Article
Microbiology
Hamzeh Mafakheri, S. Mohsen Taghavi, Sadegh Zarei, Touraj Rahimi, Mohammad Sadegh Hasannezhad, Perrine Portier, Marion Fischer-Le Saux, Ivica Dimkic, Ralf Koebnik, Nemanja Kuzmanovic, Ebrahim Osdaghi
Summary: In this study, crown gall-associated Xanthomonas strains isolated from ornamental plants in Iran were characterized and analyzed using plant inoculation assays, molecular-phylogenetic analyses, and comparative genomics. The results showed that these strains belong to two new taxonomically unique clades within the Glade IA of Xanthomonas and are genetically distinct from X. translucens. Comparative genomics analysis revealed the absence of type III secretion system genes and type III effectors in these strains. This study provides new insights into the genetic diversity and plant interactions of crown gall-associated bacteria.
MICROBIOLOGY SPECTRUM
(2022)
Article
Food Science & Technology
Yanzi Wang, Honghua Kang, Mengyi Jin, Guoliang Wang, Weifang Ma, Zhen Liu, Yuhua Xue, Cheng Li
Summary: A stable and reliable model of corneal bee sting injury was successfully established, revealing the pathogenesis and therapeutic targets. Hub genes identified in the study are expected to serve as biomarkers and therapeutic targets for the diagnosis and treatment of corneal bee sting.
Article
Biology
Helen Blank, Janine Bayer
Summary: Model-based analyses of fMRI data provide insights into the neural basis of similarity-based categorization. Prototype and exemplar representations were found in different brain areas, and some individuals formed both representation types simultaneously.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
Yuxiang Zhang, Jianping Wei, Hong Guo, Chen Niu, Yahong Yuan, Tianli Yue
Summary: This study revealed the antibacterial mechanism of cinnamic acid (CA) against food-derived Pseudomonas fragi 38-8. CA exerted its antibacterial effect mainly by disrupting cell membrane homeostasis, leading to depolarization of the cell membrane, intracellular pH reduction, and decrease in intracellular ATPase activity, ultimately inhibiting bacterial growth.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Oncology
Ellis Michiels, Hediel Madhloum, Silke Van Lint, Nouredin Messaoudi, Rastislav Kunda, Sandrina Martens, Philippe Giron, Catharina Olsen, Pierre Lefesvre, Nelson Dusetti, Leila EL Mohajer, Richard Tomasini, Lukas J. A. C. Hawinkels, Farah Ahsayni, Remy Nicolle, Tatjana Arsenijevic, Christelle Bouchart, Jean-Luc Van Laethem, Ilse Rooman
Summary: This study identifies two subtypes of pancreatic cancer and reveals spatial phenotypes within tumors through analysis of mRNA panels. These findings are important for understanding tumor heterogeneity and guiding therapeutic approaches.
JOURNAL OF PATHOLOGY
(2023)
Article
Genetics & Heredity
Shengqian Xia, Nicholas W. VanKuren, Chunyan Chen, Li Zhang, Clause Kemkemer, Yi Shao, Hangxing Jia, UnJin Lee, Alexander S. Advani, Andrea Gschwend, Maria D. Vibranovski, Sidi Chen, Yong E. Zhang, Manyuan Long
Summary: It is conventionally believed that the genetic basis of development is conserved over evolutionary time, but recent research has shown the importance of new genes in fruit fly development. Experimental and computational analyses have revealed that new genes, especially those less than 40 million years old, play essential roles in viability during fruit fly development.
