by

Impact of Ketogenic and Mediterranean Diets on Gut Microbiota Profile and Clinical Outcomes in Drug-Naïve Patients with Diabesity: A 12-Month Pilot Study
Vanessa Palmas, Andrea Deledda, Vitor Heidrich, Giuseppina Sanna, Giulia Cambarau, Michele Fosci, Lorenzo Puglia, Enrico Antonio Cappai, Alessio Lai, Andrea Loviselli, Aldo Manzin, Fernanda Velluzzi
Metabolites.2025; 15(1): 22. CrossRef
Gut microbiome links obesity to type 2 diabetes: insights from Mendelian randomization
Li Fu, Ancha Baranova, Hongbao Cao, Fuquan Zhang
BMC Microbiology.2025;[Epub] CrossRef
Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism
Runliang Zhai, Chunlin Zhao, Liming Chang, Jiongyu Liu, Tian Zhao, Jianping Jiang, Wei Zhu
Frontiers in Microbiology.2025;[Epub] CrossRef
The relationship between gut microbiome and human diseases: mechanisms, predisposing factors and potential intervention
Mohammad Shabani, Ali Ghoshehy, Amir Mohammad Mottaghi, Zahra Chegini, Azam Kerami, Aref Shariati, Majid Taati Moghadam
Frontiers in Cellular and Infection Microbiology.2025;[Epub] CrossRef
Pentachlorophenol increases diabetes risk by damaging β-cell secretion and disrupting gut microbial-related amino acids and fatty acids biosynthesis
Muke Han, Jie Yin, Xinyi Wang, Runhui Yang, Zhong Dong, Junyu Ning, Yajun Xu, Bing Shao
Journal of Hazardous Materials.2024; 480: 136103. CrossRef
Improvement of glucose metabolism disorder by wheat dietary fibre depended on the intake mode and regulated through TLRs/NF-κB/TNF pathway in db/db mice
Xinguo Liu, Shaojie Pang, Aoxiang Li, Yong Wang, Wei Fang, Wentao Qi
Food and Agricultural Immunology.2024;[Epub] CrossRef
Chemical modifications of xylan from sugarcane bagasse and their regulatory effects on gut microbiota in mice
Guozhu Zhang, Yuan Guan, Xin Zhang, Jing Li, Haishan Chen, Li Zhou, Jun Liang, Xia Li
Journal of Carbohydrate Chemistry.2024; 43(3): 90. CrossRef
Tangshen Formula alleviates inflammatory injury against aged diabetic kidney disease through modulating gut microbiota composition and related amino acid metabolism
Dan-Qian Chen, Hao-Jun Zhang, Wen Zhang, Kai Feng, Hui Liu, Hai-Ling Zhao, Ping Li
Experimental Gerontology.2024; 188: 112393. CrossRef
Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China
Yanchao Liu, Mingxiao Wang, Wuyuntana Li, Yumin Gao, Hailing Li, Ning Cao, Wenli Hao, Lingyan Zhao
BMC Microbiology.2023;[Epub] CrossRef
Bi-Directional Interactions between Glucose-Lowering Medications and Gut Microbiome in Patients with Type 2 Diabetes Mellitus: A Systematic Review
Ruolin Li, Fereshteh Shokri, Alejandro Rincon, Fernando Rivadeneira, Carolina Medina-Gomez, Fariba Ahmadizar
Genes.2023; 14(8): 1572. CrossRef
Microbe-Disease Association Prediction Using RGCN Through Microbe-Drug-Disease Network
Yueyue Wang, Xiujuan Lei, Yi Pan
IEEE/ACM Transactions on Computational Biology and Bioinformatics.2023; 20(6): 3353. CrossRef
Longitudinal Characterization of the Gut Microbiota in the Diabetic ZDSD Rat Model and Therapeutic Potential of Oligofructose
Savanna N. Weninger, Angela Ding, Elizabeth N. Browne, Morgan L. Frost, Gabriele Schiro, Daniel Laubitz, Frank A. Duca
Metabolites.2023; 13(5): 660. CrossRef
Effect of Benaglutide on Gut Microbiota and Fecal Metabolites in Patients with Type 2 Diabetes Mellitus
Chen-Yu Han, Xiao-Mei Ye, Jia-Ping Lu, Hai-Ying Jin, Ping Wang, Wei-Wei Xu, Min Zhang
Diabetes, Metabolic Syndrome and Obesity.2023; Volume 16: 2329. CrossRef
Alteration of intestinal microbiota is associated with diabetic retinopathy and its severity: Samples collected from southeast coast Chinese
Xue-Mei Gu, Chao-Yin Lu, Jian Pan, Jian-Zhong Ye, Qi-Han Zhu
World Journal of Diabetes.2023; 14(6): 862. CrossRef
Progress in research on gut microbiota in ethnic minorities in China and consideration of intervention strategies based on ethnic medicine: A review
Rong Chen, Zhong-Yu Duan, Xiao-Hua Duan, Qing-Hua Chen, Jin Zheng
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Effects of Oral Glucose-Lowering Agents on Gut Microbiota and Microbial Metabolites
Dongmei Wang, Jieying Liu, Liyuan Zhou, Qian Zhang, Ming Li, Xinhua Xiao
Frontiers in Endocrinology.2022;[Epub] CrossRef
Depletion of gut secretory immunoglobulin A coatedLactobacillus reuteriis associated with gestational diabetes mellitus-related intestinal mucosal barrier damage
Haowen Zhang, Ce Qi, Yuning Zhao, Mengyao Lu, Xinyue Li, Jingbo Zhou, Hongyang Dang, Mengjun Cui, Tingting Miao, Jin Sun, Duo Li
Food & Function.2021; 12(21): 10783. CrossRef
The Microbiota Profile Analysis of Combined Periodontal-Endodontic Lesions Using 16S rRNA Next-Generation Sequencing
Ping Sun, Zhiyong Guo, Daiping Guo, Jian Wang, Tingting Wu, Tingjun Li, Jiannan Liu, Xinhua Liu, Jôice D. Corrêa
Journal of Immunology Research.2021; 2021: 1. CrossRef

Research Support, Non-U.S. Gov'ts

Deodorization of Pig Slurry and Characterization of Bacterial Diversity Using 16S rDNA Sequence Analysis: Ok-Hwa Hwang , Sebastian Raveendar , Young-Ju Kim , Ji-Hun Kim , Tae-Hun Kim , Dong-Yoon Choi , Che Ok Jeon , Sung-Back Cho , Kyung-Tai Lee; J. Microbiol. 2014;52(11):918-929. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4251-5

422 View
0 Download
8 Crossref

Abstract PDF

The concentration of major odor-causing compounds including phenols, indoles, short-chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) in response to the addition of powdered horse radish (PHR) and spent mushroom compost (SMC) was compared with control nontreated slurry (CNS) samples. A total of 97,465 rDNAs sequence reads were generated from three different samples (CNS, n = 2; PHR, n = 3; SMC, n = 3) using bar-coded pyrosequencing. The number of operational taxonomic units (OTUs) was lower in the PHR slurry compared with the other samples. A total of 11 phyla were observed in the slurry samples, while the phylogenetic analysis revealed that the slurry microbiome predominantly comprised members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla. The rarefaction analysis showed the bacterial species richness varied among the treated samples. Overall, at the OTU level, 2,558 individual genera were classified, 276 genera were found among the three samples, and 1,832 additional genera were identified in the individual samples. A principal component analysis revealed the differences in microbial communities among the CNS, PHR, and SMC pig slurries. Correlation of the bacterial community structure with the Kyoto Encyclopedia of Genes and Genomes (KEGG) predicted pathways showed that the treatments altered the metabolic capabilities of the slurry microbiota. Overall, these results demonstrated that the PHR and SMC treatments significantly reduced the malodor compounds in pig slurry (P < 0.05).

