Journal of Microbiology

Journal Articles

Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13: Yunhee Choi , Yong-Hak Kim; J. Microbiol. 2022;60(4):411-418. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2018-y

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Bacillus velezensis strain GH1-13 contains a (2R,3R)-butanediol dehydrogenase (R-BDH) BdhA which converts acetoin to R-BD reversibly, however, little is known about its regulatory cysteine and biological significance. We performed sitedirected mutation of three cysteines in BdhA. The C37S mutant had no enzyme activity and the C34S and C177S mutants differed from each other and wild type (WT). After zinc affinity chromatography, 1 mM ZnCl2 treatment resulted in a 3-fold enhancement of the WT activity, but reduced activity of the C34S mutant by more than 2 folds compared to the untreated ones. However, ZnCl2 treatment did not affect the activity of the C177S mutant. Most of the double and triple mutant proteins (C34S/C37S, C34S/C177S, C37S/C177S, and C34S/C37S/C177S) were aggregated in zinc resins, likely due to the decreased protein stability. All of the purified WT and single mutant proteins increased multiple intermolecular disulfide bonds in the presence of H2O2 as the buffer pH decreased from 7.5 to 5.5, whereas an intramolecular disulfide bond of cysteine 177 and another cysteine in the CGIC motif region was likely formed at pH higher than pKa of 7.5. When pH varied, WT and its C34S or C177S mutants reduced acetoin to R-BD at the optimum pH 5.5 and oxidized R-BD to acetoin at the optimum pH 10. This study demonstrated that cysteine residues in BdhA play a regulatory role for the production of acetoin and R-BD depending on pH as well as metal binding and oxidative stress.

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Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
Bochun Hu, Xiaoqi Xi, Fugang Xiao, Xiaomeng Bai, Yuanyuan Gong, Yifan Li, Xueqin Qiao, Cunduo Tang, Jihong Huang
International Journal of Biological Macromolecules.2024; 281: 136443. CrossRef
Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase
Xiaofei Wang, Lingyun Jia, Fangling Ji
Biochimica et Biophysica Acta (BBA) - General Subjects.2023; 1867(4): 130326. CrossRef
Engineering a BsBDHA substrate-binding pocket entrance for the improvement in catalytic performance toward (R)-phenyl-1,2-ethanediol based on the computer-aided design
Bo-Chun Hu, Meng-Ran Li, Ying-Ying Li, Xin-Shuang Yuan, Yu-Ye Hu, Fu-Gang Xiao
Biochemical Engineering Journal.2023; 194: 108907. CrossRef

Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1: Seong Hyuk Lee , Hwan Youn , Sung Gyun Kang , Hyun Sook Lee; J. Microbiol. 2019;57(2):138-142. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8592-y

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Abstract

Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O2) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O2. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)+ from NAD(P)H. We present a plausible mechanism by which O2 serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O2-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.

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How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Jasmine S Berg, Soeren Ahmerkamp, Petra Pjevac, Bela Hausmann, Jana Milucka, Marcel M M Kuypers
FEMS Microbiology Reviews.2022;[Epub] CrossRef
Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto, Purificación López-García
Nature Communications.2021;[Epub] CrossRef

Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone: Dan Xue , Huai Chen , Xiaolin Luo , Jiuqiang Guan , Yixin He , Xinquan Zhao; J. Microbiol. 2018;56(10):734-743. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8133-0

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Abstract

The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.

