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- In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
- Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
- J. Microbiol. 2024;62(5):409-418. Published online April 30, 2024
- DOI: https://doi.org/10.1007/s12275-024-00132-1
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Abstract
- Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.
- Crystal Structures of Plk1 Polo‑Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2‑Derived Peptide
- Sujin Jung , Hye Seon Lee , Ho-Chul Shin , Joon Sig Choi , Seung Jun Kim , Bonsu Ku
- J. Microbiol. 2023;61(8):755-764. Published online September 8, 2023
- DOI: https://doi.org/10.1007/s12275-023-00071-3
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- 1 Scopus
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Abstract
- Human papillomaviruses (HPVs) can increase the proliferation of infected cells during HPV-driven abnormalities, such as cervical cancer or benign warts. To date, more than 200 HPV genotypes have been identified, most of which are classified into three major genera: Alphapapillomavirus, Betapapillomavirus, and Gammapapillomavirus. HPV genomes commonly encode two structural (L1 and L2) and seven functional (E1, E2, E4–E7, and E8) proteins. L2, the minor structural protein of HPVs, not only serves as a viral capsid component but also interacts with various human proteins during viral infection. A recent report revealed that L2 of HPV16 recruits polo-like kinase 1 (Plk1), a master regulator of eukaryotic mitosis and cell cycle progression, for the delivery of viral DNA to mitotic chromatin during HPV16 infection. In this study, we verified the direct and potent interactions between the polo-box domain (PBD) of Plk1 and PBD-binding motif (S–S–pT–P)-containing phosphopeptides derived from L2 of HPV16/HPV18 (high-risk alphapapillomaviruses), HPV5b (low-risk betapapillomavirus), and HPV4 (low-risk gammapapillomavirus). Subsequent structural determination of the Plk1 PBD bound to the HPV18 or HPV4 L2-derived phosphopeptide demonstrated that they interact with each other in a canonical manner, in which electrostatic interactions and hydrogen bonds play key roles in sustaining the complex. Therefore, our structural and biochemical data imply that Plk1 is a broad binding target of L2 of various HPV genotypes belonging to the Alpha-, Beta-, and Gammapapillomavirus genera.
- Assessment of Cre-lox and CRISPR-Cas9 as tools for recycling of multiple-integrated selection markers in Saccharomyces cerevisiae
- Hye Yun Moon† , Gyu Hun Sim† , Hyeon Jin Kim , Keunpil Kim , Hyun Ah Kang
- J. Microbiol. 2022;60(1):18-30. Published online December 29, 2021
- DOI: https://doi.org/10.1007/s12275-022-1580-7
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- 7 Crossref
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Abstract
- We evaluated the Cre-lox and CRISPR-Cas9 systems as markerrecycling tools in Saccharomyces cerevisiae recombinants containing multiple-integrated expression cassettes. As an initial trial, we constructed rDNA-nontranscribed spacer- or Ty4- based multiple integration vectors containing the URA3 marker flanked by the loxP sequence. Integrants harboring multiple copies of tHMG1 and NNV-CP expression cassettes were obtained and subsequently transformed with the Cre plasmid. However, the simultaneous pop-out of the expression cassettes along with the URA3 marker hampered the use of Cre-lox as a marker-recycling tool in multiple integrants. As an alternative, we constructed a set of CRISPR-Cas9-gRNA vectors containing gRNA targeted to auxotrophic marker genes. Transformation of multiple integrants of tHMG1 and NNV-CP cassettes by the Cas9-gRNA vector in the presence of the URA3 (stop) donor DNA fragments generated the Ura- transformants retaining multiple copies of the expression cassettes. CRISPR-Cas9-based inactivation led to the recycling of the other markers, HIS3, LEU2, and TRP1, without loss of expression cassettes in the recombinants containing multiple copies of tHMG1, NNV-CP, and SfBGL1 cassettes, respectively. Reuse of the same selection marker in marker-inactivated S. cerevisiae was validated by multiple integrations of the TrEGL2 cassette into the S. cerevisiae strain expressing SfBGL1. These results demonstrate that introducing stop codons into selection marker genes using the CRISPR-Cas9 system with donor DNA fragments is an efficient strategy for markerrecycling in multiple integrants. In particular, the continual reuse of auxotrophic markers would facilitate the construction of a yeast cell factory containing multiple copies of expression cassettes without antibiotic resistance genes.
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Citations
Citations to this article as recorded by
- Multiple metabolic engineering of Saccharomyces cerevisiae for the production of lycopene
Jiaheng Liu, Minxia Song, Xianhao Xu, Yaokang Wu, Yanfeng Liu, Guocheng Du, Jianghua Li, Long Liu, Xueqin Lv
Food Bioengineering.2024;[Epub] CrossRef - Biochemical and Biorefinery Platform for Second-Generation Bioethanol: Fermentative Strategies and Microorganisms
Karla D. González-Gloria, Elia Tomás-Pejó, Lorena Amaya-Delgado, Rosa M. Rodríguez-Jasso, Araceli Loredo-Treviño, Anusuiya Singh, Meenu Hans, Carlos Martín, Sachin Kumar, Héctor A. Ruiz
Fermentation.2024; 10(7): 361. CrossRef - CRISPR/Cas9-based toolkit for rapid marker recycling and combinatorial libraries in Komagataella phaffii
Wei Zhou, Yuanyi Li, Guosong Liu, Weichuang Qin, Dongzhi Wei, Fengqing Wang, Bei Gao
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef - Establishment, optimization, and application of genetic technology in Aspergillus spp.
Jing Gao, Huiqing Liu, Zhenzhen Zhang, Zhihong Liang
Frontiers in Microbiology.2023;[Epub] CrossRef - CRISPR-Cas Technology for Bioengineering Conventional and Non-Conventional Yeasts: Progress and New Challenges
Yuanyuan Xia, Yujie Li, Wei Shen, Haiquan Yang, Xianzhong Chen
International Journal of Molecular Sciences.2023; 24(20): 15310. CrossRef - Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products
Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-joo Jeon, Che Ok Jeon, Seong-il Eyun, Hyun Ah Kang
FEMS Yeast Research.2023;[Epub] CrossRef - Multiplex genome editing to construct cellulase engineered Saccharomyces cerevisiae for ethanol production from cellulosic biomass
Yatika Dixit, Preeti Yadav, Arun Kumar Sharma, Poornima Pandey, Arindam Kuila
Renewable and Sustainable Energy Reviews.2023; 187: 113772. CrossRef
- Multiple metabolic engineering of Saccharomyces cerevisiae for the production of lycopene
Review
- [MINIREVIEW]Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective
- Misung Kim , Jaeeun Park , Mingyeong Kang , Jihye Yang , Woojun Park
- J. Microbiol. 2021;59(6):535-545. Published online April 20, 2021
- DOI: https://doi.org/10.1007/s12275-021-1085-9
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- 32 Web of Science
- 31 Crossref
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Abstract
- The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animalenvironment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal- environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzymeinhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.