Citations

Citations to this article as recorded by

Impact of Bacillus subtilis on manure solids, odor, and microbiome
Okhwa Hwang, Yeo-Myeong Yun, Steven Trabue
Journal of Environmental Management.2023; 333: 117390. CrossRef
Isolation and identification of proteolytic bacteria from pig sludge and protease activity determination
S Hamdani, N Asstiyani, D Astriany, M Singgih, S Ibrahim
IOP Conference Series: Earth and Environmental Science.2019; 230: 012095. CrossRef
The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala
Xiaoyun Wang, Qiao Gao, Wanqiang Wang, Xiaoping Wang, Chaoliang Lei, Fen Zhu
BMC Microbiology.2018;[Epub] CrossRef
Bacterial community composition and diversity uncovered in experimental sludge treatment reed bed systems with different swine slurry hydraulic loadings
Paula Arroyo, Luis E. Sáenz de Miera, Jorge Falagán, Gemma Ansola
Ecological Engineering.2018; 123: 175. CrossRef
Effect of pH on soil bacterial diversity
Sun-Ja Cho, Mi-Hee Kim, Young-Ok Lee
Journal of Ecology and Environment.2016;[Epub] CrossRef
Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration?
Jisun Kim, Woojun Park
Journal of Microbiology.2015; 53(7): 421. CrossRef
Application of Next Generation Sequencing to Investigate Microbiome in the Livestock Sector
Minseok Kim, Youlchang Baek, Young Kyoon Oh
Journal of Animal Environmental Science.2015; 21(3): 93. CrossRef
Survival of free-living Acholeplasma in aerated pig manure slurry revealed by 13C-labeled bacterial biomass probing
Dai Hanajima, Tomo Aoyagi, Tomoyuki Hori
Frontiers in Microbiology.2015;[Epub] CrossRef

Phenotypic and Phylogenetic Analysis of Lactic Acid Bacteria Isolated from Forage Crops and Grasses in the Tibetan Plateau: Huili Pang , Zhongfang Tan , Guangyong Qin , Yanping Wang , Zongwei Li , Qingsheng Jin , Yimin Cai; J. Microbiol. 2012;50(1):63-71. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1284-5

446 View
0 Download
39 Crossref

Abstract PDF

A total of 140 lactic acid bacteria (LAB) strains were isolated from corn, alfalfa, clover, sainfoin, and Indian goosegrass in the Tibetan Plateau. According to phenotypic and chemotaxonomic characteristics, 16S rDNA sequence, and recA gene PCR amplification, these LAB isolates were identified as belonging to five genera and nine species. Corn contained more LAB species than other forage crops. Leuconostoc pseudomesenteroides, Lactococcus lactis subsp. lactis, Lactobacillus brevis, and Weissella paramesenteroides were dominant members of the LAB population on alfalfa, clover, sainfoin, and Indian goosegrass, respectively. The comprehensive 16S rDNA and recA-based approach effectively described the LAB community structure of the relatively abundant LAB species distributed on different forage crops. This is the first report describing the diversity and natural populations of LAB associated with Tibetan forage crops, and most isolates grow well at or below 10°C. The results will be valuable for the future design of appropriate inoculants for silage fermentation in this very cold area.

