Journal of Microbiology

Journal Articles

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

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First Case of Respiratory Infection in Rabbits Caused by Alcaligenes faecalis in Romania
Vlad Iorgoni, Ionica Iancu, Ionela Popa, Alexandru Gligor, Gabriel Orghici, Bogdan Sicoe, Corina Badea, Cristian Dreghiciu, Călin Pop, Timea Bochiș, Janos Degi, Luminita Costinar, Corina Pascu, Viorel Herman
Veterinary Sciences.2025; 12(1): 33. CrossRef

Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense: Keita Saito , Keiichiro Mukai , Issara Kaweewan , Hiroyuki Nakagawa , Takeshi Hosaka , Shinya Kodani; J. Microbiol. 2023;61(6):641-648. Published online June 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00059-z

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Abstract

Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.

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Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins
Issara Kaweewan, Keiichiro Mukai, Pratchaya Rukthanapitak, Hiroyuki Nakagawa, Takeshi Hosaka, Shinya Kodani
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef
Facile Method for Determining Lanthipeptide Stereochemistry
Youran Luo, Shuyun Xu, Autumn M. Frerk, Wilfred A. van der Donk
Analytical Chemistry.2024; 96(4): 1767. CrossRef
Antimicrobial Peptides Derived from Bacteria: Classification, Sources, and Mechanism of Action against Multidrug-Resistant Bacteria
Raynichka Mihaylova-Garnizova, Slavena Davidova, Yordan Hodzhev, Galina Satchanska
International Journal of Molecular Sciences.2024; 25(19): 10788. CrossRef

[PROTOCOL]Analyzing viral epitranscriptomes using nanopore direct RNA sequencing: Ari Hong , Dongwan Kim , V. Narry Kim , Hyeshik Chang; J. Microbiol. 2022;60(9):867-876. Published online August 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2324-4

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Abstract

RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N6- methyladenosine, have also been found in viral transcripts and viral RNA genomes. Some of the modifications increase the viral replication efficiency while also helping the virus to evade the host immune system. Nonetheless, there are numerous examples in which the host's RNA modification enzymes function as antiviral factors. Although established methods like MeRIP-seq and miCLIP can provide a transcriptome- wide overview of how viral RNA is modified, it is difficult to distinguish between the complex overlapping viral transcript isoforms using the short read-based techniques. Nanopore direct RNA sequencing (DRS) provides both long reads and direct signal readings, which may carry information about the modifications. Here, we describe a refined protocol for analyzing the RNA modifications in viral transcriptomes using nanopore technology.

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Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications
Lu Tan, Zhihao Guo, Xiaoming Wang, Dal Young Kim, Runsheng Li, Pedro H. Oliveira
mSystems.2024;[Epub] CrossRef
Current progress in strategies to profile transcriptomic m6A modifications
Yuening Yang, Yanming Lu, Yan Wang, Xianghui Wen, Changhai Qi, Weilan Piao, Hua Jin
Frontiers in Cell and Developmental Biology.2024;[Epub] CrossRef
Improved sub-genomic RNA prediction with the ARTIC protocol
Thomas Baudeau, Kristoffer Sahlin
Nucleic Acids Research.2024; 52(17): e82. CrossRef
Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases
Stephen Spatz, Claudio L. Afonso
Veterinary Sciences.2024; 11(6): 239. CrossRef
Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data
Shenglun Chen, Jia Meng, Yuxin Zhang
Methods.2024; 228: 30. CrossRef
Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis
Caroline A. McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N. Klink, Miten Jain, Sara H. Rouhanifard
Gigabyte.2024; 2024: 1. CrossRef
Dissecting the effects of METTL3 on alternative splicing in prostate cancer
Lin Wang, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, Yiwei Wang, Cathy Sin-Hang Fung, Peter Ka-Fung Chiu, Chi-Fai Ng, Stephen Kwok-Wing Tsui
Frontiers in Oncology.2023;[Epub] CrossRef

Review

Application of computational approaches to analyze metagenomic data: Ho-Jin Gwak , Seung Jae Lee , Mina Rho; J. Microbiol. 2021;59(3):233-241. Published online February 10, 2021; DOI: https://doi.org/10.1007/s12275-021-0632-8

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Abstract

Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of nextgeneration sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational
methods
that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.