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Citations
Citations to this article as recorded by- Removing high strength lincomycin in pharmaceutical wastewater by a bacteria microalgae consortium co-immobilized filter
Yonghong Li, Lifei Feng, Guanghua Li, Jian Wang, Keke Li
Bioresource Technology.2025; 415: 131704. CrossRef - Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment
Rui Xin, Ying Zhang, Kai Zhang, Yichen Yang, Yongzheng Ma, Zhiguang Niu
Science of The Total Environment.2024; 909: 168516. CrossRef - Hospital and municipal wastewater as a source of carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa in the environment: a review
Magdalena Męcik, Kornelia Stefaniak, Monika Harnisz, Ewa Korzeniewska
Environmental Science and Pollution Research.2024; 31(36): 48813. CrossRef -
Unexpected vulnerability of
Enterococcus faecium
to polymyxin B under anaerobic condition
Yongjun Son, Bitnara Kim, Pureun Kim, Jihyeon Min, Yerim Park, Jihye Yang, Wonjae Kim, Masanori Toyofuku, Woojun Park
Gut Microbes.2024;[Epub] CrossRef - Antimicrobial Resistance in the Context of Animal Production and Meat Products in Poland—A Critical Review and Future Perspective
Patryk Wiśniewski, Miłosz Trymers, Wioleta Chajęcka-Wierzchowska, Katarzyna Tkacz, Anna Zadernowska, Monika Modzelewska-Kapituła
Pathogens.2024; 13(12): 1123. CrossRef - Resistome Diversity in Escherichia coli Isolates of Global Wastewaters
Pavithra Anantharaman Sudhakari, Bhaskar Chandra Mohan Ramisetty
Microbial Drug Resistance.2024; 30(1): 37. CrossRef - Transfer dynamics of antimicrobial resistance among gram-negative bacteria
Bangjuan Wang, Muhammad Haris Raza Farhan, Linlin Yuan, Yuxin Sui, Jinhua Chu, Xiaohan Yang, Yuxin Li, Lingli Huang, Guyue Cheng
Science of The Total Environment.2024; 954: 176347. CrossRef -
Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx
Yerim Park, Jihyeon Min, Bitnara Kim, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef - Co-selection mechanism for bacterial resistance to major chemical pollutants in the environment
Meixia Huo, Xiangyue Xu, Kun Mi, Wenjin Ma, Qin Zhou, Xudong Lin, Guyue Cheng, Lingli Huang
Science of The Total Environment.2024; 912: 169223. CrossRef - Repeated Exposure of Vancomycin to Vancomycin-Susceptible Staphylococcus aureus (VSSA) Parent Emerged VISA and VRSA Strains with Enhanced Virulence Potentials
An Nguyen, J. Jean Sophy Roy, Ji-Hoon Kim, Kyung-Hee Yun, Wonsik Lee, Kyeong Kyu Kim, Truc Kim, Akhilesh Kumar Chaurasia
Journal of Microbiology.2024; 62(7): 535. CrossRef - Human Disturbance Increases Health Risks to Golden Snub-Nosed Monkeys and the Transfer Risk of Pathogenic Antibiotic-Resistant Bacteria from Golden Snub-Nosed Monkeys to Humans
Shuzhen Zou, Tingting Yuan, Tan Lu, Jiayu Yan, Di Kang, Dayong Li
Animals.2023; 13(19): 3083. CrossRef - Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome
Mathijs J. P. Theelen, Roosmarijn E. C. Luiken, Jaap A. Wagenaar, Marianne M. Sloet van Oldruitenborgh-Oosterbaan, John W. A. Rossen, Femke J. W. C. Schaafstra, David A. van Doorn, Aldert L. Zomer
Microbiome.2023;[Epub] CrossRef - Genomic evidences of gulls as reservoirs of critical priority CTX-M-producing Escherichia coli in Corcovado Gulf, Patagonia
Danny Fuentes-Castillo, Daniela Castro-Tardón, Fernanda Esposito, Ingrith Neves, Larissa Rodrigues, Herrison Fontana, Bruna Fuga, José L. Catão-Dias, Nilton Lincopan
Science of The Total Environment.2023; 874: 162564. CrossRef - Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms
Magdalena Męcik, Martyna Buta-Hubeny, Łukasz Paukszto, Mateusz Maździarz, Izabela Wolak, Monika Harnisz, Ewa Korzeniewska
Journal of Environmental Management.2023; 348: 119303. CrossRef - Fabrication of Co-Assembly from Berberine and Tannic Acid for Multidrug-Resistant Bacteria Infection Treatment
Tingting Zheng, Huan Chen, Chenyang Wu, Jinrui Wang, Mengyao Cui, Hanyi Ye, Yifan Feng, Ying Li, Zhengqi Dong
Pharmaceutics.2023; 15(7): 1782. CrossRef - Grazing disturbance increased the mobility, pathogenicity and host microbial species of antibiotic resistance genes, and multidrug resistance genes posed the highest risk in the habitats of wild animals
Shuzhen Zou, Tan Lu, Cailiang Huang, Jie Wang, Dayong Li
Frontiers in Environmental Science.2023;[Epub] CrossRef - Application of electrochemical oxidation for the enhancement of antibiotic resistant bacteria removal in stormwater bioretention cells
XiaoJun Zuo, SongHu Zhang, FanXin Kong, QiangQiang Xu
Science of The Total Environment.2023; 861: 160477. CrossRef - Blue Light Sensing BlsA-Mediated Modulation of Meropenem Resistance and Biofilm Formation in Acinetobacter baumannii
Jihye Yang, Sohyeon Yun, Woojun Park, Mark J. Mandel
mSystems.2023;[Epub] CrossRef - AamA-mediated epigenetic control of genome-wide gene expression and phenotypic traits in Acinetobacter baumannii ATCC 17978
Jihye Yang, Yongjun Son, Mingyeong Kang, Woojun Park
Microbial Genomics .2023;[Epub] CrossRef - Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land
Kailin Xu, Xuna Liu, Lina Pang, Yao Yue, Efthalia Chatzisymeon, Ping Yang
Science of The Total Environment.2023; 905: 166994. CrossRef - The β-Lactamase Activity at the Community Level Confers β-Lactam Resistance to Bloom-Forming Microcystis aeruginosa Cells
Yerim Park, Wonjae Kim, Minkyung Kim, Woojun Park
Journal of Microbiology.2023; 61(9): 807. CrossRef - Bactericidal activity of silver nanoparticles in drug-resistant bacteria
C. Chapa González, L. I. González García, L. G. Burciaga Jurado, A. Carrillo Castillo
Brazilian Journal of Microbiology.2023; 54(2): 691. CrossRef - Computational modelling of epithelial cell monolayers during infection with Listeria monocytogenes
Raul Aparicio-Yuste, Francisco Serrano-Alcalde, Marie Muenkel, Jose Manuel Garcia-Aznar, Effie E. Bastounis, Maria Jose Gomez-Benito
Computer Methods in Applied Mechanics and Engineering.2022; 401: 115477. CrossRef - Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
Journal of Microbiology.2022; 60(1): 128. CrossRef - Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment
Maozhen Han, Lu Zhang, Na Zhang, Yujie Mao, Zhangjie Peng, Binbin Huang, Yan Zhang, Zhi Wang
Journal of Hazardous Materials.2022; 424: 127745. CrossRef - Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes
Mingyeong Kang, Jihye Yang, Suhyun Kim, Jaeeun Park, Misung Kim, Woojun Park
Science of The Total Environment.2022; 811: 152331. CrossRef - Occurrence and spread of antibiotic-resistant bacteria on animal farms and in their vicinity in Poland and Ukraine—review