Citations

Citations to this article as recorded by

Effect of isolated lactic acid bacteria on the quality and bacterial diversity of native grass silage
Jian Bao, Gentu Ge, Zhijun Wang, Yanzi Xiao, Muqier Zhao, Lin Sun, Yu Wang, Jiawei Zhang, Yushan Jia, Shuai Du
Frontiers in Plant Science.2023;[Epub] CrossRef
Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage
Mingjian Liu, Yu Wang, Zhijun Wang, Jian Bao, Muqier Zhao, Gentu Ge, Yushan Jia, Shuai Du
Microorganisms.2022; 10(12): 2463. CrossRef
An investigation on fermentative profile, microbial numbers, bacterial community diversity and their predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) silages
Siran Wang, Junfeng Li, Jie Zhao, Zhihao Dong, Tao Shao
Animal Bioscience.2022; 35(8): 1162. CrossRef
Bacteriocin-Producing Lactic Acid Bacteria Strains with Antimicrobial Activity Screened from Bamei Pig Feces
Jun Chen, Huili Pang, Lei Wang, Cunming Ma, Guofang Wu, Yuan Liu, Yifei Guan, Miao Zhang, Guangyong Qin, Zhongfang Tan
Foods.2022; 11(5): 709. CrossRef
Effect of exogenous microorganisms on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage
Meirong Zhao, Hongyu Zhang, Gang Pan, Hang Yin, Juanjuan Sun, Zhu Yu, Chunsheng Bai, Yanlin Xue
Frontiers in Microbiology.2022;[Epub] CrossRef
Intake, digestibility rumen fermentation and nitrogen balance in lambs offered alfalfa and tall fescue-mixtures harvested and ensiled after a frost
V. Niyigena, K.P. Coffey, W.K. Coblentz, D. Philipp, C. Althaber, J. Diaz Gomez, R.T. Rhein, M.C. Pruden
Animal Feed Science and Technology.2022; 286: 115268. CrossRef
Spraying sugars, growth temperatures and N application levels change epiphytic lactic acid bacteria composition on Italian ryegrass
Xinzhu Chen, Zhaoxia Dong, Jianguo Zhang
Grassland Science.2022; 68(2): 145. CrossRef
Genotypic and Phenotypic Characterization of Lactic Acid Bacteria Associated with Silage Fermentation of Pineapple Residue
Yanli Lin, Zhumei Du, Yi Xiong, Ningwei Wang, Xuekai Wang, Xiaoli Zhou, Fuyu Yang, Kuikui Ni
Diversity.2022; 14(8): 631. CrossRef
Effect of Ensiling Density and Storage Temperature on Fermentation Quality, Bacterial Community, and Nitrate Concentration of Sorghum-Sudangrass Silage
Chunsheng Bai, Gang Pan, Ruoxuan Leng, Wenhua Ni, Jiyun Yang, Juanjuan Sun, Zhu Yu, Zhigang Liu, Yanlin Xue
Frontiers in Microbiology.2022;[Epub] CrossRef
Growth studies of dominant lactic acid bacteria in orange juice and selection of strains to ferment citric fruit juices with probiotic potential
María B. Pérez, Eloy Argañaraz Martinez, Jaime D. Babot, Adriana Pérez Chaia, Fabiana M. Saguir
Brazilian Journal of Microbiology.2022; 53(4): 2145. CrossRef
Effects of Maize Varieties on Biomass Yield and Silage Quality of Maize–Soybean Intercropping in the Qinghai–Tibet Plateau
Jiayi Li, Xingjin Wen, Jizhi Yang, Wenyu Yang, Yafen Xin, Lei Zhang, Haiping Liu, Yaling He, Yanhong Yan
Fermentation.2022; 8(10): 542. CrossRef
Microbial Community and Fermentation Characteristics of Native Grass Prepared Without or With Isolated Lactic Acid Bacteria on the Mongolian Plateau
Sihan You, Shuai Du, Gentu Ge, Tao Wan, Yushan Jia
Frontiers in Microbiology.2021;[Epub] CrossRef
A Search for Anti-Naegleria fowleri Agents Based on Competitive Exclusion Behavior of Microorganisms in Natural Aquatic Environments
Pichet Ruenchit, Narisara Whangviboonkij, Hathai Sawasdipokin, Uraporn Phumisantiphong, Wanpen Chaicumpa
Pathogens.2021; 10(2): 142. CrossRef
Selection of lactic acid bacteria from native grass silage and its effects as inoculant on silage fermentation
Sihan You, Shuai Du, Gentu Ge, Tao Wan, Yushan Jia
Agronomy Journal.2021; 113(4): 3169. CrossRef
Pediococcus acidilacticistrains as silage inoculants for improving the fermentation quality, nutritive value andin vitroruminal digestibility in different forages
S. Wang, Z. Dong, J. Li, L. Chen, T. Shao
Journal of Applied Microbiology.2019; 126(2): 424. CrossRef
Diversity of lactic acid bacteria in dadih produced by either back-slopping or spontaneous fermentation from two different regions of West Sumatra, Indonesia
Chandra Utami Wirawati, Mirnawati Bachrum Sudarwanto, Denny Widaya Lukman, Ietje Wientarsih, Eko Agus Srihanto
Veterinary World.2019; 12(6): 823. CrossRef
Improved Quality of Corn Silage When Combining Cellulose-Decomposing Bacteria andLactobacillus buchneriduring Silage Fermentation
Fanfan Zhang, Xuzhe Wang, Weihua Lu, Feifei Li, Chunhui Ma
BioMed Research International.2019; 2019: 1. CrossRef
Roles of microbes and lipolytic enzymes in changing the fatty acid profile, α-tocopherol and β-carotene of whole-crop oat silages during ensiling and after exposure to air
Q.H. Liu, J.X. Wu, T. Shao
Animal Feed Science and Technology.2019; 253: 81. CrossRef
Isolation and molecular identification of lactic acid bacteria from King grass and their application to improve the fermentation quality of sweet Sorghum
Assar Ali Shah, Yuan Xianjun, Dong Zhihao, Li Junfeng, Tao Shao
World Journal of Microbiology and Biotechnology.2018;[Epub] CrossRef
Effects of storage temperature and combined microbial inoculants on fermentation end products and microbial populations of Italian ryegrass (Lolium multiflorumLam.) silage
S. Wang, Z. Dong, J. Li, L. Chen, T. Shao
Journal of Applied Microbiology.2018; 125(6): 1682. CrossRef
Evaluation of lactic acid bacteria isolated from alfalfa for silage fermentation
Dongxia Li, Yanping Wang, Yingchao Zhang, Yanli Lin, Fuyu Yang
Grassland Science.2018; 64(3): 190. CrossRef
Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L.
Erica Pontonio, Raffaella Di Cagno, Waed Tarraf, Pasquale Filannino, Giuseppe De Mastro, Marco Gobbetti
Frontiers in Microbiology.2018;[Epub] CrossRef
Characteristics of lactic acid bacteria isolated from different sources and their effects on the silage quality of oat (Avena sativa L.) straw on the Tibetan Plateau
Siran Wang, Xianjun Yuan, Zhihao Dong, Junfeng Li, Tao Shao
Grassland Science.2018; 64(2): 128. CrossRef
The effects of lactic acid bacteria strains isolated from various substrates on the fermentation quality of common vetch (Vicia sativa L.) in Tibet
Siran Wang, Junfeng Li, Zhihao Dong, Lei Chen, Xianjun Yuan, Tao Shao
Grass and Forage Science.2018; 73(3): 639. CrossRef
Isolating and evaluating lactic acid bacteria strains for effectiveness on silage quality at low temperatures on the Tibetan Plateau
Siran Wang, Xianjun Yuan, Zhihao Dong, Junfeng Li, Tao Shao
Animal Science Journal.2017; 88(11): 1722. CrossRef
Microbial inoculant and an extract of Trichoderma longibrachiatum with xylanase activity effect on chemical composition, fermentative profile and aerobic stability of guinea grass (Pancium maximum Jacq.) silage
J. Gandra, E. de Oliveira, R. H. de Goes, K. de Oliveira, C. Takiya, T. Del Valle, H. Araki, K. Silveira, D. Silva, A. Da Silva Pause
Journal of Animal and Feed Sciences.2017; 26(4): 339. CrossRef
Microorganism profile, fermentation quality and rumen digestibility in vitro of maize-stalk silages produced at different maturity stages
Miao Zhang, Yanping Wang, Zhongfang Tan, Zongwei Li, Ya Li, Haoxin Lv, Bei Zhang, Qingsheng Jin
Crop & Pasture Science.2017; 68(3): 225. CrossRef
Characteristics of isolated lactic acid bacteria and their effects on the silage quality
Siran Wang, Xianjun Yuan, Zhihao Dong, Junfeng Li, Gang Guo, Yunfeng Bai, Junyu Zhang, Tao Shao
Asian-Australasian Journal of Animal Sciences.2016; 30(6): 819. CrossRef
The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin
Mickaël Castelain, Marie-Pierre Duviau, Alexis Canette, Philippe Schmitz, Pascal Loubière, Muriel Cocaign-Bousquet, Jean-Christophe Piard, Muriel Mercier-Bonin, Etienne Dague
PLOS ONE.2016; 11(3): e0152053. CrossRef
Drivers for the establishment and composition of the sourdough lactic acid bacteria biota
Marco Gobbetti, Fabio Minervini, Erica Pontonio, Raffaella Di Cagno, Maria De Angelis
International Journal of Food Microbiology.2016; 239: 3. CrossRef
Effect of temperature (5-25°C) on epiphytic lactic acid bacteria populations and fermentation of whole-plant corn silage
Y. Zhou, P. Drouin, C. Lafrenière
Journal of Applied Microbiology.2016; 121(3): 657. CrossRef
Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle
Fabio Minervini, Giuseppe Celano, Anna Lattanzi, Luigi Tedone, Giuseppe De Mastro, Marco Gobbetti, Maria De Angelis, M. W. Griffiths
Applied and Environmental Microbiology.2015; 81(19): 6736. CrossRef
The genus Weissella: taxonomy, ecology and biotechnological potential
Vincenzina Fusco, Grazia M. Quero, Gyu-Sung Cho, Jan Kabisch, Diana Meske, Horst Neve, Wilhelm Bockelmann, Charles M. A. P. Franz
Frontiers in Microbiology.2015;[Epub] CrossRef
Natural Lactic Acid Bacteria Population and Silage Fermentation of Whole-crop Wheat
Kuikui Ni, Yanping Wang, Yimin Cai, Huili Pang
Asian-Australasian Journal of Animal Sciences.2015; 28(8): 1123. CrossRef
Identification and Antimicrobial Activity Detection of Lactic Acid Bacteria Isolated from Corn Stover Silage
Dongxia Li, Kuikui Ni, Huili Pang, Yanping Wang, Yimin Cai, Qingsheng Jin
Asian-Australasian Journal of Animal Sciences.2015; 28(5): 620. CrossRef
Characterization, Identification and Application of Lactic Acid Bacteria Isolated from Forage Paddy Rice Silage
Kuikui Ni, Yanping Wang, Dongxia Li, Yimin Cai, Huili Pang, Daichang Yang
PLOS ONE.2015; 10(3): e0121967. CrossRef
Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese
Bei Zhang, Zhongfang Tan, Yanping Wang, Zongwei Li, Zhen Jiao, Qunce Huang
Dairy Science & Technology.2015; 95(2): 167. CrossRef
Effect of Novel Lactobacillus plantarum KCC-10 and KCC-19 on Fermentation Characterization of Alfalfa Silage
Ki Choon Choi, Soundarrajan Ilavenil, Mariadhas Valan Arasu, Hyung-Su Park, Won-Ho Kim
Journal of The Korean Society of Grassland and Forage Science.2015; 35(2): 166. CrossRef
Naturally Occurring Lactic Acid Bacteria Isolated from Tomato Pomace Silage
Jing-jing Wu, Rui-ping Du, Min Gao, Yao-qiang Sui, Lei Xiu, Xiao Wang
Asian-Australasian Journal of Animal Sciences.2014; 27(5): 648. CrossRef

Journal Article

Molecular Identification of Fecal Pollution Sources in Water Supplies by Host-Specific Fecal DNA Markers and Terminal Restriction Fragment Length Polymorphism Profiles of 16S rRNA Gene: Ju-Yong Jeong , Kyung-Ik Gil , Kyong-Hee Lee , Jong-Ok Ka; J. Microbiol. 2008;46(6):599-607. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0174-3

379 View
0 Download
2 Crossref

Abstract PDF

Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.

