Article
Immunology
Sarah A. Ahmed, Tobias Engel, Jan Zoll, Peggy C. R. Godschalk, Ruth Klaasen, Leandro Moreno, Henrich van der Lee, Paul E. Verweij, Sybren de Hoog
Summary: The study reports a case of subcutaneous phaeohyphomycosis in an immunocompetent patient and proposes a new genus and species to name the causative fungus. Whole genome analysis reveals several genes associated with pathogenicity, but further research is needed to understand the pathogenic mechanism of the fungus and the origin of pathogenicity in the family Trematosphaeriaceae.
MICROBES AND INFECTION
(2022)
Article
Microbiology
Camila Gazolla Volpiano, Fernando Hayashi Sant'Anna, Adriana Ambrosini, Jackson Freitas Brilhante de Sao Jose, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Summary: Taxonomic decisions within the order Rhizobiales are based on highly conserved 16S rRNA sequences and DNA-DNA hybridizations. By computing ANI values from genome sequences of type strains, it was found that several bacterial species exhibit synonymy, while a new classification for Aminobacter heintzii and Aminobacter cicerones is proposed. Additionally, an R package called ProKlust was introduced for downstream analysis of large ANI matrices.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Jian-Yu Jiao, Zheng-Han Lian, Ze-Tao Liu, Lan Liu, Meng-Meng Li, Ai-Ping Lv, Wen-Dong Xian, Ting Zhou, Zhitang Lyu, Nimaichand Salam, Wen-Jun Li
Summary: Phylogenomic analyses revealed classification issues in two species within the genera Meiothermus and Calidithermus, leading to a proposal for reclassification. Additionally, two heterotypic synonyms were identified within the species of Meiothermus.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Editorial Material
Radiology, Nuclear Medicine & Medical Imaging
Kathleen F. Kerr
Summary: When evaluating a new risk factor for disease, researchers often compare its value with existing biomarkers and risk factors. They use net reclassification index (NRI) statistics to compare the performance of old and new risk models. However, NRI statistics have been found to have unacceptable statistical behavior, incorrect inferences, and lack interpretability. Therefore, NRI statistics are considered unhelpful at best and misleading at worst.
Article
Microbiology
Mauricio Javier Lozano, Ezequiel Gerdardo Mogro, Walter Omar Draghi
Summary: Burkholderia novacaledonica has been reclassified as Caballeronia novacaledonica comb. nov, confirming its placement in the Caballeronia genus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Joseph Wambui, Nicole Cernela, Marc J. A. Stevens, Roger Stephan
Summary: This study identified and characterized isolates within the Clostridium estertheticum complex (CEC) through whole genome sequencing, revealing potential overlaps between different species when using different threshold values for species classification.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Xiaoying Liu, Jessica L. Sutter, Jacobo de la Cuesta-Zuluaga, Jillian L. Waters, Nicholas D. Youngblut, Ruth E. Ley
Summary: The genera Catabacter and Christensenella, both strict anaerobes within the Firmicutes phylum, are closely related. Phylogenetic analysis shows that Catabacter splits Christensenella into a polyphyletic clade. Based on evolutionary relationship, Catabacter hongkongensis should be transferred to the genus Christensenella as Christensenella hongkongensis comb. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Hisayuki Komaki, Tomohiko Tamura
Summary: In this study, it was found that Streptomyces cinnamonensis and Streptomyces virginiae share the same gene sequence and belong to the same genomospecies, leading to a reclassification of the former as a heterotypic synonym of the latter. Despite identical gene sequences among some Streptomyces species, digital DNA-DNA relatedness indicated that they are not synonymous.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Noah Hensen, Lucas Bonometti, Ivar Westerberg, Ioana Onut Brannstrom, Sonia Guillou, Sandrine Cros-Aarteil, Sara Calhoun, Sajeet Haridas, Alan Kuo, Stephen Mondo, Jasmyn Pangilinan, Robert Riley, Kurt Labutti, Bill Andreopoulos, Anna Lipzen, Cindy Chen, Mi Yan, Chris Daum, Vivian Ng, Alicia Clum, Andrei Steindorff, Robin A. Ohm, Francis Martin, Philippe Silar, Donald O. Natvig, Christophe Lalanne, Valerie Gautier, Sandra Lorena Ament-Velasquezi, Asa Kruys, Miriam I. Hutchinson, Amy Jo Powell, Kerrie Barry, Andrew N. Miller, Igor Grigoriev, Robert Debuchy, Pierre Gladieux, Markus Hiltunen Thoren, Hanna Johannesson
Summary: This study analyzed the genomes of 99 Sordariales species, including 52 newly sequenced genomes, to understand their taxonomy and genome evolution. The results revealed the variations in genomic traits among different families within the order and provided a comprehensive framework for studying genome evolution in this important group of fungi.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Paolo Pellizzoni, Giulia Muzio, Karsten Borgwardt
Summary: HOGImine is a novel algorithm that considers higher-order interactions of genes and allows multiple encodings for the genetic variants, expanding the class of discoverable genetic meta-markers. Experimental evaluation shows that it has higher statistical power compared to previous methods, enabling the discovery of previously unidentified genetic mutations associated with the phenotype. The algorithm also incorporates biological knowledge to improve search efficiency and computation time.