Karolina Jeżak, Anna Kozajda
Environmental Science and Pollution Research.2022; 29(7): 9533. CrossRef - Application of Electrochemical Oxidation for the Enhancement of Antibiotic Resistant Bacteria Removal in Stormwater Bioretention Cells
XiaoJun Zuo, SongHu Zhang, FanXin Kong, QiangQiang Xu
SSRN Electronic Journal .2022;[Epub] CrossRef - Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments
Damon C. Brown, Naomi Aggarwal, Raymond J. Turner
Microbiology .2022;[Epub] CrossRef - Small Things Matter: The 11.6-kDa TraB Protein is Crucial for Antibiotic Resistance Transfer Among Enterococci
Tamara M.I. Berger, Claudia Michaelis, Ines Probst, Theo Sagmeister, Lukas Petrowitsch, Sandra Puchner, Tea Pavkov-Keller, Bernd Gesslbauer, Elisabeth Grohmann, Walter Keller
Frontiers in Molecular Biosciences.2022;[Epub] CrossRef - The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench
Hualong Su, Chengcheng Wu, Peiyun Han, Zixuan Liu, Mincong Liang, Zheng Zhang, Zhike Wang, Guangyu Guo, Xinyi He, Jianhu Pang, Cheng Wang, Shaoping Weng, Jianguo He
Journal of Hazardous Materials.2022; 439: 129543. CrossRef
- Removing high strength lincomycin in pharmaceutical wastewater by a bacteria microalgae consortium co-immobilized filter
Journal Articles
- Mst1/2-ALK promotes NLRP3 inflammasome activation and cell apoptosis during Listeria monocytogenes infection
- Aijiao Gao , Huixin Tang , Qian Zhang , Ruiqing Liu , Lin Wang , Yashan Liu , Zhi Qi , Yanna Shen
- J. Microbiol. 2021;59(7):681-692. Published online April 20, 2021
- DOI: https://doi.org/10.1007/s12275-021-0638-2
- 57 View
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- 10 Web of Science
- 8 Crossref
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Abstract
- Listeria monocytogenes (L. monocytogenes) is a Gram-positive intracellular foodborne pathogen that causes severe diseases, such as meningitis and sepsis. The NLR family pyrin domain-containing 3 (NLRP3) inflammasome has been reported to participate in host defense against pathogen infection. However, the exact molecular mechanisms underlying NLRP3 inflammasome activation remain to be fully elucidated. In the present study, the roles of mammalian Ste20- like kinases 1/2 (Mst1/2) and Anaplastic Lymphoma Kinase (ALK) in the activation of the NLRP3 inflammasome induced by L. monocytogenes infection were investigated. The expression levels of Mst1/2, phospho (p)-ALK, p-JNK, Nek7, and NLRP3 downstream molecules including activated caspase- 1 (p20) and mature interleukin (IL)-1β (p17), were upregulated in L. monocytogenes-infected macrophages. The ALK inhibitor significantly decreased the expression of p-JNK, Nek7, and NLRP3 downstream molecules in macrophages infected with L. monocytogenes. Furthermore, the Mst1/2 inhibitor markedly inhibited the L. monocytogenes-induced activation of ALK, subsequently downregulating the expression of p-JNK, Nek7, and NLRP3 downstream molecules. Therefore, our study demonstrated that Mst1/2-ALK mediated the activation of the NLRP3 inflammasome by promoting the interaction between Nek7 and NLRP3 via JNK during L. monocytogenes infection, which subsequently increased the maturation and release of proinflammatory cytokine to resist pathogen infection. Moreover, Listeriolysin O played a key role in the process. In addition, we also found that the L. monocytogenes-induced apoptosis of J774A.1 cells was reduced by the Mst1/2 or ALK inhibitor. The present study reported, for the first time, that the Mst1/2-ALK-JNK-NLRP3 signaling pathway plays a vital proinflammatory role during L. monocytogenes infection.
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Citations
Citations to this article as recorded by- IL-18 biology in severe asthma
Sarita Thawanaphong, Aswathi Nair, Emily Volfson, Parameswaran Nair, Manali Mukherjee
Frontiers in Medicine.2024;[Epub] CrossRef - TRAF6-TAK1-IKKβ pathway mediates TLR2 agonists activating “one-step” NLRP3 inflammasome in human monocytes
Mengdan Chen, Shi Yu, Yuhui Gao, Jiaxun Li, Xun Wang, Bin Wei, Guangxun Meng
Cytokine.2023; 169: 156302. CrossRef - ALK-JNK signaling promotes NLRP3 inflammasome activation and pyroptosis via NEK7 during Streptococcus pneumoniae infection
Xia Wang, Yan Zhao, Dan Wang, Chang Liu, Zhi Qi, Huixin Tang, Yashan Liu, Shiqi Zhang, Yali Cui, Yingying Li, Ruiqing Liu, Yanna Shen
Molecular Immunology.2023; 157: 78. CrossRef - Inflammasome activation by Gram-positive bacteria: Mechanisms of activation and regulation
A. Marijke Keestra-Gounder, Prescilla Emy Nagao
Frontiers in Immunology.2023;[Epub] CrossRef - Toxoplasma gondii profilin induces NLRP3 activation and IL-1β production/secretion in THP-1 cells
Hossein Pazoki, Hamed Mirjalali, Maryam Niyyati, Seyed Javad Seyed Tabaei, Nariman Mosaffa, Shabnam Shahrokh, Hamid Asadzadeh Ahdaei, Andreas Kupz, Mohammad Reza Zali
Microbial Pathogenesis.2023; 180: 106120. CrossRef - The Critical Role of Potassium Efflux and Nek7 in Pasteurella multocida-Induced NLRP3 Inflammasome Activation
Yu Wang, Zheng Zeng, Jinrong Ran, Lianci Peng, Xingping Wu, Chao Ye, Chunxia Dong, Yuanyi Peng, Rendong Fang
Frontiers in Microbiology.2022;[Epub] CrossRef - Coral and it's symbionts responses to the typical global marine pollutant BaP by 4D-Proteomics approach
Yuebin Pei, Shuai Chen, Yuting Zhang, Volovych Olga, Yuanchao Li, Xiaoping Diao, Hailong Zhou
Environmental Pollution.2022; 307: 119440. CrossRef - NEK7-Mediated Activation of NLRP3 Inflammasome Is Coordinated by Potassium Efflux/Syk/JNK Signaling During Staphylococcus aureus Infection
Ruiqing Liu, Yashan Liu, Chang Liu, Aijiao Gao, Lin Wang, Huixin Tang, Qiang Wu, Xia Wang, Derun Tian, Zhi Qi, Yanna Shen
Frontiers in Immunology.2021;[Epub] CrossRef
- IL-18 biology in severe asthma
- Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti
- Olga Y. Burenina , Daria A. Elkina , Anzhela Y. Migur , Tatiana S. Oretskaya , Elena Evguenieva-Hackenberg , RolK. Hartmann , Elena A. Kubareva
- J. Microbiol. 2020;58(11):945-956. Published online October 30, 2020
- DOI: https://doi.org/10.1007/s12275-020-0283-1
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- 5 Web of Science
- 6 Crossref
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Abstract
- 6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ~13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ~75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.