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A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data
Arunmozhi Bharathi Achudhan, Priya Kannan, Annapurna Gupta, Lilly M. Saleena
Biochemical Genetics.2024; 62(2): 621. CrossRef
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities
Alexander Van Uffelen, Andrés Posadas, Nancy H. C. Roosens, Kathleen Marchal, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Scientific Data.2024;[Epub] CrossRef
Metagenomic approaches and opportunities in arid soil research
Muhammad Riaz Ejaz, Kareem Badr, Zahoor Ul Hassan, Roda Al-Thani, Samir Jaoua
Science of The Total Environment.2024; 953: 176173. CrossRef
DeepCheck: multitask learning aids in assessing microbial genome quality
Guo Wei, Nannan Wu, Kunyang Zhao, Sihai Yang, Long Wang, Yan Liu
Briefings in Bioinformatics.2024;[Epub] CrossRef
Integrated multi-omics analyses of microbial communities: a review of the current state and future directions
Muzaffer Arıkan, Thilo Muth
Molecular Omics.2023; 19(8): 607. CrossRef
Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
Juan José González-Plaza, Cristina Furlan, Tomaž Rijavec, Aleš Lapanje, Rocío Barros, Juan Antonio Tamayo-Ramos, Maria Suarez-Diez
Frontiers in Microbiology.2022;[Epub] CrossRef
Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests
Sylvie Buffet-Bataillon, Guillaume Rizk, Vincent Cattoir, Mohamed Sassi, Vincent Thibault, Jennifer Del Giudice, Jean-Pierre Gangneux
Microorganisms.2022; 10(4): 711. CrossRef
Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms
Feng Chen, Xianjin Wang, Guiping Qiu, Haida Liu, Yingquan Tan, Beijiu Cheng, Guomin Han
International Journal of Molecular Sciences.2022; 23(22): 14223. CrossRef
Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease
Alba Boix-Amorós, Hilary Monaco, Elisa Sambataro, Jose C. Clemente
Gut Microbes.2022;[Epub] CrossRef
Current Understanding on the Genetic Basis of Key Metabolic Disorders: A Review
Kenneth Francis Rodrigues, Wilson Thau Lym Yong, Md. Safiul Alam Bhuiyan, Shafiquzzaman Siddiquee, Muhammad Dawood Shah, Balu Alagar Venmathi Maran
Biology.2022; 11(9): 1308. CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef

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

Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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Abstract