Article
Oncology
Andrea Casadei-Gardini, Sara Lonardi, Valeria Smiroldo, Matteo Canale, Alessandro Passardi, Nicola Silvestris, Giulia Orsi, Floriana Nappo, Lorenza Rimassa, Matteo Fassan, Paola Spaggiari, Oronzo Brunetti, Kalliopi Andrikou, Stefano Cascinu
Summary: The study identified three distinct subtypes of SBA based on genetic analysis: immunological subtype, DNA Damage Repair (DDR) like subtype, and Colon-like subtype. These findings suggest potential targeted therapy options for patients beyond chemotherapy.
Article
Biology
Jacqueline Heckenhauer, Paul B. Frandsen, John S. Sproul, Zheng Li, Juraj Paule, Amanda M. Larracuente, Peter J. Maughan, Michael S. Barker, Julio Schneider, Russell J. Stewart, Steffen U. Pauls
Summary: The size of genomes in caddisflies varies greatly, and the expansion of repetitive elements, particularly transposable elements, is identified as a major driver of larger genome sizes. The association between transposable elements and genome size shows a linear relationship. Moreover, expanded genomes are more likely to occur in caddisfly lineages with higher ecological diversity.
Article
Microbiology
Haoyu Wang, Xiaoling Sha, Rui Li, Yijing Li, Himel Nahreen Khaleque, Yuxiu Zhang, Tsing Bohu, Zhihui Bai, Xuliang Zhuang
Summary: This study conducted a genome-wide comparative analysis of the strain EBL0706, confirming it as a strain of Luteovulum azotoformans. The genome of EBL0706 contains 4034 protein-coding genes, including a complete photosynthetic gene cluster.
Article
Microbiology
Ekaterina M. Semenova, Denis S. Grouzdev, Diyana S. Sokolova, Tatiyana P. Tourova, Andrey B. Poltaraus, Natalia Potekhina, Polina N. Shishina, Maria A. Bolshakova, Alexander N. Avtukh, Elena A. Ianutsevich, Vera M. Tereshina, Tamara N. Nazina
Summary: This study aimed to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. A new species Actinotalea subterranea was isolated and characterized, and taxonomic revision of the genera Actinotalea and Pseudactinotalea was proposed based on phylogenomic analysis of Actinobacteria.
Review
Biochemistry & Molecular Biology
Ahmad Ibrahim, Philippe Colson, Vicky Merhej, Rita Zgheib, Mohamad Maatouk, Sabrina Naud, Fadi Bittar, Didier Raoult
Summary: Living organisms interact and transfer genetic sequences, resulting in mosaic genomes that challenge traditional classification schemes. By integrating representative genomes and constructing a genetic network, a more accurate understanding of evolutionary relationships among species is achieved. The discovery of a separate taxon, fifth TRUC, highlights the importance of updating classification systems to accommodate new organisms and advances in evolutionary studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Alexandra Pitt, Ulrike Koll, Johanna Schmidt, Meina Neumann-Schaal, Jacqueline Wolf, Sophia Krausz, Martin W. Hahn
Summary: Two bacterial strains isolated from freshwater habitats near Salzburg, Austria were identified as new species of the genus Aquirufa through genome-based phylogenetic reconstructions. They exhibited distinct phenotypic and genomic features compared to other members of the genus.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Antonio Camacho
Summary: This study characterized 14 strains of freshwater bacteria through genomic, phylogenetic, and phenotypic analyses. The results indicate that these strains represent 14 new species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Qi Liu, Zichen He, Takeshi Naganuma, Ryosuke Nakai, Luz Maria Rodriguez, Rafael Carreno, Franco Urbani
Summary: This study investigated the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands and found that the microbial composition in silicate caves is similar to that in limestone and other silicate caves. Additionally, the study inferred metabolic features and found that membrane transport and amino acid metabolism may play important roles in the formation and weathering of silicate speleothems.