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Citations
Citations to this article as recorded by- Bacteria Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Биоорганическая химия.2023; 49(6): 555. CrossRef - Bacterial Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation (A Review)
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2023; 49(6): 1198. CrossRef - Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase
Sweetha Ganapathy, Philipp G. Hoch, Marcus Lechner, Malte Bussiek, Roland K. Hartmann
Non-Coding RNA.2022; 8(1): 20. CrossRef - Involvement of E. coli 6S RNA in Oxidative Stress Response
Olga Y. Burenina, Daria A. Elkina, Anna Ovcharenko, Valeria A. Bannikova, M. Amri C. Schlüter, Tatiana S. Oretskaya, Roland K. Hartmann, Elena A. Kubareva
International Journal of Molecular Sciences.2022; 23(7): 3653. CrossRef - Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
Viola Vaňková Hausnerová, Olga Marvalová, Michaela Šiková, Mahmoud Shoman, Jarmila Havelková, Milada Kambová, Martina Janoušková, Dilip Kumar, Petr Halada, Marek Schwarz, Libor Krásný, Jarmila Hnilicová, Josef Pánek
Frontiers in Microbiology.2022;[Epub] CrossRef - Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization
O. Y. Burenina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2021; 47(2): 478. CrossRef
- Bacteria Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation
- Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes
- Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul
- J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019
- DOI: https://doi.org/10.1007/s12275-019-9217-1
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- 20 Web of Science
- 21 Crossref
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Abstract
- Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.
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Citations
Citations to this article as recorded by- Metagenomic insights into the lignocellulose degradation mechanism during short-term composting of peach sawdust: Core microbial community and carbohydrate-active enzyme profile analysis
Wei-Wei Zhang, Yu-Xin Guo, Qing-Jun Chen, Yi-Yang Wang, Qiu-Ying Wang, Ya-Ru Yang, Guo-Qing Zhang
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- Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation
- Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha
- J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018
- DOI: https://doi.org/10.1007/s12275-018-8372-0
- 43 View
- 0 Download
- 21 Crossref
-
Abstract
- The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.
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Review
- REVIEW] The Ruminococci: key symbionts of the gut ecosystem
- Alex J. La Reau , Garret Suen
- J. Microbiol. 2018;56(3):199-208. Published online February 28, 2018
- DOI: https://doi.org/10.1007/s12275-018-8024-4
- 46 View
- 0 Download
- 213 Crossref
-
Abstract
- Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant- associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.
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Nutrients.2024; 16(6): 891. CrossRef - Causal relationship between gut microbiota and gastric cancer: A two‑sample Mendelian randomization analysis
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Molecular and Clinical Oncology.2024;[Epub] CrossRef - Metabolism of quercitrin in the colon and its beneficial regulatory effects on gut microbiota
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Journal of the Science of Food and Agriculture.2024; 104(15): 9255. CrossRef - Diverse mechanisms by which chemical pollutant exposure alters gut microbiota metabolism and inflammation
Menna Teffera, Alex C. Veith, Sean Ronnekleiv-Kelly, Christopher A. Bradfield, Maria Nikodemova, Lisa Tussing-Humphreys, Kristen Malecki
Environment International.2024; 190: 108805. CrossRef - Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities
Maoping Li, Suqin Wang, Liang Zhong, Petr Heděnec, Zhaoxian Tan, Rong Wang, Xinyang Chen, Yan Zhang, Bingmin Tang, Huakun Zhou, Jiapeng Qu
Frontiers in Microbiology.2024;[Epub] CrossRef - Inhalation of 2,2′,5,5′-tetrachlorobiphenyl (PCB52) causes changes to the gut microbiome throughout the gastrointestinal tract
Laura E. Dean, Hui Wang, Amanda J. Bullert, Hui Wang, Andrea Adamcakova-Dodd, Ashutosh K. Mangalam, Peter S. Thorne, James A. Ankrum, Aloysius J. Klingelhutz, Hans-Joachim Lehmler
Journal of Hazardous Materials.2024; 480: 135999. CrossRef - Association of gut microbiome and oral cavity cancer: A two sample mendelian randomization and case-control study
Xinpeng Liu, Xinping Li, Menglan Xie, Jinyuan Guo, Xianghuai Zheng, Shanwei Shi, Qiuju Cui, Danya Zhang, Zhaoqiang Zhang, Zhiping Wang
Journal of Stomatology, Oral and Maxillofacial Surgery.2024; 125(4): 101736. CrossRef - Bridging the Gap: Harnessing Plant Bioactive Molecules to Target Gut Microbiome Dysfunctions in Amyotrophic Lateral Sclerosis
Mirela Pribac, Anca Motataianu, Sebastian Andone, Elena Mardale, Sebastian Nemeth
Current Issues in Molecular Biology.2024; 46(5): 4471. CrossRef - Temporal changes in the mouse gut bacteriota influenced by host sex, diet, and exercise
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Journal of Applied Physiology.2024; 137(5): 1374. CrossRef - The Ruminal Microbiome Alterations Associated with Diet-Induced Milk Fat Depression and Milk Fat Globule Size Reduction in Dairy Goats
Menglu Zhang, Zhentao Liu, Kuixian Wu, Chuankai Zhang, Tong Fu, Yu Sun, Tengyun Gao, Liqiang Han
Animals.2024; 14(17): 2614. CrossRef - Oral administration of lysozyme protects against injury of ileum via modulating gut microbiota dysbiosis after severe traumatic brain injury
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Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef - Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou
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Frontiers in Microbiology.2024;[Epub] CrossRef -
The colibactin-producing
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Nilmara de Oliveira Alves, Guillaume Dalmasso, Darja Nikitina, Amaury Vaysse, Richard Ruez, Lea Ledoux, Thierry Pedron, Emma Bergsten, Olivier Boulard, Lora Autier, Sofian Allam, Laurence Motreff, Pierre Sauvanet, Diane Letourneur, Pragya Kashyap, Johan G
Gut Microbes.2024;[Epub] CrossRef - Firmicutes and Bacteroidetes contribute to mass gain variation in female obligate hibernators
Samuel Degregori, Gina C Johnson, Paul H Barber, Daniel T Blumstein, Elizabeth Flaherty
Journal of Mammalogy.2024; 105(1): 2. CrossRef - Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People
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Probiotics and Antimicrobial Proteins.2024; 16(4): 1240. CrossRef - Characterization of the Effects of a Novel Probiotic on Salmonella Colonization of a Piglet-Derived Intestinal Microbiota Using Improved Bioreactor
Amely Grandmont, Mohamed Rhouma, Marie-Pierre Létourneau-Montminy, William Thériault, Isabelle Mainville, Yves Arcand, Roland Leduc, Bruno Demers, Alexandre Thibodeau
Animals.2024; 14(5): 787. CrossRef - INDICATORS OF THE QUALITATIVE AND QUANTITATIVE COMPOSITION OF THE GUT COMMENSAL MICROBIOTA AS BIOMARKERS OF HOMEOSTASIS (Part 1)
M.M. Ananieva, G.A. Loban, M.O. Faustova, Y.V. Chumak, S.M. Losev
Актуальні проблеми сучасної медицини: Вісник Української медичної стоматологічної академії.2024; 24(1): 239. CrossRef -
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Critical Reviews in Food Science and Nutrition.2024; 64(18): 6432. CrossRef -
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Gut Microbes.2024;[Epub] CrossRef - Ruminococcus gnavus in the gut: driver, contributor, or innocent bystander in steatotic liver disease?