Citations

Citations to this article as recorded by

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing
Ju-Yong Jeong, Hee-Deung Park, Kyong-Hee Lee, Hang-Yeon Weon, Jong-Ok Ka
The Journal of Microbiology.2011; 49(4): 585. CrossRef
Application of an Integrated Community Analysis Approach for Microbial Source Tracking in a Coastal Creek
Yiping Cao, Laurie C. Van De Werfhorst, Bram Sercu, Jill L. S. Murray, Patricia A. Holden
Environmental Science & Technology.2011; 45(17): 7195. CrossRef

Research Support, Non-U.S. Gov'ts

An Examination of the Bacteriophages and Bacteria of the Namib Desert: Eric Prestel , Sylvie Salamitou , Michael S. DuBow; J. Microbiol. 2008;46(4):364-372. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0007-4

360 View
0 Download
58 Crossref

Abstract PDF

Bacteria and their viruses (called bacteriophages, or phages), have been found in virtually every ecological niche on Earth. Arid regions, including their most extreme form called deserts, represent the single largest ecosystem type on the Earth''s terrestrial surface. The Namib desert is believed to be the oldest (80 million years) desert. We report here an initial analysis of bacteriophages isolated from the Namib desert using a combination of electron microscopy and genomic approaches. The virus-like particles observed by electron microscopy revealed 20 seemingly different phage-like morphologies and sizes belonging to the Myoviridae and Siphoviridae families of tailed phages. Pulsed-field gel electrophoresis revealed a majority of phage genomes of 55~65 kb in length, with genomes of approximately 200, 300, and 350 kb also observable. Sample sequencing of cloned phage DNA fragments revealed that approximately 50% appeared to be of bacterial origin. Of the remaining DNA sequences, approximately 50% displayed no significant match to any sequence in the databases. The majority of the 16S rDNA sequences amplified from DNA extracted from the sand displayed considerable (94~98%) homology to members of the Firmicutes, and in particular to members of the genus Bacillus, though members of the Bacteroidetes, Planctomycetes, Chloroflexi, and delta-Proteobacteria groups were also observed.