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Pengujian Potensi Cairan Omasum Sapi untuk Ketercernaan Tiga Jenis Bahan Organik sebagai Sumber Bioetanol Generasi Ke-2
Endah Dwi Hastuti, Riska Amalia, Munifatul Izzati
Buletin Anatomi dan Fisiologi.2024; 9(1): 75. CrossRef
Effects of Two Feeding Patterns on Growth Performance, Rumen Fermentation Parameters, and Bacterial Community Composition in Yak Calves
Qin Li, Yan Tu, Tao Ma, Kai Cui, Jianxin Zhang, Qiyu Diao, Yanliang Bi
Microorganisms.2023; 11(3): 576. CrossRef
Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks
Yili Liu, Qi Min, Jiao Tang, Lu Yang, Xinxin Meng, Tao Peng, Mingfeng Jiang
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep
Yuqi Li, Jian Gao, Yihan Xue, Ruolin Sun, Xiaoni Sun, Zhanying Sun, Suozhu Liu, Zhankun Tan, Weiyun Zhu, Yanfen Cheng
BMC Microbiology.2023;[Epub] CrossRef
Review: Effect of Experimental Diets on the Microbiome of Productive Animals
Rodrigo Huaiquipán, John Quiñones, Rommy Díaz, Carla Velásquez, Gastón Sepúlveda, Lidiana Velázquez, Erwin A. Paz, Daniela Tapia, David Cancino, Néstor Sepúlveda
Microorganisms.2023; 11(9): 2219. CrossRef
“The Yak”—A remarkable animal living in a harsh environment: An overview of its feeding, growth, production performance, and contribution to food security
Ali Mujtaba Shah, Iqra Bano, Izhar Hyder Qazi, Maharach Matra, Metha Wanapat
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Effects of Two Different Straw Pellets on Yak Growth Performance and Ruminal Microbiota during Cold Season
Xiangyan Wang, Bingang Shi, Zhi Zuo, Youpeng Qi, Shijie Zhao, Xueping Zhang, Lijuan Lan, Yu Shi, Xiu Liu, Shaobin Li, Jiqing Wang, Jiang Hu
Animals.2023; 13(3): 335. CrossRef
Isoacids supplementation improves growth performance and feed fiber digestibility associated with ruminal bacterial community in yaks
Fei Jiang, Yanhua Gao, Zhongli Peng, Xiulian Ma, Yinjie You, Zhibin Hu, Anxiang He, Yupeng Liao
Frontiers in Microbiology.2023;[Epub] CrossRef
Representativeness of Fecal Microbiota Is Limited to Cecum and Colon in Domestic Yak
Wen Qin, Pengfei Song, Jirong Li, Jiuxiang Xie, Shoudong Zhang
Sustainability.2022; 14(16): 10263. CrossRef
Dynamic changes in the yak rumen eukaryotic community and metabolome characteristics in response to feed type
Xiaojing Cui, Yue Liu, Hao Wu, Qingxiang Meng, Shujie Liu, Shatuo Chai, Lizhuang Hao, Zhenming Zhou
Frontiers in Veterinary Science.2022;[Epub] CrossRef
The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau
Xungang Wang, Tianwei Xu, Xiaoling Zhang, Na Zhao, Linyong Hu, Hongjin Liu, Qian Zhang, Yuanyue Geng, Shengping Kang, Shixiao Xu
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Yak Gut Microbiota: A Systematic Review and Meta-Analysis
Yuxin Su, Junhong Su, Fanglin Li, Xiaojing Tian, Zewen Liu, Gongtao Ding, Jialin Bai, Zhuo Li, Zhongren Ma, Maikel P. Peppelenbosch
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon)
Xiaolong Hu, Yuting Wei, Tianxiang Zhang, Xiaoguo Wang, Yongtao Xu, Weiwei Zhang, Yunlin Zheng, Martha Vives
Applied and Environmental Microbiology.2022;[Epub] CrossRef
Comparison of Microbial Community and Metabolites in Four Stomach Compartments of Myostatin-Gene-Edited and Non-edited Cattle
Xinyu Zhou, Mingjuan Gu, Lin Zhu, Di Wu, Miaomiao Yang, Yajie Gao, Xueqiao Wang, Chunling Bai, Zhuying Wei, Lei Yang, Guangpeng Li
Frontiers in Microbiology.2022;[Epub] CrossRef