Article
Multidisciplinary Sciences
Cunmin Qu, Meichen Zhu, Ran Hu, Yongchao Niu, Si Chen, Huiyan Zhao, Chengxiang Li, Zhen Wang, Nengwen Yin, Fujun Sun, Zhiyou Chen, Shulin Shen, Guoxia Shang, Yan Zhou, Xingying Yan, Lijuan Wei, Liezhao Liu, Bin Yi, Jinmin Lian, Jiang Li, Zhanglin Tang, Ying Liang, Xinfu Xu, Rui Wang, Jiaming Yin, Huafang Wan, Hai Du, Wei Qian, Yourong Chai, Qingyuan Zhou, Yajun He, Silin Zhong, Xiao Qiu, Hao Yu, Hon-Ming Lam, Kun Lu, Fuyou Fu, Jiana Li
Summary: In this study, high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821) rapeseed were assembled, and a quantitative trait locus (QTL) controlling seed color was finely mapped. The BnA09MYB47a gene encoding a transcription factor was identified as the causal gene for the yellow-seed trait. Functional studies revealed that sequence variation of BnA09MYB47a leads to the functional divergence between yellow- and black-seeded rapeseed.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Jiani Yang, Shuang Zhang, Yu Zhang, Dan Zhao, Tao Liu, Xindi Sun, Lei Yan
Summary: Understanding the molecular mechanism of magnetite (Fe3O4) nanoparticle synthesis in Acidithiobacillus ferrooxidans BYM is crucial for the commercial development of biogenic Fe(3)O(4) nanoparticles. Different treatment conditions, such as FeSO4 center dot 7H(2)O concentrations, growth times, and magnetic field intensities, significantly affected intracellular iron content and the number and size of Fe3O4 nanoparticles. Transcriptome analysis identified differentially expressed genes (DEGs) and significant expression profiles, enriching ion transport, oxidation-reduction process, membrane structure, signal transduction, and quorum sensing. Gene regulatory networks associated with Fe3O4 nanoparticle synthesis revealed modules significantly correlated with phenomic parameters. Ten hub genes significantly correlated with Fe3O4 nanoparticle phenomic parameters were selected from 24 eigengenes related to iron metabolism. Based on previous research and present findings, a hypothetical molecular model for Fe3O4 nanoparticle synthesis mediated by these hub genes was proposed, involving membrane formation, iron uptake and transport, iron redox, and crystal maturity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Genetics & Heredity
Yiwen Ju, Zhenling Wan, Qin Zhang, Si Li, Bingshu Wang, Jianmin Qiu, Shaojiang Zheng, Shuo Gu
Summary: By analyzing the proteomics of cerebrospinal fluid from patients with hydrocephalus and arachnoid cyst, differentially expressed proteins related to the diseases were identified, and potential therapeutic drugs were uncovered. These findings provide valuable resources for investigating the molecular pathways in hydrocephalus and offer potential biomarkers for clinical diagnosis and therapy.
CURRENT GENE THERAPY
(2023)
Article
Microbiology
Eom-Ji Oh, In Sun Hwang, In Woong Park, Chang-Sik Oh
Summary: Through the analysis of the genome sequence of Clavibacter michiganensis strain LMG7333(T), it was found that its plasmids carry distinct gene content compared to other strains. This information is important for understanding the genetic diversity of Clavibacter species.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Ali Bahadur, Ting Li, Wasim Sajjad, Fahad Nasir, Muhammad Amir Zia, Minghui Wu, Gaosen Zhang, Guangxiu Liu, Tuo Chen, Wei Zhang
Summary: This study investigated the transcriptional response of Planomicrobium strain AX6, isolated from a cold-desert ecosystem in the Qinghai-Tibet Plateau, China, to H2O2 stress. The results revealed that the strain utilizes up-regulated genes involved in antioxidant defense pathways to scavenge H2O2, providing a competitive advantage for its survival in H2O2-polluted environments.
Article
Microbiology
Miryam Valenzuela, Marianela Gonzalez, Alexis Velasquez, Fernando Dorta, Ivan Montenegro, Ximena Besoain, Francisco Salva-Serra, Daniel Jaen-Luchoro, Edward R. B. Moore, Michael Seeger
Summary: This study characterized nine strains of Clavibacter michiganensis subsp. michiganensis isolated in Chile, revealing differences in virulence. Two highly virulent strains showed increased cellulase activity, while a strain causing mild symptoms had no cellulase activity. PCR and gene sequence analysis indicated correlations between disease severity differences and the presence/absence of specific genes. Deletions in virulence genes were also observed in the Chilean strains.
Article
Medicine, Research & Experimental
Sheng-Qing Lv, Zhen Fu, Lin Yang, Qing-Rui Li, Jiang Zhu, Qu-Jing Gai, Min Mao, Jiang He, Yan Qin, Xiao-Xue Yao, Xi Lan, Yan-Xia Wang, Hui-Min Lu, Yan Xiang, Zuo-Xin Zhang, Guo-Hao Huang, Wei Yang, Ping Kang, Zhijian Sun, Yu Shi, Xiao-Hong Yao, Xiu-Wu Bian, Yan Wang
Summary: This study comprehensively analyzed the genetic, DNA methylomic, and transcriptomic characteristics of multifocal glioblastoma (mGBM), revealing specific genetic features and DNA methylation changes in mGBM. Different tumor foci in mGBM exhibited distinct molecular subtypes, and components of the extracellular microenvironment, such as LIF and CCL2, were found to contribute to the evolution and prognosis of tumor foci in mGBM patients.