Citations

Citations to this article as recorded by

Condensation nucleation and water collection performance of functional surfaces with hydrophilic-hydrophobic patterns inspired by desert beetle elytra
Xiaoya Guan, Yi Peng, Shixian Liu, Jie Ran, Jianlong Yang, Zhankun Wang
Chemical Engineering Science.2026; 326: 123576. CrossRef
Temperature as a Driver of Phage Ecology and Evolution
Samuel T.E. Greenrod, Tobias E. Hector, Michael Blazanin, Daniel Cazares, Kayla C. King
Annual Review of Microbiology .2025; 79(1): 497. CrossRef
Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems
Xiang Tang, Han‐Peng Liao, Jiang‐Tao Gao, Qiu‐E Yang, Christopher Rensing, Shun‐Gui Zhou
Environmental Microbiology.2025;[Epub] CrossRef
Bacterial Diversity Profiles of Desert Sand and Salt Crusts from the Gran Desierto de Altar, Sonora, Mexico
Cristal Ramos-Madrigal, Esperanza Martínez-Romero, Yunuen Tapia-Torres, Luis E. Servín-Garcidueñas
Diversity.2024; 16(12): 745. CrossRef
Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site
Stéphane Boivin, Amélia Bourceret, Kenji Maurice, Liam Laurent‐Webb, Tomáš Figura, Julie Bourillon, Jérôme Nespoulous, Odile Domergue, Clémence Chaintreuil, Hassan Boukcim, Marc‐André Selosse, Zbigniew Fiema, Emmanuel Botte, Laila Nehme, Marc Ducousso
Environmental Microbiology.2024;[Epub] CrossRef
Biocrust succession significantly influences soil virus composition and alpha diversity in a sandy desert
Yang Zhao, Yu-Chao Lian, Yan-Qiao Zhao, Wen-Wen Xu, Yi-Xue Zhao, Zhi-Shan Zhang
Applied Soil Ecology.2024; 195: 105255. CrossRef
Bacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States
Leigh H. Magness, Véronique A. Delesalle, Albert C. Vill, Madison S. Strine, Brianne E. Chaudhry, Katherine B. Lichty, Alexandra A. Guffey, Jenna M. DeCurzio, Greg P. Krukonis
PHAGE.2023; 4(4): 165. CrossRef
Comparative Genomics of Bacillus subtilis Phages Related to phiNIT1 from Desert Soils of the Southwest United States
Albert C. Vill, Véronique A. Delesalle, Leigh H. Magness, Brianne E. Chaudhry, Katherine B. Lichty, Madison S. Strine, Alexandra A. Guffey, Jenna M. DeCurzio, Greg P. Krukonis
PHAGE.2023; 4(4): 173. CrossRef
A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations
Rachel E. Loney, Véronique A. Delesalle, Brianne E. Chaudry, Megan Czerpak, Alexandra A. Guffey, Leo Goubet-McCall, Michael McCarty, Madison S. Strine, Natalie T. Tanke, Albert C. Vill, Greg P. Krukonis
Viruses.2023; 15(11): 2267. CrossRef
Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities
Leora Busse, Mike Tisza, Jocelyne DiRuggiero
Viruses.2022; 14(9): 1983. CrossRef
Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States
Albert C. Vill, Véronique A. Delesalle, Brianne E. Tomko, Katherine B. Lichty, Madison S. Strine, Alexandra A. Guffey, Elizabeth A. Burton, Natalie T. Tanke, Greg P. Krukonis
PHAGE.2022; 3(3): 171. CrossRef
Complete Genome Sequences of Two Temperate Bacillus subtilis Phages Isolated at Tumamoc Hill Desert Laboratory
Greg P. Krukonis, Amanda K. Kemp, Katie F. Storrie, Vivian R. Chavira, Hayden W. Lantrip, Victoria D. Perez, Desiree A. Reyes, Julian A. Truax, Rachel Loney, Véronique A. Delesalle, Simon Roux
Microbiology Resource Announcements.2022;[Epub] CrossRef
Response of soil bacterial community to agricultural reclamation in the Tengger desert, northwestern China
Lin Ye, Xue Wu, Cuinan Wu, Yi Zhang, Lili Meng, Encai Bao, Kai Cao
Applied Soil Ecology.2022; 169: 104189. CrossRef
Partners to survive: Hoffmannseggia doellii root‐associated microbiome at the Atacama Desert
Jonathan E. Maldonado, Alexis Gaete, Dinka Mandakovic, Constanza Aguado‐Norese, Melissa Aguilar, Rodrigo A. Gutiérrez, Mauricio González
New Phytologist.2022; 234(6): 2126. CrossRef
An Appraisal of Bacteriophage Isolation Techniques from Environment
Aparna Nair, Gaurav S. Ghugare, Krishna Khairnar
Microbial Ecology.2022; 83(3): 519. CrossRef
Response of soil viral communities to land use changes
Hu Liao, Hu Li, Chen-Song Duan, Xin-Yuan Zhou, Qiu-Ping Luo, Xin-Li An, Yong-Guan Zhu, Jian-Qiang Su
Nature Communications.2022;[Epub] CrossRef
Do bacterial viruses affect framboid-like mineral formation?
Paweł Działak, Marcin D. Syczewski, Kamil Kornaus, Mirosław Słowakiewicz, Łukasz Zych, Andrzej Borkowski
Biogeosciences.2022; 19(18): 4533. CrossRef
Plant ecological genomics at the limits of life in the Atacama Desert
Gil Eshel, Viviana Araus, Soledad Undurraga, Daniela C. Soto, Carol Moraga, Alejandro Montecinos, Tomás Moyano, Jonathan Maldonado, Francisca P. Díaz, Kranthi Varala, Chase W. Nelson, Orlando Contreras-López, Henrietta Pal-Gabor, Tatiana Kraiser, Gabriela
Proceedings of the National Academy of Sciences.2021;[Epub] CrossRef
ISOLATION AND PHYSICOCHEMICAL CHARACTERIZATION OF BRUCELLA PHAGES
A.Y. Shaheen, A.A. Sheikh, M Rabbani, W Shehzad, Z Abbas, M Maqbool
The Journal of Animal and Plant Sciences.2021; 31(5): 1277. CrossRef
Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach
Narender Kumar, Amit Kumar Gupta, Sarabjeet Kour Sudan, Deepika Pal, Vinay Randhawa, Girish Sahni, Shanmugam Mayilraj, Manoj Kumar
Microbial Drug Resistance.2021; 27(10): 1336. CrossRef
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
Yunha Hwang, Janina Rahlff, Dirk Schulze-Makuch, Michael Schloter, Alexander J. Probst, Joanne B. Emerson
mSystems.2021;[Epub] CrossRef
Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities
Alexis Gaete, Rodrigo Pulgar, Christian Hodar, Jonathan Maldonado, Leonardo Pavez, Denisse Zamorano, Claudio Pastenes, Mauricio González, Nicolás Franck, Dinka Mandakovic
Frontiers in Plant Science.2021;[Epub] CrossRef
Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China
Ke Wu, Wenxuan Xu, Weikang Yang
PeerJ.2020; 8: e8433. CrossRef
Microbiomics of Namib Desert habitats
D. A. Cowan, D. W. Hopkins, B. E. Jones, G. Maggs-Kölling, R. Majewska, J.-B. Ramond
Extremophiles.2020; 24(1): 17. CrossRef
Application of Adaptive Evolution to Improve the Stability of Bacteriophages during Storage
Kelvin K. Kering, Xiaoxu Zhang, Raphael Nyaruaba, Junping Yu, Hongping Wei
Viruses.2020; 12(4): 423. CrossRef
Abiotic and plant gender effects on the structure and function of soil microbial communities associated with Acanthosicyos horridus (Nara) in the Namibian sand-dune desert ecosystem
Chen Sherman, Eugene Marais, Gillian Maggs-Kölling, Jonathan Adams, Yosef Steinberger
Journal of Arid Environments.2019; 163: 50. CrossRef
Virus-Like Particle Production in Atmospheric Eubacteria Isolates
Nuria Teigell-Perez, Cristina Gonzalez-Martin, Basilio Valladares, David J. Smith, Dale W. Griffin
Atmosphere.2019; 10(7): 417. CrossRef
Soil bacterial community associated with the dioecious Acanthosicyos horridus in the Namib Desert
Adrian Unc, Gillian Maggs-Kölling, Eugene Marais, Chen Sherman, Tirza Doniger, Yosef Steinberger
Biology and Fertility of Soils.2019; 55(4): 393. CrossRef
Examination of the Bacterial Biodiversity of Coastal Eroded Surface Soils from the Padza de Dapani (Mayotte Island)
Jorge R. Osman, Gustavo Fernandes, Christophe Regeard, Chloé Jaubert, Michael S. DuBow
Geomicrobiology Journal.2018; 35(5): 355. CrossRef
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
Ulas Karaoz, Estelle Couradeau, Ulisses Nunes da Rocha, Hsiao-Chien Lim, Trent Northen, Ferran Garcia-Pichel, Eoin L. Brodie, Mark J. Bailey
mBio.2018;[Epub] CrossRef
Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert
Dinka Mandakovic, Jonathan Maldonado, Rodrigo Pulgar, Pablo Cabrera, Alexis Gaete, Viviana Urtuvia, Michael Seeger, Verónica Cambiazo, Mauricio González
Extremophiles.2018; 22(4): 665. CrossRef
Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments
Steffi Genderjahn, Mashal Alawi, Kai Mangelsdorf, Fabian Horn, Dirk Wagner
Frontiers in Microbiology.2018;[Epub] CrossRef
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisca P. Díaz, Beatriz Fernández-Gómez, Pablo Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A. Gutiérrez, Alejandro
Scientific Reports.2018;[Epub] CrossRef
An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Current Microbiology.2018; 75(2): 132. CrossRef
Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient
Olivier Zablocki, Evelien M. Adriaenssens, Aline Frossard, Mary Seely, Jean-Baptiste Ramond, Don Cowan
Genome Announcements.2017;[Epub] CrossRef
Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters
Riegardt M. Johnson, Jean-Baptiste Ramond, Eoin Gunnigle, Mary Seely, Don A. Cowan
Extremophiles.2017; 21(2): 381. CrossRef
Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils
Li-Li Han, Dan-Ting Yu, Li-Mei Zhang, Ju-Pei Shen, Ji-Zheng He
Scientific Reports.2017;[Epub] CrossRef
Virome Assembly and Annotation: A Surprise in the Namib Desert
Uljana Hesse, Peter van Heusden, Bronwyn M. Kirby, Israel Olonade, Leonardo J. van Zyl, Marla Trindade
Frontiers in Microbiology.2017;[Epub] CrossRef
Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics
Krupa M. Parmar, Saurabh L. Gaikwad, Prashant K. Dhakephalkar, Ramesh Kothari, Ravindra Pal Singh
Frontiers in Microbiology.2017;[Epub] CrossRef
Unique community structure of viruses in a glacier soil of the Tianshan Mountains, China
Li-Li Han, Dan-Ting Yu, Li-Mei Zhang, Jun-Tao Wang, Ji-Zheng He
Journal of Soils and Sediments.2017; 17(3): 852. CrossRef
Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata
Jens A. Hammerl, Cornelia Göllner, Sascha Al Dahouk, Karsten Nöckler, Jochen Reetz, Stefan Hertwig
Frontiers in Microbiology.2016;[Epub] CrossRef
Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses
Evelien Adriaenssens, Leonardo Van Zyl, Don Cowan, Marla Trindade
Viruses.2016; 8(1): 14. CrossRef
Diversity and Ecology of Viruses in Hyperarid Desert Soils
Olivier Zablocki, Evelien M. Adriaenssens, Don Cowan, F. E. Löffler
Applied and Environmental Microbiology.2016; 82(3): 770. CrossRef
Microbial ecology of hot desert edaphic systems
Thulani P. Makhalanyane, Angel Valverde, Eoin Gunnigle, Aline Frossard, Jean-Baptiste Ramond, Don A. Cowan
FEMS Microbiology Reviews.2015; 39(2): 203. CrossRef
The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of theCentralNamibDesert
S. Gombeer, J.‐B. Ramond, F. D. Eckardt, M. Seely, D. A. Cowan
Geobiology.2015; 13(5): 494. CrossRef
Metagenomic analysis of the viral community in Namib Desert hypoliths
Evelien M. Adriaenssens, Lonnie Van Zyl, Pieter De Maayer, Enrico Rubagotti, Ed Rybicki, Marla Tuffin, Don A. Cowan
Environmental Microbiology.2015; 17(2): 480. CrossRef
Environmental bacteriophages: viruses of microbes in aquatic ecosystems
TÃ©lesphore Sime-Ngando
Frontiers in Microbiology.2014;[Epub] CrossRef
The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert
Eric Prestel, Christophe Regeard, Sylvie Salamitou, Julie Neveu, Michael S. DuBow
Antonie van Leeuwenhoek.2013; 103(6): 1329. CrossRef
Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara
Laura Fancello, Sébatien Trape, Catherine Robert, Mickaël Boyer, Nikolay Popgeorgiev, Didier Raoult, Christelle Desnues
The ISME Journal.2013; 7(2): 359. CrossRef
Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert
Francesca Stomeo, Angel Valverde, Stephen B. Pointing, Christopher P. McKay, Kimberley A. Warren-Rhodes, Marla I. Tuffin, Mary Seely, Don A. Cowan
Extremophiles.2013; 17(2): 329. CrossRef
Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils
David R. Andrew, Robert R. Fitak, Adrian Munguia-Vega, Adriana Racolta, Vincent G. Martinson, Katerina Dontsova
Applied and Environmental Microbiology.2012; 78(21): 7527. CrossRef
A Novel Bacteriophage Morphotype with a Ribbon-like Structure at the Tail Extremity
Eric Prestel, Christophe Regeard, James Andrews, Philippe Oger, Michael S. DuBow
Research Journal of Microbiology.2012; 7(1): 75. CrossRef
A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station (Utah)
Susana O.L. Direito, Pascale Ehrenfreund, Andries Marees, Martijn Staats, Bernard Foing, Wilfred F.M. Röling
International Journal of Astrobiology.2011; 10(3): 191. CrossRef
Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts
Julie Neveu, Christophe Regeard, Michael S. DuBow
Applied Microbiology and Biotechnology.2011; 91(3): 635. CrossRef
Mineral and Bacterial Diversities of Desert Sand Grains from South-East Morocco
Maxime Gommeaux, Mohamed Barakat, Gilles Montagnac, Richard Christen, François Guyot, Thierry Heulin
Geomicrobiology Journal.2010; 27(1): 76. CrossRef
Occurrence of Vibrio parahaemolyticus and Its Specific Phages from Shrimp Ponds in East Coast of India
K. M. Alagappan, B. Deivasigamani, S. T. Somasundaram, S. Kumaran
Current Microbiology.2010; 61(4): 235. CrossRef
Soil Microbial Abundance and Diversity Along a Low Precipitation Gradient
Ami Bachar, Ashraf Al-Ashhab, M. Ines M. Soares, Menachem Y. Sklarz, Roey Angel, Eugene D. Ungar, Osnat Gillor
Microbial Ecology.2010; 60(2): 453. CrossRef
Current insights into phage biodiversity and biogeography
Rebecca Vega Thurber
Current Opinion in Microbiology.2009; 12(5): 582. CrossRef