Effects of trace minerals supply from rumen sustained release boluses on milk yields and components, rumen fermentation and the rumen bacteria in lactating yaks (Bos grunniens)
Z.W. Zhao, Z.Y. Ma, H.C. Wang, C.F. Zhang
Animal Feed Science and Technology.2022; 283: 115184. CrossRef
Characterization of the bacterial microbiota across the different intestinal segments of the Qinghai semi-fine wool sheep on the Qinghai-Tibetan Plateau
Xungang Wang, Linyong Hu, Hongjin Liu, Tianwei Xu, Na Zhao, Xiaoling Zhang, Yuanyue Geng, Shengping Kang, Shixiao Xu
Animal Bioscience.2021; 34(12): 1921. CrossRef
Multi-Omics Analysis Reveals a Dependent Relationship Between Rumen Bacteria and Diet of Grass- and Grain-Fed Yaks
Chenchen Xu, Wenwen Liu, Baozhong Sun, Songshan Zhang, Shou Zhang, Yuanli Yang, Yuanhua Lei, Lan Chang, Peng Xie, Huayi Suo
Frontiers in Microbiology.2021;[Epub] CrossRef
Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China
Xueping Han, Hongjin Liu, Linyong Hu, Na Zhao, Shixiao Xu, Zhijia Lin, Yongwei Chen
Animals.2021; 11(8): 2243. CrossRef
Effects of rumen-protected methionine and lysine supplementation on milk yields and components, rumen fermentation, and the rumen microbiome in lactating yaks (Bos grunniens)
Z.W. Zhao, Z.Y. Ma, H.C. Wang, C.F. Zhang
Animal Feed Science and Technology.2021; 277: 114972. CrossRef
Response of sheep rumen fermentation and microbial communities to feed infected with the endophyte Epichloë gansuensis as evaluated with rumen-simulating technology
Yaling Ma, Hucheng Wang, Chunjie Li
Journal of Microbiology.2021; 59(8): 718. CrossRef
Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers
Naren Gaowa, Kevin Panke-Buisse, Shuxiang Wang, Haibo Wang, Zhijun Cao, Yajing Wang, Kun Yao, Shengli Li
Animals.2020; 10(9): 1712. CrossRef
A Mixed Phytogenic Modulates the Rumen Bacteria Composition and Milk Fatty Acid Profile of Water Buffaloes
Faiz-ul Hassan, Hossam M. Ebeid, Zhenhua Tang, Mengwei Li, Lijuan Peng, Kaiping Peng, Xin Liang, Chengjian Yang
Frontiers in Veterinary Science.2020;[Epub] CrossRef
Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai–Tibetan Plateau
Jian Ma, Yixiao Zhu, Zhisheng Wang, Xiong Yu, Rui Hu, Xueying Wang, Guang Cao, Huawei Zou, Ali Mujtaba Shah, Quanhui Peng, Bai Xue, Lizhi Wang, Suonan Zhao, Xiangying Kong
Frontiers in Microbiology.2020;[Epub] CrossRef
Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen
Qingmiao Ren, Huazhe Si, Xiaoting Yan, Chang Liu, Luming Ding, Ruijun Long, Zhipeng Li, Qiang Qiu
MicrobiologyOpen.2020;[Epub] CrossRef
Interactions Between Rumen Microbes, VFAs, and Host Genes Regulate Nutrient Absorption and Epithelial Barrier Function During Cold Season Nutritional Stress in Tibetan Sheep
Xiu Liu, Yuzhu Sha, Renqing Dingkao, Wei Zhang, Weibing Lv, Hong Wei, Hao Shi, Jiang Hu, Jiqing Wang, Shaobin Li, Zhiyun Hao, Yuzhu Luo
Frontiers in Microbiology.2020;[Epub] CrossRef
Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau
Li Ma, Shixiao Xu, Hongjin Liu, Tianwei Xu, Linyong Hu, Na Zhao, Xueping Han, Xiaoling Zhang
PeerJ.2019; 7: e7645. CrossRef
Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau
Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Jincheng Zhong, Qiumei Ji
Frontiers in Microbiology.2019;[Epub] CrossRef
Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type
Chang Liu, Hao Wu, Shujie Liu, Shatuo Chai, Qingxiang Meng, Zhenming Zhou
Frontiers in Microbiology.2019;[Epub] CrossRef

Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea: Jin-Woo Lee , Kae Kyoung Kwon , Jang-Jun Bahk , Dong-Hun Lee , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee; J. Microbiol. 2016;54(12):814-822. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6379-y

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Abstract

We have previously identified a sulfate methane transition zone (SMTZ) within the methane hydrate-bearing sediment in the Ulleung Basin, East Sea of Korea, and the presence of ANME-1b group in the sediment has been shown by phylogenetic analysis of a 16S rRNA gene. Herein, we describe taxonomic and functional profiling in the SMTZ sample by metagenomic analysis, comparing with that of surface sediment. Metagenomic sequences of 115 Mbp and 252 Mbp were obtained from SMTZ and surface sediments, respectively. The taxonomic profiling using BLASTX against the SEED within MG-RAST showed the prevalence of methanogens (19.1%), such as Methanosarcinales (12.0%) and Methanomicrobiales (4.1%) predominated within the SMTZ metagenome. A number of 185,200 SMTZ reads (38.9%) and 438,484 surface reads (62.5%) were assigned to functional categories, and methanogenesis-related reads were statistically significantly overrepresented in the SMTZ metagenome. However, the mapping analysis of metagenome reads to the reference genomes, most of the sequences of the SMTZ metagenome were mapped to ANME-1 draft genomes, rather than those of methanogens. Furthermore, the two copies of the methyl-coenzyme M reductase gene (mcrA) segments of the SMTZ metagenome were clustered with ANME-1b in the phylogenetic cluster. These results indicate that ANME- 1b reads were miss-annotated to methanogens due to limitation of database. Many of key genes necessary for reverse methanogenesis were present in the SMTZ metagenome, except for N5,N10-methenyl-H4MPT reductase (mer) and CoBCoM heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary player the anaerobic methane oxidation in the SMTZ, of the methane hydrate-bearing sediment at the Ulleung Basin, East Sea of Korea.

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Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough
Youzhi Xin, Nengyou Wu, Zhilei Sun, Hongmei Wang, Ye Chen, Cuiling Xu, Wei Geng, Hong Cao, Xilin Zhang, Bin Zhai, Dawei Yan
Science of The Total Environment.2022; 851: 158213. CrossRef
Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments
Anna J. Wallenius, Paula Dalcin Martins, Caroline P. Slomp, Mike S. M. Jetten
Frontiers in Microbiology.2021;[Epub] CrossRef
Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling
Yi Yang, Robert Sanford, Jun Yan, Gao Chen, Natalie L. Cápiro, Xiuying Li, Frank E. Löffler, Nick Bouskill
mSystems.2020;[Epub] CrossRef
Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico
Santiago Cadena, M. Leopoldina Aguirre-Macedo, Daniel Cerqueda-García, Francisco J. Cervantes, Jorge A. Herrera-Silveira, José Q. García-Maldonado
Estuarine, Coastal and Shelf Science.2019; 230: 106433. CrossRef

Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits: Brigita Nograsek , Tomaz Accetto , Lijana Fanedl , Gorazd Avgustin; J. Microbiol. 2015;53(8):503-510. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5142-0