Review
Biochemistry & Molecular Biology
Hugo Maruyama, Takayuki Nambu, Chiho Mashimo, Toshinori Okinaga, Kunio Takeyasu
Summary: Comparative structural and molecular biology using single-molecule analyses, combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution, have been powerful tools for elucidating the mechanisms underlying genome DNA folding in all three domains of life. Key protein players such as histone, Alba, HU, and SMC proteins have been identified as fundamental structural units involved in genome folding. Recent studies have revealed the involvement of archaeal SMC proteins in higher-order genome folding, and detailed functions of bacterial and eukaryotic SMC proteins have been uncovered using single-molecule tracking techniques. The similarities and differences in DNA-folding mechanisms in the three domains of life have been highlighted.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Yuta Aoyagi Blue, Junko Kusumi, Akiko Satake
Summary: The study reveals the expansion of the PARP gene family in trees compared to annual and perennial herbs, with PARP1 showing a close association with growth rate. The findings suggest a conserved role of PARPs in longevity between plants and animals.
Article
Biotechnology & Applied Microbiology
Appadurai Muthamil Iniyan, Joachim Wink, Wiebke Landwehr, Eedara Veera Venkata Ramprasad, Chintalapati Sasikala, Chintalapati Venkata Ramana, Peter Schumann, Cathrin Sproer, Boyke Bunk, Francis-Joseph Rosemary Sharmila Joseph, Sam Albert Joshua, Eby-Nesar Stella-Glory Deepak Shyl, Rajaretinam Rajesh Kannan, Samuel Gnana Prakash Vincent
Summary: A novel marine actinomycete strain ICN19(T) was isolated and identified, showing distinct differences from previously described Streptomyces species at both phenotypic and molecular levels. The strain represents a new species within the genus Streptomyces based on physiological, biochemical, chemotaxonomic, and genomic characteristics. The proposed name for this novel species is Streptomyces marianii sp. nov. (ICN19(T) = MCC 3599(T) = KCTC 39749(T)).
JOURNAL OF ANTIBIOTICS
(2021)
Editorial Material
Microbiology
Markus Goeker
Summary: This is the record of the online meeting of the Judicial Commission of the International Committee on Systematics of Prokaryotes held on August 4, 2021 via video conference.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Eduarda Almeida, Valentina Henriques, Sandra Wiegand, Luciana Albuquerque, Peter Schumann, Timo Kohn, Christian Jogler, Milton Simoes da Costa, Alexandre Lobo-da-Cunha, Maria de Fatima Carvalho, Olga Maria Lage
Summary: A novel micro-organism named Salsipaludibacter albus was isolated from dry salt in Portugal. It is a Gram-stain-positive, rod-shaped bacterium that requires oxygen for growth. The strain exhibits pleomorphism, with long filaments of rod-shaped cells and coccoid cellular forms at the end of the filaments. It grows best at temperatures between 20-30 degrees C, NaCl concentrations of 2%, and pH values of 8.0-11.0. Based on genomic, phylogenetic, phenotypic, and chemotaxonomic studies, it is proposed that Salsipaludibacter albus represents a new genus, species, family, and order.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Sara Szuroczki, Gorkhmaz Abbaszade, Karoly Boka, Peter Schumann, Meina Neumann-Schaal, Erika Toth
Summary: A new bacterial strain, named Szabonella alba gen. nov., sp. nov., was isolated from a water sample in Hungary. Phylogenetic analysis revealed that it is distinct from its closest relatives in the family Rhodobacteraceae based on 16S rRNA gene sequences and genome-related indices.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
David R. Arahal, Hans-Jurgen Busse, Carolee T. Bull, Henrik Christensen, Maria Chuvochina, Svetlana N. Dedysh, Pierre-Edouard Fournier, Konstantinos T. Konstantinidis, Charles T. Parker, Ramon Rossello-Mora, Antonio Ventosa, Markus Goeker
Summary: These Opinions address multiple requests, including the designation of neotypes and name corrections. The Judicial Commission concludes that certain names did not meet the requirements for valid publication.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Letter
Microbiology
Iain C. Sutcliffe, David R. Arahal, Markus Goeker, Aharon Oren
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jan P. Meier-Kolthoff, Joaquim Sarda Carbasse, Rosa L. Peinado-Olarte, Markus Goeker
Summary: Microbial systematics is influenced by genome-based methods and faces challenges from the increasing number of taxon names and associated sequences. Accurate and reliable high-throughput platforms like LPSN and TYGS are essential for handling the data efficiently. The updates include new features and expanded database content to provide easy access to the data.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Johannes Sikorski, Vanessa Baumgartner, Klaus Birkhofer, Runa S. Boeddinghaus, Boyke Bunk, Markus Fischer, Baerbel U. Foesel, Michael W. Friedrich, Markus Goeker, Norbert Hoelzel, Sixing Huang, Katharina J. Huber, Ellen Kandeler, Valentin H. Klaus, Till Kleinebecker, Sven Marhan, Christian von Mering, Yvonne Oelmann, Daniel Prati, Kathleen M. Regan, Tim Richter-Heitmann, Joao F. Matias Rodrigues, Barbara Schmitt, Ingo Schoening, Marion Schrumpf, Elisabeth Schurig, Emily F. Solly, Volkmar Wolters, Joerg Overmann