Vik Meadows, Jayson M. Antonio, Ronaldo P. Ferraris, Nan Gao
The FEBS Journal.2024;[Epub] CrossRef - INDICATORS OF QUANTITATIVE AND QUALITATIVE COMPOSITION OF THE GUT COMMENSAL MICROBIOTA AS BIOMARKERS OF HOMEOSTASIS
M.M. Ananieva, G.A. Loban, M.O. Faustova, Y.V. Chumak, S.M. Losev
Актуальні проблеми сучасної медицини: Вісник Української медичної стоматологічної академії.2024; 24(2): 277. CrossRef - Enteromorpha prolifera Polysaccharide Alleviates Acute Alcoholic Liver Injury in C57 BL/6 Mice through the Gut–Liver Axis and NF-κB Pathway
Tingting Yan, Jinghe Sun, Yuying Zhang, Chengrong Wen, Jingfeng Yang
Journal of Agricultural and Food Chemistry.2024; 72(42): 23258. CrossRef - Chlorella and vegetable oil inclusion in diets for growing rabbits: effects on growth, digestibility, plasma metabolites, and caecal fermentations and microbiota
F. Bordignon, A. Trocino, P.J. Marín García, T. Larsen, G. Zardinoni, M. Molin, M. Birolo, P. Stevanato, G. Xiccato
animal.2024; 18(12): 101365. CrossRef - Hawthorn pectin plays a protective role in myocardial ischaemia by regulating intestinal flora and short chain fatty acids
Jiayue Lou, Baojie Zhang, Yu Zheng, Meiqi Liu, Yang Qu
Current Research in Food Science.2024; 9: 100863. CrossRef - Blackcurrants shape gut microbiota profile and reduce risk of postmenopausal osteoporosis via the gut-bone axis: Evidence from a pilot randomized controlled trial
Briana M. Nosal, Staci N. Thornton, Manije Darooghegi Mofrad, Junichi R. Sakaki, Kyle J. Mahoney, Zachary Macdonald, Lauren Daddi, Thi Dong Binh Tran, George Weinstock, Yanjiao Zhou, Elaine Choung-Hee Lee, Ock K. Chun
The Journal of Nutritional Biochemistry.2024; 133: 109701. CrossRef - Characterization of the follicular fluid microbiota based on culturomics and sequencing analysis
Wenting Wei, Yazhou Zhou, Haiyang Zuo, Min Li, Zhiyuan Pan, Bin Liu, Lu Wang, Yafang Tan, Ruifu Yang, Wei Shang, Yujing Bi, Weizhou Wang
Journal of Medical Microbiology .2023;[Epub] CrossRef - Oral intake of Lactiplantibacillus pentosus LPG1 Produces a Beneficial Regulation of Gut Microbiota in Healthy Persons: A Randomised, Placebo-Controlled, Single-Blind Trial
Elio López-García, Antonio Benítez-Cabello, Antonio Pablo Arenas-de Larriva, Francisco Miguel Gutierrez-Mariscal, Pablo Pérez-Martínez, Elena María Yubero-Serrano, Antonio Garrido-Fernández, Francisco Noé Arroyo-López
Nutrients.2023; 15(8): 1931. CrossRef - Polysaccharides from small black soybean alleviating type 2 diabetes via modulation of gut microbiota and serum metabolism
Zhouya Bai, Xiaojun Huang, Guangjie Wu, Yanli Zhang, Hedi Xu, Yang Chen, Huayu Yang, Shaoping Nie
Food Hydrocolloids.2023; 141: 108670. CrossRef - Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients
Lauma Jagare, Maija Rozenberga, Ivars Silamikelis, Laura Ansone, Ilze Elbere, Monta Briviba, Kaspars Megnis, Ilze Konrade, Ilze Birka, Zane Straume, Janis Klovins
Journal of Medical Microbiology .2023;[Epub] CrossRef - Gut bacteria of adult and larval Cotinis nitida Linnaeus (Coleoptera: Scarabaeidae) demonstrate community differences according to respective life stage and gut region
Roy A. Kucuk, Barbara J. Campbell, Nicholas J. Lyon, Emily A. Shelby, Michael S. Caterino
Frontiers in Microbiology.2023;[Epub] CrossRef - Definition of a microbial signature as a predictor of endoscopic post-surgical recurrence in patients with Crohn’s disease
Lia Oliver, Blau Camps, David Julià-Bergkvist, Joan Amoedo, Sara Ramió-Pujol, Marta Malagón, Anna Bahí, Paola Torres, Eugeni Domènech, Jordi Guardiola, Mariona Serra-Pagès, Jesus Garcia-Gil, Xavier Aldeguer
Frontiers in Molecular Medicine.2023;[Epub] CrossRef - Integrated Analysis of the Effects of Cecal Microbiota and Serum Metabolome on Market Weights of Chinese Native Chickens
Shenghong Yang, Yongxian Yang, Xiaoxia Long, Hui Li, Fuping Zhang, Zhong Wang
Animals.2023; 13(19): 3034. CrossRef - Effects of different manganese sources on nutrient digestibility, fecal bacterial community, and mineral excretion of weaning dairy calves
Huimin Ji, Dejin Tan, Yuhua Chen, Zhiqiang Cheng, Jingwen Zhao, Miao Lin
Frontiers in Microbiology.2023;[Epub] CrossRef - Effects of an inulin fiber diet on the gut microbiome, colon, and inflammatory biomarkers in aged mice
Noah T. Hutchinson, Selena S. Wang, Laurie A. Rund, Maria Elisa Caetano-Silva, Jacob M. Allen, Rodney W. Johnson, Jeffrey A. Woods
Experimental Gerontology.2023; 176: 112164. CrossRef - Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs
Lydia K. Greene, Erin A. McKenney, William Gasper, Claudia Wrampelmeier, Shivdeep Hayer, Erin E. Ehmke, Jonathan B. Clayton
Microbial Ecology.2023; 85(4): 1608. CrossRef - Metaproteomic Analysis of Gut Resistome in the Cecal Microbiota of Fattening Pigs Raised without Antibiotics
Pamornya Buthasane, Sittiruk Roytrakul, Narumon Phaonakrop, Paiboon Tunsagool, Wannapol Buthasane, Nutthee Am-in, Gunnaporn Suriyaphol, Montarop Yamabhai
Microbiology Spectrum.2023;[Epub] CrossRef - Captivity restructures the gut microbiota of François' langurs (Trachypithecus francoisi)
Fengxiang Mo, Yuhui Li, Zheng Liu, Jingjin Zheng, Zhonghao Huang
Frontiers in Microbiology.2023;[Epub] CrossRef - Effects of dietary Chinese herbal mixtures on productive performance, egg quality, immune status, caecal and offspring meconial microbiota of Wenchang breeder hens
Mengjie Liu, Jieyi Huang, Ming Ma, Gengxiong Huang, Yingwen Zhang, Yiqing Ding, Qian Qu, Weijie Lv, Shining Guo
Frontiers in Veterinary Science.2023;[Epub] CrossRef - Associations of the gut microbiome with psychoneurological symptom cluster in women with gynecologic cancers: a longitudinal study
Zahra Amirkhanzadeh Barandouzi, Tony Eng, Joseph Shelton, Namita Khanna, Isabelle Scott, Rebecca Meador, Deborah Watkins Bruner
Supportive Care in Cancer.2023;[Epub] CrossRef - Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition
Sayaka Katagiri, Yujin Ohsugi, Takahiko Shiba, Kanako Yoshimi, Kazuharu Nakagawa, Yuki Nagasawa, Aritoshi Uchida, Anhao Liu, Peiya Lin, Yuta Tsukahara, Takanori Iwata, Haruka Tohara
Frontiers in Microbiology.2023;[Epub] CrossRef - Drinking Warm Water Promotes Performance by Regulating Ruminal Microbial Composition and Serum Metabolites in Yak Calves
Tianxu Liu, Qianqian Wang, Chenxi Gao, Shenfei Long, Tengfei He, Zhenlong Wu, Zhaohui Chen
Microorganisms.2023; 11(8): 2092. CrossRef - Effect of Clindamycin on Intestinal Microbiome and Miltefosine Pharmacology in Hamsters Infected with Leishmania infantum
Ana Isabel Olías-Molero, Pedro Botías, Montserrat Cuquerella, Jesús García-Cantalejo, Emilia Barcia, Susana Torrado, Juan José Torrado, José María Alunda