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Abstract

Five strictly anaerobic Gram-negative bacterial strains, P4-65, P4-76T, P5-60, P5-119, and P5-125, presumably belonging to the genus Prevotella were isolated from pig fecal samples. Strains were tested for various phenotypic traits and nearcomplete genome sequences were obtained and analyzed. Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis based on five conserved genes confirmed that the strains belong to the genus Prevotella, revealing that they represent a novel and discrete lineage distinct from other known species of this genus. The size of the genome of the isolated strains is 3?.3 Mbp, and the DNA G+C content is 47.5?8.1 mol%. The isolates are strictly anaerobic, rod-shaped with rounded ends, non-motile and non-spore-forming. The main fermentation products are succinate and acetate, with minor concentrations of isovalerate, propionate and isobutyrate. Hydrogen is also produced. Major cellular fatty acids consist of anteiso-C15:0 and iso-C15:0, and a number of additional acids are present in lower concentrations. A substantial portion of genes involved in carbohydrate utilization is devoted to pectin degradation and utilization, while those supporting growth on xylan in ruminal Prevotella could not have been revealed. On the basis of the presented results, a novel species, Prevotella pectinovora sp. nov. is proposed. The type strain is P4-76T (=DSM 29996T =ZIM B1020T).

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Sathya Sujani, Claire B Gleason, Barbara R dos Reis, Robin R White
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Changes in Gene Expression of Actinobacillus pleuropneumoniae in Response to Anaerobic Stress Reveal Induction of Central Metabolism and Biofilm Formation: Lu Li , Jiawen Zhu , Kui Yang , Zhuofei Xu , Ziduo Liu , Rui Zhou; J. Microbiol. 2014;52(6):473-481. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3456-y

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Abstract

Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry worldwide. Oxygen deprivation is a stress that A. pleuropneumoniae will encounter during both early infection and the later, persistent stage. To understand modulation of A. pleuropneumoniae gene expression in response to the stress caused by anaerobic conditions, gene expression profiles under anaerobic and aerobic conditions were compared in this study. The microarray results showed that 631 genes (27.7% of the total ORFs) were differentially expressed in anaerobic conditions. Many genes encoding proteins involved in glycolysis, carbon source uptake systems, pyruvate metabolism, fermentation and the electron respiration transport chain were up-regulated. These changes led to an increased amount of pyruvate, lactate, ethanol and acetate in the bacterial cells as confirmed by metabolite detection. Genes encoding proteins involved in cell surface structures, especially biofilm formation, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis were up-regulated as well. Biofilm formation was significantly enhanced under anaerobic conditions. These results indicate that induction of central metabolism is important for basic survival of A. pleuropneumoniae after a shift to an anaerobic environment. Enhanced biofilm formation may contribute to the persistence of this pathogen in the damaged anaerobic host tissue and also in the early colonization stage. These discoveries give new insights into adaptation mechanisms of A. pleuropneumoniae in response to environmental stress.

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PLOS ONE.2016; 11(3): e0152363. CrossRef
Regulation of Escherichia coli RNase III activity
Boram Lim, Minji Sim, Howoon Lee, Seogang Hyun, Younghoon Lee, Yoonsoo Hahn, Eunkyoung Shin, Kangseok Lee
Journal of Microbiology.2015; 53(8): 487. CrossRef
Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae
Louise Brogaard, Kirstine Klitgaard, Peter MH Heegaard, Mette Sif Hansen, Tim Kåre Jensen, Kerstin Skovgaard
BMC Genomics.2015;[Epub] CrossRef
Identification and characterization of a novel stress-responsive outer membrane protein Lip40 from Actinobacillus pleuropneumoniae
Xuehe Hu, Hao Yan, Ke Liu, Jiansheng Hu, Chao Qi, Jihong Yang, Yanli Liu, Jin Zhao, Jinlin Liu
BMC Biotechnology.2015;[Epub] CrossRef
Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes
Maksim Shestov, Santiago Ontañón, Aydin Tozeren
BMC Genomics.2015;[Epub] CrossRef

Paenibacillus xylaniclasticus sp. nov., a Xylanolytic-Cellulolytic Bacterium Isolated from Sludge in an Anaerobic Digester: Chakrit Tachaapaikoon , Somboon Tanasupawat , Patthra Pason , Somphit Sornyotha , Rattiya Waeonukul , Khin Lay Kyu , Khanok Ratanakhanokchai; J. Microbiol. 2012;50(3):394-400. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1480-3

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Abstract: A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1T, was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C15:0, iso-C16:0, anteiso-C17:0, and C16:0 were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1T belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1T were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1T should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1T (=NBRC 106381T =KCTC 13719T =TISTR 1914T).