The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

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Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield
Qiushuang Li, Zhiyuan Ma, Jiabin Huo, Xiumin Zhang, Rong Wang, Shizhe Zhang, Jinzhen Jiao, Xiyang Dong, Peter H Janssen, Emilio M Ungerfeld, Chris Greening, Zhiliang Tan, Min Wang
The ISME Journal.2024;[Epub] CrossRef
The Effect of Direct-Fed Microbials on In-Vitro Rumen Fermentation of Grass or Maize Silage
Rajan Dhakal, Giuseppe Copani, Bruno Ieda Cappellozza, Nina Milora, Hanne Helene Hansen
Fermentation.2023; 9(4): 347. CrossRef
Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?
Ana Margarida Pereira, Maria de Lurdes Nunes Enes Dapkevicius, Alfredo E. S. Borba
Animal Microbiome.2022;[Epub] CrossRef
Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization
Jing Ma, Pei Zhong, Yuqi Li, Zhanying Sun, Xiaoni Sun, Min Aung, Lizhuang Hao, Yanfen Cheng, Weiyun Zhu
Journal of Fungi.2022; 8(4): 338. CrossRef
Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows
Keith W. Savin, Peter J. Moate, S. R. O. Williams, Carolyn Bath, Joanne Hemsworth, Jianghui Wang, Doris Ram, Jody Zawadzki, Simone Rochfort, Benjamin G. Cocks, James E. Wells
PLOS ONE.2022; 17(5): e0268157. CrossRef
Effect of Autochthonous Nepalese Fruits on Nutrient Degradation, Fermentation Kinetics, Total Gas Production, and Methane Production in In-Vitro Rumen Fermentation
Rajan Dhakal, Manuel Gonzalez Ronquillo, Einar Vargas-Bello-Pérez, Hanne Helene Hansen
Animals.2022; 12(17): 2199. CrossRef
Reducing Enteric Methanogenesis through Alternate Hydrogen Sinks in the Rumen
Prasanta Kumar Choudhury, Rajashree Jena, Sudhir Kumar Tomar, Anil Kumar Puniya
Methane.2022; 1(4): 320. CrossRef
Methane Emissions Regulated by Microbial Community Response to the Addition of Monensin and Fumarate in Different Substrates
Dan Xue, Huai Chen, Xiaolin Luo
Applied Sciences.2021; 11(14): 6282. CrossRef
Different milk replacers alter growth performance and rumen bacterial diversity of dairy bull calves
Yangdong Zhang, Jing Cheng, Nan Zheng, Yuanqing Zhang, Di Jin
Livestock Science.2020; 231: 103862. CrossRef
Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions
Emilio M. Ungerfeld
Frontiers in Microbiology.2020;[Epub] CrossRef
Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation
Lovelia L. Mamuad, Seon Ho Kim, Ashraf A. Biswas, Zhongtang Yu, Kwang-Keun Cho, Sang-Bum Kim, Kichoon Lee, Sang Suk Lee
AMB Express.2019;[Epub] CrossRef
Advanced estimation and mitigation strategies: a cumulative approach to enteric methane abatement from ruminants
Mahfuzul Islam, Sang-Suk Lee
Journal of Animal Science and Technology.2019; 61(3): 122. CrossRef
Recent insight and future techniques to enhance rumen fermentation in dairy goats
Lovelia L. Mamuad, Sung Sill Lee, Sang Suk Lee
Asian-Australasian Journal of Animal Sciences.2019; 32(8): 1321. CrossRef
Effects of illite supplementation on in vitro and in vivo rumen fermentation, microbial population and methane emission of Hanwoo steers fed high concentrate diets
Ashraf A. Biswas, Sung‐Sill Lee, Lovelia L. Mamuad, Seon‐Ho Kim, Yeon‐Jae Choi, Chanhee Lee, Kichoon Lee, Gui‐Seck Bae, Sang‐Suk Lee
Animal Science Journal.2018; 89(1): 114. CrossRef
Effect of different concentrate diet levels on rumen fluid inoculum used for determination of in vitro rumen fermentation, methane concentration, and methanogen abundance and diversity
Seon-Ho Kim, Lovelia L. Mamuad, Eun-Joong Kim, Ha-Guyn Sung, Gui-Seck Bae, Kwang-Keun Cho, Chanhee Lee, Sang-Suk Lee
Italian Journal of Animal Science.2018; 17(2): 359. CrossRef
Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review
P Chellapandi, M Bharathi, C Sangavai, R Prathiviraj
Veterinary and Animal Science.2018; 6: 86. CrossRef
Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau
Dan Xue, Huai Chen, Xinquan Zhao, Shixiao Xu, Linyong Hu, Tianwei Xu, Lin Jiang, Wei Zhan
Systematic and Applied Microbiology.2017; 40(4): 227. CrossRef
Increased propionate concentration inLactobacillus mucosae-fermented wet brewers grains and duringin vitrorumen fermentation
L.L. Mamuad, S.H. Kim, Y.J. Choi, A.P. Soriano, K.K. Cho, K. Lee, G.S. Bae, S.S. Lee
Journal of Applied Microbiology.2017; 123(1): 29. CrossRef
Use of Lysozyme as a Feed Additive on In vitro Rumen Fermentation and Methane Emission
Ashraf A. Biswas, Sung Sill Lee, Lovelia L. Mamuad, Seon-Ho Kim, Yeon-Jae Choi, Gui-Seck Bae, Kichoon Lee, Ha-Guyn Sung, Sang-Suk Lee
Asian-Australasian Journal of Animal Sciences.2016; 29(11): 1601. CrossRef
Quantification of organic acids in ruminal in vitro batch culture fermentation supplemented with fumarate using a herb mix as a substrate
J. Pisarčíková, Z. Váradyová, K. Mihaliková, S. Kišidayová, J. Plaizier
Canadian Journal of Animal Science.2016; 96(1): 60. CrossRef
Rumen fermentation and performance of Hanwoo steers fed total mixed ration with Korean rice wine residue
Chang-Dae Jeong, Lovelia L. Mamuad, Jong Youl Ko, Ha Guyn Sung, Keun Kyu Park, Yoo Kyung Lee, Sang-Suk Lee
Journal of Animal Science and Technology.2016;[Epub] CrossRef
Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation
Emilio M. Ungerfeld
Frontiers in Microbiology.2015;[Epub] CrossRef
Effect of Soybean Meal and Soluble Starch on Biogenic Amine Production and Microbial Diversity Using In vitro Rumen Fermentation
Chang-Dae Jeong, Lovelia L. Mamuad, Seon-Ho Kim, Yeon Jae Choi, Alvin P. Soriano, Kwang Keun Cho, Che-Ok Jeon, Sung Sil Lee, Sang-Suk Lee
Asian-Australasian Journal of Animal Sciences.2014; 28(1): 50. CrossRef