Summary: This study used a culture-independent niche modeling approach to investigate the ecological adaptations and evolution of Acidobacteria in grassland soils in Germany. The results revealed a pronounced ecological diversification among acidobacterial sister clades and showed that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation. The niche modeling approach correctly predicted the physiological properties of cultivated species of Acidobacteria and provided novel information on ecological adaptations that cannot be inferred from standard taxonomic descriptions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Moussa Louati, Karima Hezbri, Maria del Carmen Montero-Calasanz, Manfred Rohde, Markus Goeker, Faten Ghodhbane-Gtari, Hans-Peter Klenk, Imen Nouioui, Maher Gtari
Summary: A new actinobacterium strain, Blastococcus tunisiensis sp. nov., was isolated from a limestone sample collected in Tunisia, which has distinct phenotypic and genotypic features.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Infectious Diseases
Gabriele Margos, Gary P. Wormser, Ira Schwartz, Mateusz Markowicz, Anna J. Henningsson, Reto Lienhard, Brian Stevenson, Agustin Estrada-Pena, Andreas Sing, Volker Fingerle, Markus Goker
Summary: The taxon names used in public databases are critical for linking organisms to sequence data. Simplistic approaches for determining preferred synonyms can introduce biases in taxonomic opinions. It is not necessary or possible to generate newer validly published names for reverting to the previous merged genus. The policy of always preferring the latest validly published name may render the database oblivious to reversals in taxonomic opinion.
TICKS AND TICK-BORNE DISEASES
(2022)
Article
Microbiology
Markus Goeker
Summary: This article discusses the major modifications made to the International Code of Nomenclature for Prokaryotes (ICNP) regarding higher taxonomic ranks. The introduction of the phylum category and the clarification of naming rules for classes have resolved uncertainties in taxonomy. However, there are still some issues surrounding the validity and legitimacy of certain names at the class, order, and family levels. This article aims to provide missing formal descriptions and attribute taxon names to their original authors.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Editorial Material
Microbiology
Markus Goeker, Edward R. B. Moore, Aharon Oren, Martha E. Trujillo
Summary: The recent publication of the alternative nomenclatural code SeqCode raises questions about how to treat names 'validly published' under that code in IJSEM. It is reiterated that IJSEM must adhere to the ICNP and assign a nomenclatural status to all prokaryotic names, including those 'validly published' under SeqCode. Such names should be marked as Candidatus names or printed in quotation marks.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Maria del Carmen Montero-Calasanz, Adnan Yaramis, Manfred Rohde, Peter Schumann, Hans-Peter Klenk, Jan P. Meier-Kolthoff
Summary: Integrating genomic information into microbial systematics allows for reliable prokaryotic classification. In silico chemotaxonomic analysis is being introduced to replace traditional laboratory methods for characterizing taxa, increasing speed and accuracy of taxonomic reports. Genomics has already played a role in taxonomic rearrangement, highlighting the need for revisiting taxonomy in light of new genomic data.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Markus Goeker, Aharon Oren
Summary: Observations show that adding a category should be done before informal names at that rank are widely used, based on the introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP). An extrapolation from the number of validly published names under the ICNP at different categories suggests that adding kingdom and domain as separate principal ranks would be beneficial. By examining taxonomic activity and associated nomenclatural problems above the phylum level, it is confirmed that introducing these ranks would help stabilize prokaryotic nomenclature. Proposed amendments to the ICNP include the inclusion of kingdom and domain as additional categories.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Cell Biology
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rudiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sarda, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Goeker, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The study presents a comprehensive analysis of actinobacterial diversity, showing that only a small portion of this diversity is represented by sequenced genomes. The comparison of gene functions reveals novel determinants of host-microbe interaction and environment-specific adaptations. The analysis of biosynthetic gene clusters highlights the role of horizontal gene transfer and gene loss in shaping secondary metabolite repertoire.