Antibiotics.2023; 12(2): 362. CrossRef - Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019–2020 Australian Megafire
Jordyn Clough, Sibylle Schwab, Katarina Mikac
Animals.2023; 13(22): 3583. CrossRef - Orally Administrated Lactiplantibacillus plantarum BGAN8-Derived EPS-AN8 Ameliorates Cd Hazards in Rats
Emilija Brdarić, Dušanka Popović, Svetlana Soković Bajić, Dina Tucović, Jelena Mutić, Maja Čakić-Milošević, Slađana Đurđić, Maja Tolinački, Aleksandra Popov Aleksandrov, Nataša Golić, Ivana Mirkov, Milica Živković
International Journal of Molecular Sciences.2023; 24(3): 2845. CrossRef - Ligularia virgaurea improved nutrient digestion, ruminal fermentation, and bacterial composition in Tibetan sheep grazing on the Qinghai–Tibetan plateau in winter
Xiongxiong Cui, Zhaofeng Wang, Qingshan Fan, Shenghua Chang, Tianhai Yan, Fujiang Hou
Animal Feed Science and Technology.2023; 299: 115628. CrossRef - Characterization of the Gut Microbiota in Urban Thai Individuals Reveals Enterotype-Specific Signature
Jiramaetha Sinsuebchuea, Prasobsook Paenkaew, Montree Wutthiin, Thatchawanon Nantanaranon, Kiattiyot Laeman, Weerayuth Kittichotirat, Songsak Wattanachaisaereekul, Sudarat Dulsawat, Montira Nopharatana, Namol Vorapreeda, Sakarindr Bhumiratana, Supapon Che
Microorganisms.2023; 11(1): 136. CrossRef - Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses
Javad Gharechahi, Mohammad Farhad Vahidi, Golandam Sharifi, Shohreh Ariaeenejad, Xue-Zhi Ding, Jian-Lin Han, Ghasem Hosseini Salekdeh
Environmental Research.2023; 229: 115925. CrossRef - Associations between the Gut Microbiome and Migraines in Children Aged 7-18 Years: An Analysis of the American Gut Project Cohort
Jinbing Bai, Natalie Shen, Yanqun Liu
Pain Management Nursing.2023; 24(1): 35. CrossRef - Invited review: Rumen modifiers in today's dairy rations
J.L. Firkins, K.E. Mitchell
Journal of Dairy Science.2023; 106(5): 3053. CrossRef - Exploration of the Gut Microbiome in Thai Patients with Major Depressive Disorder Shows a Specific Bacterial Profile with Depletion of the Ruminococcus Genus as a Putative Biomarker
Michael Maes, Asara Vasupanrajit, Ketsupar Jirakran, Pavit Klomkliew, Prangwalai Chanchaem, Chavit Tunvirachaisakul, Sunchai Payungporn
Cells.2023; 12(9): 1240. CrossRef - Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity
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Medicine & Science in Sports & Exercise.2023; 55(4): 680. CrossRef - Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies
Yanjiao Li, Kang Mao, Yitian Zang, Guwei Lu, Qinghua Qiu, Kehui Ouyang, Xianghui Zhao, Xiaozhen Song, Lanjiao Xu, Huan Liang, Mingren Qu
Microbiome.2023;[Epub] CrossRef - Analysis of microbial colonies from the first-pass meconium of healthy neonates: Comparison of vaginally and cesarean section born
Hueng-Chuen Fan, Ying-Ru Pan, Pei-Ling Lai, Win-Lin Yeh, Shu-Wei Hu, Ming-Yuan Hsu, Wei-Kian Chua
Tungs' Medical Journal.2023; 17(2): 76. CrossRef - Food desert residence has limited impact on veteran fecal microbiome composition: a U.S. Veteran Microbiome Project study
Diana P. Brostow, Meghan Donovan, Molly Penzenik, Christopher E. Stamper, Talia Spark, Christopher A. Lowry, Suzanne L. Ishaq, Andrew J. Hoisington, Lisa A. Brenner, Thomas J. Sharpton
mSystems.2023;[Epub] CrossRef - The gut microbiome dysbiosis is recovered by restoring a normal diet in hypercholesterolemic pigs
Leonie Schoch, Pablo Sutelman, Rosa Suades, Lina Badimon, Isabel Moreno‐Indias, Gemma Vilahur
European Journal of Clinical Investigation.2023;[Epub] CrossRef - Partially Alternative Feeding with Fermented Distillers’ Grains Modulates Gastrointestinal Flora and Metabolic Profile in Guanling Cattle
Guangxia He, Chao Chen, Shihui Mei, Ze Chen, Rong Zhang, Tiantian Zhang, Duhan Xu, Mingming Zhu, Xiaofen Luo, Chengrong Zeng, Bijun Zhou, Kaigong Wang, Erpeng Zhu, Zhentao Cheng
Animals.2023; 13(22): 3437. CrossRef - Dysbiosis in gastrointestinal pathophysiology: Role of the gut microbiome in Gulf War Illness
Elise Slevin, Sachiko Koyama, Kelly Harrison, Ying Wan, James E. Klaunig, Chaodong Wu, Ashok K. Shetty, Fanyin Meng
Journal of Cellular and Molecular Medicine.2023; 27(7): 891. CrossRef - Gastrointestinal Degradation and Toxicity of Disinfection Byproducts in Drinking Water Using In Vitro Models and the Roles of Gut Microbiota
Jinbao Yin, Dingxin Li, Tianming Zheng, Bin Hu, Peifang Wang
Environmental Science & Technology.2023; 57(43): 16219. CrossRef - Enhanced lupus progression in alcohol‐administered Fc gamma receptor‐IIb–deficiency lupus mice, partly through leaky gut‐induced inflammation
Wiwat Chancharoenthana, Supitcha Kamolratanakul, Phatcharapon Yiengwattananon, Pornpimol Phuengmaung, Kanyarat Udompornpitak, Wilasinee Saisorn, Pratsanee Hiengrach, Peerapat Visitchanakun, Marcus J Schultz, Asada Leelahavanichkul
Immunology & Cell Biology.2023; 101(8): 746. CrossRef - Deciphering salivary microbiome signature in Crohn’s disease patients with different factors contributing to dysbiosis
Hala Elzayat, Talha Malik, Haifa Al-Awadhi, Mazen Taha, Gehad Elghazali, Farah Al-Marzooq
Scientific Reports.2023;[Epub] CrossRef - Apolipoprotein E gene variants shape the association between dietary fibre intake and cognitive decline risk in community-dwelling older adults
Andrea Unión-Caballero, Tomás Meroño, Cristina Andrés-Lacueva, Nicole Hidalgo-Liberona, Montserrat Rabassa, Stefania Bandinelli, Luigi Ferrucci, Massimiliano Fedecostante, Raúl Zamora-Ros, Antonio Cherubini
Age and Ageing.2023;[Epub] CrossRef - Alfalfa hay substitution for wheat straw improves beef quality via rumen microflora alteration
Zimin Gao, Boshuai Liu, Shaokai La, Defeng Li, Xiaoyan Zhu, Hao Sun, Sen Ma, Yalei Cui, Yinghua Shi
Heliyon.2023; 9(10): e20803. CrossRef - Altered gut microbiota in older adults with mild cognitive impairment: a case-control study
Kang-Chen Fan, Chen-Ching Lin, Yi-Chien Liu, Yi-Ping Chao, Yen-Jun Lai, Yen-Ling Chiu, Yi-Fang Chuang
Frontiers in Aging Neuroscience.2023;[Epub] CrossRef - Changes of gut microbiota under different nutritional methods in elderly patients with severe COVID-19 and their relationship with prognosis
Jiawei Zhang, Jiaxin Deng, Juan Li, Yuping Su, Jiancong Hu, Dezheng Lin, Mingli Su, Yongcheng Chen, Sen Liao, Xuhao Bai, Miwei Lv, Tian Xu, Qinghua Zhong, Xuefeng Guo
Frontiers in Immunology.2023;[Epub] CrossRef - Stall-Feeding of Sheep on Restricted Grazing: Effects on Performance and Serum Metabolites, Ruminal Fermentation, and Fecal Microbiota
Mengyu Zhao, Xiaoan Zhang, Yao Chen, Chunhuan Ren, Yiming Sun, Penghui Wang, Xiao Cheng, Zijun Zhang, Jiahong Chen, Yafeng Huang