Journal Articles

Effects of Nicotine on the Growth and Protein Expression of Porphyromonas gingivalis: Orson Baek , Weidong Zhu , Hyeong C. Kim Kim , Seok-Woo Lee Lee; J. Microbiol. 2012;50(1):143-148. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1212-8

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Abstract: Tobacco smoking is considered one of the most significant environmental risk factors for destructive periodontal disease. The effect of smoking on periodontopathic microbiota has not yet been elucidated, as previous studies failed to identify a concrete relationship between periodontopathic microorganisms and smoking. However, it is likely that smoking, as an environmental stress factor, may affect the behavior of dental plaque microorganisms, ultimately leading to alteration of the host-parasite interaction. The goal of this study was to examine the effect of nicotine, a major component of tobacco, on the growth and protein expression of the crucial periodontal pathogen Porphyromonas gingivalis. The growth of P. gingivalis 381 was measured after bacterial cells were cultivated in liquid broth containing various nicotine concentrations. First, P. gingivalis cells were allowed to grow in the presence of a single dose of nicotine (the single exposure protocol) at 0, 1, 2, 4, and 8 mg/L, respectively. Second, P. gingivalis cells were exposed to five consecutive doses of nicotine (the multiple exposure protocol) at 0, 1, 2, and 4 mg/L, respectively. Bacterial growth was measured by optical density and protein expression was analyzed by SDS-PAGE and 2-D gel electrophoresis. In the single nicotine exposure protocol, it was observed that the growth of P. gingivalis 381 was inhibited by nicotine in a dose-dependent manner. In the multiple nicotine exposure protocol, the growth rate of P. gingivalis increased with each subsequent nicotine exposure, even though bacterial growth was also inhibited in a dose dependent fashion. SDS-PAGE and 2-D gel electrophoresis analyses revealed a minor change in the pattern of protein expression, showing differences in proteins with low molecular weights (around 20 kDa) on exposure to nicotine. The results of this study suggest that nicotine exerts an inhibitory effect on the growth of P. gingivalis, and has a potential to modulate protein expression in P. gingivalis.

Monitoring Nutrient Impact on Bacterial Community Composition during Bioremediation of Anoxic PAH-Contaminated Sediment: Myungsu Kim , Seung Seob Bae , Mijin Seol , Jung-Hyun Lee , Young-Sook Oh; J. Microbiol. 2008;46(6):615-623. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0097-z