Rapid Detection of Virulence Factors of Aeromonas Isolated from a Trout Farm by Hexaplex-PCR: In-Young Nam , Kiseong Joh; J. Microbiol. 2007;45(4):297-304.; DOI: https://doi.org/2569 [pii]

272 View
0 Download

Abstract PDF: The detection of virulence factors of Aeromonas is a key component in determining potential pathogenicity because these factors act multifunctionally and multifactorially. In this study water samples were collected from a trout farm on a seasonal basis, and diseased fish and Aeromonas species were isolated and identified. For rapid detection of six virulence factors of isolated Aeromonas, a hexaplex-polymerase chain reaction (hexaplex-PCR) assay was used. The detected virulence factors include aerolysin (aer), GCAT (gcat), serine protease (ser), nuclease (nuc) lipase (lip) and lateral flagella (laf). The dominant strain found in our isolates was Aeromonas sobria, and the dominant virulence factors were aer and nuc for all seasons. We confirmed that A. sobria and two of the virulence genes (aer and nuc) are related. We proposed a method by which one can identify the major strains of Aeromonas: A. hydrophila, A. sobria, A. caviae, and A. veronii, using hexaplex-PCR.

Isolation and Characterization of the Mutans Streptococci from the Dental Plaques in Koreans: So Young Yoo , Seon Joo Park , Dong Ki Jeong , Kwang-Won Kim , Sung-Hoon Lim , Sang-Ho Lee , Son-Jin Choe , Young-Hyo Chang , Insoon Park , Joong-Ki Kook; J. Microbiol. 2007;45(3):246-255.; DOI: https://doi.org/2535 [pii]

317 View
2 Download

Abstract PDF: Mutans streptococci have been implicated as cariogenic bacteria in dental caries because they can produce high levels of dental caries-causing lactic acid and extracellular polysaccharide. The aim of this study was to isolate and characterize the mutans streptococci from the dental plaque obtained from Koreans. The dental plaque samples were collected from the anterior and molar teeth of both jaws in 155 subjects (aged 2 to 33.2 years, average age 13.7±4.7 years). The samples were diluted by 100-fold in 1x PBS and plated on mitis-salivarius bacitracin (MSB) agar plates. The mutans streptococci grown on MSB plates were screened by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) targeting dextranase gene (dex). The mutans streptococci were identified at the species level using a 16S rDNA sequencing comparison method. The biochemical tests were carried out to biotype the mutans streptococci. Ninety-five strains of the mutans streptococci out of 358 colonies, which were derived from 141 subjects, were isolated. Of them, 77 strains and 18 strains were Streptococcus mutans and Streptococcus sobrinus, respectively. The biotyping data showed that 62, 1, 20, 10, and 2 strains were biotypes I, II, IV, V and variant, respectively. Of the two strains of variant biotype, one strains was similar to biotype IV except that it was positive to the arginine hydrolysis test. We considered this one strain a new biotype, and classified it as biotype VII. In conclusion, S. mutans and its biotype I was most frequently isolated in Korean dental plaque. The mutans streptococci strains isolated in this study might be useful for the study of the pathogenesis and the prevention of dental caries.

Journal Article

Kosinostatin, a Major Secondary Metabolite Isolated from the Culture Filtrate of Streptomyces violaceusniger Strain HAL64: Moustafa Y. El-Naggar; J. Microbiol. 2007;45(3):262-267.; DOI: https://doi.org/2533 [pii]

275 View
0 Download

Abstract PDF: During a screening program, an actinomycete strain isolated from the Egyptian soil was investigated for its potential to show antimicrobial activity. The identification of this isolate was performed according to spore morphology and cell wall chemo-type, which suggested that this strain is a streptomycete. Further cultural, physiological characteristics and the analysis of the nucleotide sequence of the 16S rRNA gene (1480 bp) of this isolate indicated that this strain is identical to Streptomyces violaceusniger (accession number EF063682) and then designated S. violaceusniger strain HAL64. In its culture supernatant, this organism could produce one major compound strongly inhibits the growth of Gram-positive but the inhibition of Gram-negative indicator bacteria was lower. The antibiotic was separated by silica gel column chromatography and then purified on a sephadex LH-20 column and finally the purity was checked by HPLC. The chemical structure of the purified compound was determined using spectroscopic analyses (molecular formula of C33H32N2O10 and molecular weight of 617.21) and found to be identical to the kosinostatin, a quinocycline antibiotic which is known to be produced by Micromonspora sp. TP-A0468 (Igarashi et al., 2002) and to quinocycline B isolated from Streptomyces aureofaciens (Celmer et al., 1958). Although the antibiotic is known, the newly isolated strain was able to produce the antibiotic as a major product providing an important biotechnological downstream advantage.