Animals.2023; 13(16): 2644. CrossRef - Causal Link between Gut Microbiota, Neurophysiological States, and Bone Diseases: A Comprehensive Mendelian Randomization Study
Shaoting Luo, Zhiyang Chen, Linfang Deng, Yufan Chen, Weizheng Zhou, Federico Canavese, Lianyong Li
Nutrients.2023; 15(18): 3934. CrossRef - Individual and combined effects of fluoride and arsenic on gut bacteria: a recent update
Sunanda Mukherjee, Olivia Sarkar, Ansuman Chattopadhyay
The Nucleus.2023;[Epub] CrossRef - Microbe-mineral interactions in the Plastisphere: Coastal biogeochemistry and consequences for degradation of plastics
Maya S. Dodhia, Kelsey L. Rogers, Victor Fernández-Juárez, Joan A. Carreres-Calabuig, Carolin R. Löscher, Amandine A. Tisserand, Nynke Keulen, Lasse Riemann, Yvonne Shashoua, Nicole R. Posth
Frontiers in Marine Science.2023;[Epub] CrossRef - Different roles of host and habitat in determining the microbial communities of plant-feeding true bugs
Zi-Wen Yang, Jiu-Yang Luo, Yu Men, Zhi-Hui Liu, Zi-Kai Zheng, Yan-Hui Wang, Qiang Xie
Microbiome.2023;[Epub] CrossRef - Gut Microbiome Transplants and Their Health Impacts across Species
Benjamin H. Levine, Jessica M. Hoffman
Microorganisms.2023; 11(6): 1488. CrossRef - Causal effects of gut microbiome on autoimmune liver disease: a two-sample Mendelian randomization study
Yugang Fu, Jiacheng Li, Yingying Zhu, Chong Chen, Jing Liu, Simin Gu, Yiyuan Zheng, Yong Li
BMC Medical Genomics.2023;[Epub] CrossRef - Targeting gut microbiota to alleviate neuroinflammation in Alzheimer’s disease
Vu Thu Thuy Nguyen, Kristina Endres
Advanced Drug Delivery Reviews.2022; 188: 114418. CrossRef - Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet
Tiziana Maria Mahayri, Kateřina Olša Fliegerová, Silvana Mattiello, Stefania Celozzi, Jakub Mrázek, Chahrazed Mekadim, Hana Sechovcová, Simona Kvasnová, Elie Atallah, Giuseppe Moniello
Animals.2022; 12(16): 2011. CrossRef - Zinc Biofortified Cowpea (Vigna unguiculata L. Walp.) Soluble Extracts Modulate Assessed Cecal Bacterial Populations and Gut Morphology In Vivo (Gallus gallus)
Mariana Juste Contin Gomes, Hércia Stampini Duarte Martino, Nikolai Kolba, Jacquelyn Cheng, Nikita Agarwal, Maurisrael de Moura Rocha, Elad Tako
Frontiers in Bioscience-Landmark.2022;[Epub] CrossRef - Microbial gut evaluation in an angolan paediatric population with sickle cell disease
Mariana Delgadinho, Catarina Ginete, Brígida Santos, Joana Mendes, Armandina Miranda, Jocelyne Vasconcelos, Miguel Brito
Journal of Cellular and Molecular Medicine.2022; 26(21): 5360. CrossRef -
Survival Strategies and Metabolic Interactions between Ruminococcus gauvreauii and
Ruminococcoides bili
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Natalia Molinero, Elena Conti, Alan W. Walker, Abelardo Margolles, Sylvia H. Duncan, Susana Delgado, Jeffrey A. Gralnick
Microbiology Spectrum.2022;[Epub] CrossRef - Chlorogenic acid improves growth performance of weaned rabbits via modulating the intestinal epithelium functions and intestinal microbiota
Jiali Chen, Zhicheng Song, Rongmei Ji, Yongxu Liu, Hong Zhao, Lei Liu, Fuchang Li
Frontiers in Microbiology.2022;[Epub] CrossRef - Changes to the microbiome of alfalfa during the growing season and after ensiling with Lentilactobacillus buchneri and Lentilactobacillus hilgardii inoculant
Pascal Drouin, Julien Tremblay, Érica Benjamim da Silva, Emmanuelle Apper
Journal of Applied Microbiology.2022; 133(4): 2331. CrossRef - Evaluation of Antioxidant Capacity and Gut Microbiota Modulatory Effects of Different Kinds of Berries
Jiebiao Chen, Yichen Shu, Yanhong Chen, Zhiwei Ge, Changfeng Zhang, Jinping Cao, Xian Li, Yue Wang, Chongde Sun
Antioxidants.2022; 11(5): 1020. CrossRef - Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection
Sean T. Jones, Kejun Guo, Emily H. Cooper, Stephanie M. Dillon, Cheyret Wood, David H. Nguyen, Guannan Shen, Bradley S. Barrett, Daniel N. Frank, Miranda Kroehl, Edward N. Janoff, Katerina Kechris, Cara C. Wilson, Mario L. Santiago, Frank Kirchhoff
Journal of Virology.2022;[Epub] CrossRef - Effects of lactic acid-producing bacteria as direct-fed microbials on the ruminal microbiome
H.F. Monteiro, A.L.J. Lelis, P. Fan, B. Calvo Agustinho, R.R. Lobo, J.A. Arce-Cordero, X. Dai, K.C. Jeong, A.P. Faciola
Journal of Dairy Science.2022; 105(3): 2242. CrossRef - Saccharomyces cerevisiae boulardiiCNCM I-1079 supplementation in finishing male pigs helps to cope with heat stress through feeding behaviour and gut microbiota modulation
Etienne Labussière, Caroline Achard, Serge Dubois, Sylvie Combes, Mathieu Castex, David Renaudeau
British Journal of Nutrition.2022; 127(3): 353. CrossRef - Specific Alterations of Gut Microbiota in Chinese Patients with Hypertension: A Systematic Review and Meta-Analysis
Yunlong Qin, Jin Zhao, Yuwei Wang, Ming Bai, Shiren Sun
Kidney and Blood Pressure Research.2022; 47(7): 433. CrossRef - 2-Hydroxy-4-(Methylthio) Butanoic Acid Isopropyl Ester Supplementation Altered Ruminal and Cecal Bacterial Composition and Improved Growth Performance of Finishing Beef Cattle
Xiaoli Qin, Depeng Zhang, Xinjun Qiu, Kai Zhao, Siyu Zhang, Chunlan Liu, Lianqiang Lu, Yafang Cui, Changxiao Shi, Zhiming Chen, Rikang Hao, Yingqi Li, Shunran Yang, Lina Wang, Huili Wang, Binghai Cao, Huawei Su
Frontiers in Nutrition.2022;[Epub] CrossRef - Heat Stress Affects Jejunal Immunity of Yellow-Feathered Broilers and Is Potentially Mediated by the Microbiome
Wen-Chao Liu, Meng-Yi Huang, Balamuralikrishnan Balasubramanian, Rajesh Jha
Frontiers in Physiology.2022;[Epub] CrossRef - Red Raspberry and Fructo-Oligosaccharide Supplementation, Metabolic Biomarkers, and the Gut Microbiota in Adults with Prediabetes: A Randomized Crossover Clinical Trial
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Journal Articles
- Promising cellulolytic fungi isolates for rice straw degradation
- Diana Catalina Pedraza-Zapata , Andrea Melissa Sánchez-Garibello , Balkys Quevedo-Hidalgo , Nubia Moreno-Sarmiento , Ivonne Gutiérrez-Rojas
- J. Microbiol. 2017;55(9):711-719. Published online September 2, 2017
- DOI: https://doi.org/10.1007/s12275-017-6282-1
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Abstract
