Article
Microbiology
Jutta Wiese, Johannes F. Imhoff, Hannes Horn, Erik Borchert, Nikos C. Kyrpides, Markus Goeker, Hans-Peter Klenk, Tanja Woyke, Ute Hentschel
ARCHIVES OF MICROBIOLOGY
(2020)
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
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
Stefan Spring, Manfred Rohde, Boyke Bunk, Cathrin Sproeer, Sabine Eva Will, Meina Neumann-Schaal
Summary: Strain L21-Ace-BEST, isolated from a lithifying cyanobacterial mat, belongs to a novel species and genus within the class Deferribacteres. It is an important model organism for studying anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized using biochemical studies, comparative genome analyses, and gene expression pattern evaluations. The potential use of a reversed oxidative citric acid cycle to fix CO2 was revealed through genome analysis.
ENVIRONMENTAL 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
Biochemistry & Molecular Biology
Julia Koblitz, Philipp Halama, Stefan Spring, Vera Thiel, Christiane Baschien, Richard L. Hahnke, Michael Pester, Joerg Overmann, Lorenz Christian Reimer
Summary: We present Media Dive, a comprehensive and expert-curated cultivation media database that provides recipes, instructions, and molecular compositions of over 3200 standardized cultivation media for more than 40,000 microbial strains from all domains of life. MediaDive is designed to support a wide range of applications, from everyday use in research and diagnostic laboratories to knowledge-driven support for new media design and artificial intelligence-driven data mining.
NUCLEIC ACIDS RESEARCH
(2023)
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
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
Microbiology
Nathalie Pradel, Marie-Laure Fardeau, Boyke Bunk, Cathrin Sproeer, Christian Boedeker, Jacqueline Wolf, Meina Neumann-Schaal, Michael Pester, Stefan Spring
Summary: A novel sulphur-reducing bacterium was isolated from sewage sludge in a wastewater treatment plant. It belongs to the phylum Synergistota and is anaerobic with a fermentative metabolism using peptides and amino acids as substrates. We propose the new species and genus Aminithiophilus ramosus and suggest reclassifying certain members of the Synergistaceae into new families based on phylogenomic data.
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.