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Abstract

Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

Citations

Citations to this article as recorded by

Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments
Qingguo Chen, Zhenzhen Li, Yu Chen, Mei Liu, Qiao Yang, Baikang Zhu, Jun Mu, Lijuan Feng, Zhi Chen
Marine Pollution Bulletin.2024; 199: 115925. CrossRef
Electrical current generation from a continuous flow macrophyte biocathode sediment microbial fuel cell (mSMFC) during the degradation of pollutants in urban river sediment
Felix Tetteh Kabutey, Jing Ding, Qingliang Zhao, Philip Antwi, Frank Koblah Quashie
Environmental Science and Pollution Research.2020; 27(28): 35364. CrossRef
Application of in situ Solid-Phase Microextraction on Mediterranean Sponges for Untargeted Exometabolome Screening and Environmental Monitoring
Barbara Bojko, Bora Onat, Ezel Boyaci, Eleftheria Psillakis, Thanos Dailianis, Janusz Pawliszyn
Frontiers in Marine Science.2019;[Epub] CrossRef
Effect of carbonyl cyanide m-chlorophenylhydrazone (CCCP) on microbial activity and polycyclic aromatic hydrocarbons (PAH) degradation in contaminated river sediments
G. Patricia Johnston, Z. Kalik, C. G. Johnston
Environmental Earth Sciences.2016;[Epub] CrossRef
Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil
Przemyslaw Sawulski, Nicholas Clipson, Evelyn Doyle
Biodegradation.2014; 25(6): 835. CrossRef
Anthracene biodegradation under nitrate-reducing condition and associated microbial community changes
Ying Wang, Rui Wan, Shuying Zhang, Shuguang Xie
Biotechnology and Bioprocess Engineering.2012; 17(2): 371. CrossRef
Molecular characterization of phenanthrene-degrading methanogenic communities in leachate-contaminated aquifer sediment
S. Y. Zhang, Q. F. Wang, S. G. Xie
International Journal of Environmental Science and Technology.2012; 9(4): 705. CrossRef
Increment in Anaerobic Hydrocarbon Degradation Activity of Halic Bay Sediments via Nutrient Amendment
Mustafa Kolukirik, Orhan Ince, Bahar K. Ince
Microbial Ecology.2011; 61(4): 871. CrossRef
Revealing archaeal diversity patterns and methane fluxes in Admiralty Bay, King George Island, and their association to Brazilian Antarctic Station activities
C.R. Nakayama, E. Kuhn, A.C.V. Araújo, P.C. Alvalá, W.J. Ferreira, R.F. Vazoller, V.H. Pellizari
Deep Sea Research Part II: Topical Studies in Oceanography.2011; 58(1-2): 128. CrossRef
Bioremediation of marine sediments contaminated by hydrocarbons: Experimental analysis and kinetic modeling
Francesca Beolchini, Laura Rocchetti, Francesco Regoli, Antonio Dell’Anno
Journal of Hazardous Materials.2010; 182(1-3): 403. CrossRef

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

Effects of Sulfate Concentration on the Anaerobic Dechlorination of Polychlorinated Biphenyls in Estuarine Sediments: Young-Cheol Cho , Kyoung-Hee Oh; J. Microbiol. 2005;43(2):166-171.; DOI: https://doi.org/2167 [pii]

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Abstract: In order to determine the effects of sulfate concentration on the anaerobic dechlorination of polychlorinated biphenyls, sediments spiked with Aroclor 1242 were made into slurries using media which had various sulfate concentrations ranging from 3 to 23 mM. The time course of dechlorination clearly demonstrated that dechlorination was inhibited at high concentration of sulfate due to less dechlorination of meta-substituted congeners. When the dechlorination patterns were analyzed by the calculation of Euclidean distance, the dechlorination pathway in the 3 mM sulfate samples was found to be different from that observed in the 13 mM samples, although the extent of dechlorination in these two samples was similar. It is possible that the dechlorination in the high sulfate concentration samples is inhibited by the suppression of growth of methanogen, which have been shown to be meta-dechlorinating microorganisms.

Development of a Bottle-Free Multipurpose Incubator for Generating Various Bacterial Culture Conditions: Nam Woong Yang , Yong Lim; J. Microbiol. 2005;43(1):28-33.; DOI: https://doi.org/2142 [pii]

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Abstract: The purpose of this study was to develop a multipurpose incubator, without the gas cylinders (bottles) which are required for H_2 and CO_2 supplementation. In our bottle-free multipurpose incubator, the H_2 and CO_2 were generated by chemical reactions induced within the chamber. The reaction between sodium borohydride and acetic acid at a molar ratio of 1:1 was used to generate H_2, according to the following formula: 4NaBH_4 + 2CH_3COOH + 7H_2O → 2CH_3COONa + Na_2B_4O_7 + 16H_2, whereas the other reaction, citric acid and sodium bicarbonate at a 1:1 molar ratio, was used to generate CO_2, according to the following formula: C_6H_8O_7 + 3NaHCO_3 → Na_3(C_6H_5O_7) + 3H_2O + 3CO_2. Five species of obligate anaerobic bacteria, one strain of capnophilic bacterium, and one strain of microaerophilic bacterium were successfully cultured in the presence of their respective suitable conditions, all of which were successfully generated by our bottle-free multipurpose incubator. We conclude that, due to its greater safety, versatility, and significantly lower operating costs, this bottle-free multipurpose incubator can be used for the production of fastidious bacterial cultures, and constitutes a favorable step above existing anaerobic incubators. <br>

The effect of oxygen on NAD breakdown in Salmonella typhimurium: Park , Uhnmee; J. Microbiol. 1995;33(3):234-238.