Isolation and Identification of an Anticancer Drug, Taxol from Phyllosticta tabernaemontanae, a Leaf Spot Fungus of an Angiosperm, Wrightia tinctoria: Rangarajulu Senthil Kumaran , Johnpaul Muthumary , Byung-Ki Hur; J. Microbiol. 2009;47(1):40-49. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0127-x

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Abstract: Phyllosticta tabernaemontanae, a leaf spot fungus isolated from the diseased leaves of Wrightia tinctoria, showed the production of taxol, an anticancer drug, on modified liquid medium (M1D) and potato dextrose broth (PDB) medium in culture for the first time. The presence of taxol was confirmed by spectroscopic and chromatographic methods of analysis. The amount of taxol produced by this fungus was quantified using high performance liquid chromatography (HPLC). The maximum amount of taxol production was recorded in the fungus grown on M1D medium (461 ug/L) followed by PDB medium (150 ug/L). The production rate was increased to 9.2x103 fold than that found in the culture broth of earlier reported fungus, Taxomyces andreanae. The results designate that P. tabernaemontanae is an excellent candidate for taxol production. The fungal taxol extracted also showed a strong cytotoxic activity in the in vitro culture of tested human cancer cells by apoptotic assay.

Generation of Infectious Transcripts from Korean Strain and Mild Mottle Strain of Potato Virus X: Sun Hee Choi , Ki Hyun Ryu; J. Microbiol. 2008;46(5):502-507. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0078-2

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Abstract: Full-length cDNAs of two different strains of Potato virus X (PVX-Kr and PVX-Mo) have been directly amplified by long template reverse transcription polymerase chain reaction (RT-PCR) using the 5’-end primer containing a SP6 or T7 RNA promoter sequence and the virus-specific 3’-end primer, and then constructed in plasmid vectors. Capped in vitro transcripts from cloned full-length cDNAs as well as those RTPCR amplicons proved to be infectious systemically on tobacco plants. Symptom expression on tobacco plants from PVX-Mo transcripts was faster and severer than that from PVX-Kr. In replication stability test of transcripts derived from PVX clones, progeny viruses showed stable replication according to sequencing through passages. This highly infectious transcript system from the full-length cDNA clones for PVX can be useful for recombinant molecules for functional analysis of viral proteins in plant-virus interaction study as well as for expression of foreign protein in planta.

Factors Influencing Preferential Utilization of RNA Polymerase Containing Sigma-38 in Stationary-Phase Gene Expression in Escherichia coli: Eun Young Kim , Min-Sang Shin , Joon Haeng Rhee , Hyon E. Choy; J. Microbiol. 2004;42(2):103-110.; DOI: https://doi.org/2037 [pii]

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Abstract: In order to understand the molecular basis of selective expression of stationary-phase genes by RNA polymerase containing [sigma]^38 (E[sigma]^38) in Escherichia coli, we examined transcription from the stationaryphase promoters, katEP, bolAP, hdeABP, csgBAP, and mcbP, in vivo and in vitro. Although these promoters are preferentially recognized in vivo by E[sigma]^38, they are transcribed in vitro by both E[sigma]^38 and E[sigma]^70 containing the major exponential [sigma], [sigma]^70. In the presence of high concentrations of glutamate salts, however, only E[sigma]^38 was able to efficiently transcribe from these promoters, which supports the concept that the promoter selectivity of [sigma]^38 -containing RNA polymerase is observed only under specific reaction conditions. The examination of 6S RNA, which is encoded by the ssr1 gene in vivo, showed that it reduced E[sigma]^70 activity during the stationary phase, but this reduction of activity did not result in the elevation of E[sigma]^38 activity. Thus, the preferential expression of stationary-phase genes by E[sigma]^38 is unlikely the consequence of selective inhibition of E[sigma]^70 by 6S RNA.

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; J. Microbiol. 2021;59(8):719-728.; DOI: https://doi.org/10.1007/s12275-021-1113-9