Research Support, Non-U.S. Gov'ts

Comparison of Bacterial Composition between Human Saliva and Dental Unit Water System: Eun-Hyoung Jeon , Ji-Hye Han , Tae-Young Ahn; J. Microbiol. 2007;45(1):1-5.; DOI: https://doi.org/2500 [pii]

276 View
0 Download

Abstract PDF: The bacterial compositions between the dental unit water system and human saliva were characterized and compared by direct sequence analysis of 16S rDNA clone libraries. Based on the species richness estimation, bacterial diversity in the dental unit water system (DUW) was more diverse than that of the human saliva (HS). The Chao1 estimates of species richness in HS and DUW samples were 12.0 and 72.4, respectively. The total numbers of OTUs observed in the combined libraries accounted for 83% (HS) and 59% (DUW) of the Chao1 diversity estimate as defined at the 80% similarity threshold. Based on the sequence analysis, the phylum Proteobacteria was the major group in both clone libraries at phylum level. DUW clone library contained 80.0% Proteobacteria, 8.0% Bacteroides, 4.0% Nitrospira, 4.0% Firmicutes, 2.0% Planctomycetes and 2.0% Acidobacteria. On the other hand, human saliva (HS) clone library contained 55.5% Proteobacteria, 36.1% Firmicutes and 8.4% Bacteroides. The majority of bacteria identified belonged to phylum Proteobacteria in both samples. In dental unit water system (DUW), Alphaproteobacteria was detected as the major group. There was no evidence of the bacterial contamination due to a dental treatment. Most sequences were related to microorganisms derived from biofilm in oligotrophic environments.

Archaeal Communities in Mangrove Soil Characterized by 16S rRNA Gene Clones: Bing Yan , Kui Hong , Zi-Niu Yu; J. Microbiol. 2006;44(5):566-571.; DOI: https://doi.org/2439 [pii]

279 View
0 Download

Abstract PDF: An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

A Bacterium Belonging to the Burkholderia cepacia Complex Associated with Pleurotus ostreatus: Ricardo Yara , Walter Maccheroni Junior , Jorge Horii , Joao Lucio Azevedo; J. Microbiol. 2006;44(3):263-268.; DOI: https://doi.org/2387 [pii]

273 View
0 Download

Abstract PDF: Pleurotus ostreatus is a widely cultivated white-rot fungus. Owing to its considerable enzymatic versatility P. ostreatus has become the focus of increasing attention for its possible utility in biobleaching and bioremediation applications. Interactions between microorganisms can be an important factor in those processes. In this study, we describe the presence of a bacterial species associated with P. ostreatus strain G2. This bacterial species grew slowly (approximately 30 days) in theliquid and semi-solid media tested. When P. ostreatus was inoculated in solid media containing Tween 80 or Tween 20, bacterial microcolonies were detected proximal to the fungal colonies, and the relevant bacterium was identified via the analysis of a partial 16S rDNA sequence; it was determined to belong to the Burkholderia cepacia complex, but was not closely related to other fungus-isolated Burkholderiaceae. New specific primers were designed, and confirmed the presence of in vitro P. ostreatus cultures. This is the first time that a bacterial species belonging to the B. cepacia complex has been found associated with P. ostreatus.

Molecular Analysis of Colonized Bacteria in a Human Newborn Infant Gut: Hee-Kyung Park , Sung-Sub Shim , Su-Yung Kim , Jae-Hong Park , Su-Eun Park , Hak-Jung Kim , Byeong-Chul Kang , Cheol-Min Kim; J. Microbiol. 2005;43(4):345-353.; DOI: https://doi.org/2255 [pii]

274 View
0 Download

Abstract PDF: The complex ecosystem of intestinal microflora is estimated to harbor approximately 400 different microbial species, mostly bacteria. However, studies on bacterial colonization have mostly been based on culturing methods, which only detect a small fraction of the whole microbiotic ecosystem of the gut. To clarify the initial acquisition and subsequent colonization of bacteria in an infant within the few days after birth, phylogenetic analysis was performed using 16S rDNA sequences from the DNA isolated from feces on the 1st, 3rd, and 6th day. 16S rDNA libraries were constructed with the amplicons of PCR conditions at 30 cycles and 50^oC annealing temperature. Nine independent libraries were produced by the application of three sets of primers (set A, set B, and set C) combined with three fecal samples for day 1, day 3, and day 6 of life. Approximately 220 clones (76.7%) of all 325 isolated clones were characterized as known species, while other 105 clones (32.3%) were characterized as unknown species. The library clone with set A universal primers amplifying 350 bp displayed increased diversity by days. Thus, set A primers were better suited for this type of molecular ecological analysis. On the first day of the life of the infant, Enterobacter, Lactococcus lactis, Leuconostoc citreum, and Streptococcus mitis were present. The largest taxonomic group was L. lactis. On the third day of the life of the infant, Enterobacter, Enterococcus faecalis, Escherichia coli, S. mitis, and Streptococcus salivarius were present. On the sixth day of the life of the infant, Citrobacter, Clostridium difficile, Enterobacter sp., Enterobacter cloacae, and E. coli were present. The largest taxonomic group was E. coli. These results showed that microbiotic diversity changes very rapidly in the few days after birth, and the acquisition of unculturable bacteria expanded rapidly after the third day.

Isolation and Characterization of Bacteria Associated with Two Sand Dune Plant Species, Calystegia soldanella and Elymus mollis: Myung Soo Park , Se Ra Jung , Myoung Sook Lee , Kyoung Ok Kim , Jin Ok Do , Kang Hyun Lee , Seung Bum Kim , Kyung Sook Bae; J. Microbiol. 2005;43(3):219-227.; DOI: https://doi.org/2223 [pii]

262 View
0 Download

Abstract PDF: Little is known about the bacterial communities associated with the plants inhabiting sand dune ecosystems. In this study, the bacterial populations associated with two major sand dune plant species, Calystegia soldanella (beach morning glory) and Elymus mollis (wild rye), growing along the costal areas in Tae-An, Chungnam Province, were analyzed using a culture-dependent approach. A total of 212 bacteria were isolated from the root and rhizosphere samples of the two plants, and subjected to further analysis. Based on the analysis of the 16S rDNA sequences, all the bacterial isolates were classified into six major phyla of the domain Bacteria. Significant differences were observed between the two plant species, and also between the rhizospheric and root endophytic communities. The isolates from the rhizosphere of the two plant species were assigned to 27 different established genera, and the root endophytic bacteria were assigned to 21. Members of the phylum Gammaproteobacteria, notably the Pseudomonas species, comprised the majority of both the rhizospheric and endophytic bacteria, followed by members of Bacteroidetes and Firmicutes in the rhizosphere and Alphaproteobacteria and Bacteroidetes in the root. A number of isolates were recognized as potentially novel bacterial taxa. Fifteen out of 27 bacterial genera were commonly found in the rhizosphere of both plants, which was comparable to 3 out of 21 common genera in the root, implying the host specificity for endophytic populations. This study of the diversity of culturable rhizospheric and endophytic bacteria has provided the basis for further investigation aimed at the selection of microbes for the facilitation of plant growth.