- The objective of this study was to evaluate the potential of eight fungal isolates obtained from soils in rice crops for straw degradation in situ. From the initial eight isolates, Pleurotus ostreatus T1.1 and Penicillium sp. HC1 were selected for further characterization based on qualitative cellulolytic enzyme production and capacity to use rice straw as a sole carbon source. Subsequently, cellulolytic, xylanolytic, and lignolytic (Pleurotus ostreatus) activity on carboxymethyl cellulose, oat xylan, and rice straw with different nitrogen sources was evaluated. From the results obtained it was concluded both isolates are capable to produce enzymes necessary for rice straw degradation. However, their production is dependent upon carbon and nitrogen source. Last, it was established that Pleurotus ostreatus T1.1 and Penicillium sp. HC1 capability to colonize and mineralize rice straw, in mono-and co-culture, without affecting nitrogen soil content.
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Citations
Citations to this article as recorded by- Unravelling of cellulolytic fungal consortium from humus soil for efficient lignocellulosic waste degradation
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- DOI: https://doi.org/10.1007/s12275-017-6265-2
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Abstract
- Efficiency of Enterobacter cloacae KU923381 isolated from petroleum hydrocarbon contaminated soil was evaluated in batch culture and bioreactor mode. The isolate were screened for biofilm formation using qualitative and quantitative assays. Response surface methodology (RSM) was used to study the effect of pH, temperature, glucose concentration, and sodium chloride on diesel degradation. The predicted values for diesel oil degradation efficiency by the statistical designs are in a close agreement with experimental data (R2 = 99.66%). Degradation efficiency is increased by 36.78% at pH = 7, temperature = 35°C, glucose = 5%, and sodium chloride concentration = 5%. Under the optimized conditions, the experiments were performed for diesel oil degradation by gas chromatographic mass spectrometric analysis (GC-MS). GC-MS analysis confirmed that E. cloacae had highly degrade hexadecane, heptadecane, tridecane, and docosane by 99.71%, 99.23%, 99.66%, and 98.34% respectively. This study shows that rapid bioremoval of hydrocarbons in diesel oil is acheived by E. cloacae with abet of biofilm formation. The potential use of the biofilms for preparing trickling filters (gravel particles) for the degradation of hydrocarbons from petroleum wastes before their disposal in the open environment is highly suggested. This is the first successful attempt for artificially establishing petroleum hydrocarbon degrading bacterial biofilm on solid substrates in bioreactor.
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- 5 Crossref
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Abstract
- This study was carried out to better understand the characteristic modification mechanisms of monolignols by enzyme system of Abortiporus biennis and to induce the degradation of monolignols. Degradation and polymerization of monolignols were simultaneously induced by A. biennis. Whole cells of A. biennis degraded coniferyl alcohol to vanillin and coniferyl aldehyde, and degraded sinapyl alcohol to 2,6-dimethoxybenzene- 1,4-diol, with the production of dimers. The molecular weight of monolignols treated with A. biennis increased drastically. The activities of lignin degrading enzymes were monitored for 24 h to determine whether there was any correlation between monolignol biomodification and ligninolytic enzymes. We concluded that complex enzyme systems were involved in the degradation and polymerization of monolignols. To degrade monolignols, ascorbic acid was added to the culture medium as a reducing agent. In the presence of ascorbic acid, the molecular weight was less increased in the case of coniferyl alcohol, while that of sinapyl alcohol was similar to that of the control. Furthermore, the addition of ascorbic acid led to the production of various degraded compounds: syringaldehyde and acid compounds. Accordingly, these results demonstrated that ascorbic acid prevented the rapid polymerization of monolignols, thus stabilizing radicals generated by enzymes of A. biennis. Thereafter, A. biennis catalyzed the oxidation of stable monolignols. As a result, ascorbic acid facilitated predominantly monolignols degradation by A. biennis through the stabilization of radicals. These findings showed outstanding ability of A. biennis to modify the lignin compounds rapidly and usefully.
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Research Support, U.S. Gov't, Non-P.H.S.
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Abstract
- bacterial synergism, lignocellulose degradation, bacterial activity, enzyme production, microbial interaction
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Journal Articles
- 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
- 65 View
- 0 Download
- 14 Crossref
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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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Citations
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- Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation
- Application of Response Surface Methodology for Rapid Chrysene Biodegradation by Newly Isolated Marine-derived Fungus Cochliobolus lunatus Strain CHR4D
- Jwalant K. Bhatt , Chirag M. Ghevariya , Dushyant R. Dudhagara , Rahul K. Rajpara , Bharti P. Dave
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- 50 View
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- 16 Crossref
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Abstract
- For the first time, Cochliobolus lunatus strain CHR4D, a marine-derived ascomycete fungus isolated from historically contaminated crude oil polluted shoreline of Alang-Sosiya ship-breaking yard, at Bhavnagar coast, Gujarat has been reported showing the rapid and enhanced biodegradation of chrysene, a four ringed high molecular weight (HMW) polycyclic aromatic hydrocarbon (PAH). Mineral Salt Broth (MSB) components such as ammonium tartrate and glucose along with chrysene, pH and trace metal solution have been successfully optimized by Response Surface Methodology (RSM) using central composite design (CCD). A validated, two-step optimization protocol has yielded a substantial 93.10% chrysene degradation on the 4th day, against unoptimized 56.37% degradation on the 14th day. The results depict 1.65 fold increase in chrysene degradation and 1.40 fold increase in biomass with a considerable decrement in time. Based on the successful laboratory experiments, C. lunatus strain CHR4D can thus be predicted as a potential candidate for mycoremediation of HMW PAHs impacted environments.
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