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Abstract

Achnatherum inebrians, a perennial grass, is widely distributed in China. When infected by the endophyte Epichloë gansuensis, A. inebrians produces an abundance of alkaloids that enhance plant survival but are toxic to animals. Here we used in vitro fermentation to study the impact of endophyte- infected A. inebrians (E+) addition on rumen fermentation characteristics and on microbial community and diversity as assessed with amplicon sequencing technology. We examined E+ addition at five levels, E0, E25, E50, E75, and E100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Both the fermentation characteristics and rumen microbial community structure differed significantly among treatments. E100 resulted in the highest values for pH, the Shannon index, Kiritimatiellaeota, and Lentisphaerae levels relative to the other treatments. In contrast, E25 was associated with higher levels of ammonia nitrogen, total volatile fatty acid, propionate, butyrate, isobutyrate, valerate, of the phyla Bacteroidetes and Firmicutes, and of the genus Prevotella_1, Succiniclasticum, Family_XIII_AD3011_group, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-001, and Pyramidobacter as compared with other treatments. E50 resulted in the greatest values for the abundance-based coverage estimator (ACE) and the Chao1 index as compared with other treatments. E0 resulted in the greatest values for digestibility of dry matter, gas production, acetate, and Ruminobacter as compared with other treatments. This approach avoided animal toxicity experiments and confirmed that rumen fermentation characteristics and rumen microbiota were affected by E+ toxin. Therefore, E25 showed higher abundance in Prevotella_1, Prevotellaceae_ UCG-001, and Lachnospiraceae_XPB1014_group that implied they should play significant roles in E+ alkaloids degradation. And then, we can infer that rumen microorganisms should function as an antidote with respect to this poisoning reaction at moderate dietary percentages of E+.

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Effect of Potato Vine and Leaf Mixed Silage to Whole Corn Crops on Rumen Fermentation and the Microbe of Fatten Angus Bulls
Siyu Zhang, Jiajie Deng, Yafang Cui, Lina Wang, Yingqi Li, Xianli Wang, Shengnan Min, Huili Wang, Qianzi Zhang, Peiqi Li, Yawen Luo, Xinjun Qiu, Yang He, Binghai Cao, Huawei Su
Fermentation.2023; 9(8): 704. CrossRef
Yeast (Saccharomyces cerevisiae) Culture Promotes the Performance of Fattening Sheep by Enhancing Nutrients Digestibility and Rumen Development
Jie Wang, Guohong Zhao, Yimin Zhuang, Jianmin Chai, Naifeng Zhang
Fermentation.2022; 8(12): 719. CrossRef
The effects of fermented pineapple residue on growth performance, meat quality, and rumen microbiota of fattening Simmental bull
Ming Deng, Zupeng Xiao, Guangbin Liu, Baoli Sun, Yongqing Guo, Xian Zou, Dewu Liu, Zhenwei Yang, Yaokun Li
Frontiers in Microbiology.2022;[Epub] CrossRef
The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation
Yaling Ma, Hucheng Wang, Chunjie Li, Kamran Malik
Fermentation.2022; 8(9): 419. CrossRef

Isolation and Characterization of the New Conditional-lethal Mutations in byr4 of Schizosaccharomyces pombe by in vitro Mutagenesis: Song, Ki Won , Shin, Se Jong , Albright, Charles F.; J. Microbiol. 1998;36(4):296-302.

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Abstract: Coordination of nuclear division, cytokinesis, and septation is essential for maintaining the genomic stability during the cell division cycle. byr4 in fission yeas schizosaccharomyced pombe encodes an essential gene that regulates the timing of cytokinesis and septation in a dosage-de-pendent manner (Song et al., 1996). The knock-out of byr4 causes cell cycle arrest in late mitosis with multiple cytokinesis and septation, while byr4 is an essential gene, characterization of the byr4 null phenotypes and inbestigation of its genetic interactions with other mutants entail technical limitations. To better characterize the functional mechanisms of byr4 through phenotypic and genetic analyses, we generated five temperature-sensitive byr4 mutant alleles. A truncated byr4 with a deletion corresponding to the N-terminal 29 amino acids was randomly mutagenized by hydrocylamine in vitro. The mutagenized byr4 with an N-treminal truncation was integrated into the byr4 locus of S. pombe genome. Cells that formed colonies at the permissive temperature, 25℃, but could not grow at the restrictive temperatures, 18℃ or 35℃, were isolated. We successfully isolated five temperature-sensitive byr4 alleles (KSY1-5) that could not grow at 35℃. In the restrictive temperature, KSY1, KSY3, and KSY5 alleles arrested cells with multiple septation while chromosome segregation was normal in these alleles. KSY2 and KSY4 alleles exhibited two phenotypes at the restrictive temperature: cells were arrested with multiple nuclei due to the inhibition of cytokinesis or with multiple nuclei that were separated by septum. These newly isolated byr4 conditional alleles will be useful for the deduction of cellular processes where byr4 functions. Genetic studies and suppressor screens of the conditional alleles can provide useful tools for the isolation of interacting proteins with Byr4p.

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