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Abstract: The breakdown rate of NAD in Salmonella typhimurium was investigated both in aerobic and anaerobic conditions. After NAD is broken down to nicotinamide ring containing moiety, almost all the nicotinamide ring containing moiety recycles back to NAD pool. However almost none of the adenine containing moiety recycles back. We pulse-label the endogeneous NAD with [¹⁴C]-adenine and [³H]- niacin. The remaining [¹⁴C]-radioactivity in NAD pool at each time was regarded as unbroken portion of NAD, Where ad that of [³H] was served as a total amount of NAD to start with. Under aerobic condition, the half-life of NAD was around 2 hours. However, the breakdown rate was significantly reduced (around 3-5 fold) under anaerobic condition. The observation that under aerobic conditions, NAD turnover is considerably faster than under anaerobic conditions suggests that oxygen has important effect in NAD breakdown.

Growth Properties of the Iron-reducing Bacteria, Shewanella putrefaciens IR-1 and MR-1 Coupling to Reduction of Fe(III) to Fe(II): Doo Hyun Park , Byung Hong Kim; J. Microbiol. 2001;39(4):273-278.

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Abstract: Shewanella putrefaciens IR-1 and MR-1 were cultivated by using various combinations of electron donor-acceptor, lactate-Fe(III), lactate-nitrate, pyruvate-Fe(III), pyruvate-nitrate, H_2 -acetate-Fe(III) and H_2 -acetate-nitrate. Both strains grew fermentatively on pyruvate but not on lactate without an electron acceptor. In culture with Fe(III), both strains grew on pyruvate and lactate but not on H_2 -acetate-CO_2 . In cultivation with nitrate, both strains grew on pyruvate, lactate and on H_2 -acetate-CO_2 . The growth yields of IR-1 on pyruvate, pyruvate-Fe(III) and lactate-Fe(III) were about 3.4, 3.5, and 3.6 (g cell/M substrate), respectively, but the yields on lactate-nitrate, pyruvate-nitrate and H_2 -acetate-CO_2 ?trate were about 6.8, 5.9, and 9.4 (g cell/M substrate), respectively. From the growth properties of both strains on media with Fe(III) as an electron acceptor, the bacterial growth was confirmed not to be increased by addition of Fe(III) as an electron acceptor to the growth medium, which indicates a possibility that the dissimilatory reduction of Fe(III) to Fe(II) may not be coupled to free energy production.

Transformations of 2,4,6-Trinitrotoluene in Various Conditions by Klebsiella sp. Strain C1 Isolated from Activated Sludge: Chong-Suk Chang , Hyoun-Young Kim , Yang-Mi Kang , Kyung Sook Bae , Hong-Gyu Song; J. Microbiol. 2002;40(3):193-198.

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Abstract: Several 2,4,6-Trinitrotoluene (TNT) degrading bacteria were isolated from an activated sludge by an enrichment culture technique, and their TNT removal activities were examined. Among the isolates, strain C1 showed the highest degrading capability, and completely removed 100 or 200 mg l^-1 of TNT within 6 hours of incubation. This bacterium was identified as Klebsiella sp. The effects of different carbon sources on the removal of the parent TNT by Klebsiella sp. C1 were negligible, but the transformation rates of TNT metabolites such as amino-dinitrotoluenes and diamino-nitrotoluenes were higher with fructose addition compared to glucose addition. When nitrate was used as the nitrogen source, the degradation rates of TNT and hydroxylamino-dinitrotoluenes were higher than those with the ammonium addition. Although the TNT removal rate of Klebsiella sp. C1 was slightly higher in anaerobic conditions, the further transformations of TNT metabolites were more favorable in aerobic conditions.

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