Journal Article

Prevalence of Putative Periodontopathogens in Subgingival Dental Plaques from Gingivitis Lesions in Korean Orthodontic Patients: Seung Mi Lee , So Young Yoo , Hwa-Sook Kim , Kwang-Won Kim , Young-Joo Yoon , Sung-Hoon Lim , Hee-Young Shin , Joong-Ki Kook; J. Microbiol. 2005;43(3):260-265.; DOI: https://doi.org/2215 [pii]

261 View
0 Download

Abstract PDF: The objective of this study was to detect and compare the presence of periodontopathogens in the subgingival plaques of gingivitis lesions in adults who wore fixed orthodontic appliances, as opposed to adults who did not wear any orthodontic appliances. Thirty-six individuals participated in this study. Ninteen of these subjects did not wear any orthodontic appliances, and these subjects comprised the control group. The other 17 individuals had been wearing fixed orthodontic appliances for at least 3 months each. After a periodontal examination, we collected subgingival plaque samples from the gingivitis lesions of each patient. Using PCR based on 16S rDNA, we detected the presence of 6 putative periodontopathogenic species, Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia (formerly Bacteroides forsythus), Prevotella nigrescens, Prevotella intermedia, and Actinobacillus actinomycetemcomitans. With regard to the presence of individual periodontopathogens, we found that T. forsythia, T. denticola, and P. nigrescens were significantly more common in the samples obtained from the orthodontic patients than in the samples obtained from the non-orthodontic patient controls. Our results indicate that the local changes associated with the wearing of fixed orthodontic appliances may affect the prevalence of periodontopathogens in subgingival dental plaques.

Research Support, Non-U.S. Gov't

Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis: Bong-Soo Kim , Huyn-Myung Oh , Hojeong Kang , Jongsik Chun; J. Microbiol. 2005;43(2):144-151.; DOI: https://doi.org/2170 [pii]

286 View
0 Download

Abstract PDF: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25 - 100%) to sequences from other environments in the public database than did those (75.22 - 98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.

Journal Article

Identification of Non-mutans Streptococci Organisms in Dental Plaques Recovering on Mitis-Salivarius Bacitracin Agar Medium: So Young Yoo , Pyung Sik Kim , Ho-Keel Hwang , Seong-Hoon Lim , Kwang-Won Kim , Son-Jin Choe , Byung-Moo Min , Joong-Ki Kook; J. Microbiol. 2005;43(2):204-208.; DOI: https://doi.org/2160 [pii]

296 View
0 Download

Abstract PDF: The objective of this study was to both isolate and identify non-mutans streptococci organisms (non-MSO) from dental plaques recovered on mitis-salivarius sucrose bacitracin agar (MSB) plates. The dental plaque samples, which had been collected from 63 human subjects, were diluted and plated on MSB. The bacteria growing on the MSB plates were then identified with biochemical tests, as well as with 16S rDNA cloning and sequencing techniques. Our data indicated that bacteria from 30 subjects had been recovered on the MSB plates. Among the 21 typical colonies selected from the 30 subjects, 12 colonies, derived from 10 subjects, were identified as non-MSO. These 12 colonies were determined to be Streptococcus anginosus (8 colonies), S. sanguinis (1 colony), and Pantoea agglomerans (3 colonies). These results strongly suggest that a new selective medium will be required for the reliable isolation of mutans streptococci.

Research Support, Non-U.S. Gov'ts

Identification of Actinobacillus actinomycetemcomitans Using Species-Specific 16S rDNA Primers: Su-Gwan Kim , Soo-Heung Kim , Mi-Kwang Kim , Hwa-Sook Kim , Joong-Ki Kook; J. Microbiol. 2005;43(2):209-212.; DOI: https://doi.org/2159 [pii]

282 View
0 Download

Abstract PDF: The purpose of this study was to develop species-specific PCR primers for use in the identification and detection of Actinobacillus actinomycetemcomitans. These primers target variable regions of the 16S ribosomal RNA coding gene (rDNA). We assessed the specificity of the primers against 9 A. actinomycetemcomitans strains and 11 strains (3 species) of the Haemophilus genus. Primer sensitivity was determined by testing serial dilutions of the purified genomic DNAs of A. actinomycetemcomitans ATCC 33384^T. Our obtained data revealed that we had obtained species-specific amplicons for all of the tested A. actinomycetemcomitans strains, and that none of these amplicons occurred in any of the other species. Our PCR protocol proved able to detect as little as 4 fg of A. actinomycetemcomitans chromosomal DNA. Our findings suggest that these PCR primers are incredibly sensitive, and should prove suitable for application in epidemiological studies, as well as the diagnosis and monitoring of periodontal pathogens after treatment for periodontitis.

The Diversity of Culturable Organotrophic Bacteria from Local Solar Salterns: Sun-Hee Yeon , Won-Jin Jeong , Jin-Sook Park; J. Microbiol. 2005;43(1):1-10.; DOI: https://doi.org/2146 [pii]

264 View
0 Download

Abstract PDF: We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of [gammar]-Proteobacteria (70.3%) and 19 strains of Firmicutes (29.7%). The [alpha]-Proteobacteria and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The [gammar]-Proteobacteria group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Populations in 5-Stage Biological Nutrient Removal Process with Step Feed System for Wastewater Treatment: Soo-Youn Lee , Hyeon-Guk Kim , Jong Bok Park , Yong Keun Park; J. Microbiol. 2004;42(1):1-8.; DOI: https://doi.org/2009 [pii]

252 View
0 Download

Abstract PDF: Changes in the bacterial populations of a 5-stage biological nutrient removal (BNR) process, with a step feed system for wastewater treatment, were monitored by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments. DGGE analysis indicated seasonal community changes were observed, however, community profiles of the total bacteria of each reactor showed only minor differences in the samples obtained from the same season. The number of major bands was higher in the summer samples, and decreased during the winter period, indicating that the microbial community structure became simpler at low temperatures. Since the nitrogen and phosphate removal efficiencies were highly maintained throughout the winter operation period, the bacteria which still remaining in the winter sample can be considered important, playing a key role in the present 5-stage BNR sludge. The prominent DGGE bands were excised, and sequenced to gain insight into the identities of the predominant bacterial populations present, and most were found to not be closely related to previously characterized bacteria. These data suggest the importance of culture independent methods for the quality control of wastewater treatment

Bacterial Diversity of Culturable Isolates from Seawater and a Marine Coral, Plexauridae sp., near Mun-Sum, Cheju-Island: Jung-Hyun Lee , Hyun-Hee Shin , Deuk-Soo Lee , Kae Kyung Kwon , Sang-Jin Kim , Hong Kum Lee; J. Microbiol. 1999;37(4):193-199.

281 View
0 Download

Abstract PDF: Fifty-eight strains showing different colony morphological characteristics on various media were isolated from marine coral (Plexauridae sp.) and ambient seawater near Mun-Sum, Cheju-Island in 1998. Bacterial diversity was studies by phylogenetic analysis of the partial 16S rRNA gene sequences. All isolates representing the bacterial domain included affiliates of the high G+C (59%) and los G+C (3%) subdivision of Gram positive bacteria, and the alpha (33%) and gamma (5%) subdivision of the Proteobacteria. The 16S rDNA sequence similarity of the isolates was in the 88.3 to 100% range (average, 95.6%) to reported sequence data. In the comparison of the isolates from marine coarl and ambient seawater, more diverse groups belonging to alpha-proteobacteria were preferentially obtained from seawater.

First
Prev
Page of 1
Next
Last

Search