Article
Microbiology
Zichen He, Takeshi Naganuma, Ryosuke Nakai, Satoshi Imura, Megumu Tsujimoto, Peter Convey
Summary: This study compared the bacterial floras and potential metabolism of rock tripe lichens from two distinct Antarctic biological regions. The results showed clear differences in bacterial communities between the two regions and suggested that the sampling area's climate may influence the metabolism of the lichen-associated bacteria.
Article
Microbiology
Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Ulrike Koll, Jacqueline Wolf, William B. Whitman, Paul L. E. Bodelier, Meina Neumann-Schaal
Summary: This study presents two strains affiliated with the GKS98 cluster. Phylogenetic analysis suggests that these strains are closely related to the family Alcaligenaceae and previously described species Orrella amnicola and Orrella marina. Based on the phylogenomic trees and other characteristics, the authors propose the establishment of new genera Zwartia gen. nov. and Jezberella gen. nov., and the reclassification of Orrella amnicola into the new genus Sheuella gen. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Ecology
Masaru Konishi Nobu, Ryosuke Nakai, Satoshi Tamazawa, Hiroshi Mori, Atsushi Toyoda, Akira Ijiri, Shino Suzuki, Ken Kurokawa, Yoichi Kamagata, Hideyuki Tamaki
Summary: The serpentinization of ultramafic rocks can provide molecular hydrogen (H-2) for microorganisms, but the conditions in these environments are extremely challenging. Through metagenomics and thermodynamics, researchers have discovered unique microbial taxa in serpentinization-active systems that are adapted to these conditions. These microorganisms utilize alternative modes of H-2-utilizing lithotrophy, specifically using reduced carbon compounds rather than CO2. This research sheds light on potential strategies that extremophiles may employ in serpentinization-associated environments, which could also be relevant to primordial lithotrophy on early Earth.
Article
Microbiology
Kyohei Kuroda, Kyosuke Yamamoto, Ryosuke Nakai, Yuga Hirakata, Kengo Kubota, Masaru K. Nobu, Takashi Narihiro
Summary: Ca. Patescibacteria is a highly diverse group of bacteria that has symbiotic or parasitic relationships with other bacteria or even eukarya. By amending wastewater treatment sludge samples, researchers discovered a novel cross-domain parasitic interaction between Ca. Patescibacteria and an isolate archaeon closely related to a methanogen population. This finding sheds light on the potential strategies for culturing Ca. Patescibacteria and highlights the importance of cross-domain symbiosis.
Review
Microbiology
Zichen He, Takeshi Naganuma
Summary: Lichens are symbiotic systems consisting of fungal and algal symbionts. The plasticity in the combination of fungal and algal species contributes to the worldwide distribution of lichens, while the association between non-cyanobacterial bacteria and lichens has attracted attention.
Article
Microbiology
Akio Ueno, Satoshi Tamazawa, Shuji Tamamura, Takuma Murakami, Tamotsu Kiyama, Hidenori Inomata, Noritaka Aramaki, Kunihiko Yoshida, Shinji Yamaguchi, Hideo Aoyama, Takeshi Naganuma, Toshifumi Igarashi
Summary: This study reported the effective conversion of chemically solubilized lignite into methane using methanogenic consortia. Adding pulverized lignite as conductive material significantly increased methane production by approximately 50-fold. This method provides an effective utilization of the neglected subterranean lignite resource.
Article
Microbiology
Sho Shimada, Kotaro Aoki, Ryosuke Nakai, Shota Miura, Kohji Komori, Sakae Kudoh, Satoshi Imura, Yoshikazu Ishii, Kazuhiro Tateda
Summary: We report the whole-genome sequences of three psychrotolerant Mycolicibacterium strains, TUM20983, TUM20984, and TUM20985, isolated from Antarctic soils. Taxonomic analyses indicate that these strains are putative new species. These genome sequences may provide insight into the cold adaptation mechanisms of Mycolicibacterium spp. through future comparative genomic studies.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Sho Shimada, Ryosuke Nakai, Kotaro Aoki, Shota Miura, Kohji Komori, Sakae Kudoh, Satoshi Imura, Yoshikazu Ishii, Kazuhiro Tateda
Summary: In this study, the complete genome sequence of Polynucleobacter sp. strain TUM22923, isolated from Antarctic lake sediment, was reported. The genome of this strain is 1,860,127 bp in length, consisting of 1,848 protein-coding sequences. These data provide insights into the genome streamlining and low-temperature adaptation mechanisms in members of the cosmopolitan group of ultramicrobacteria, Polynucleobacter.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biotechnology & Applied Microbiology
Shuka Kagemasa, Kyohei Kuroda, Ryosuke Nakai, Yu-You Li, Kengo Kubota
Summary: This study reveals a higher diversity of Ca. Patescibacteria in activated sludge than previously expected through genetic analysis.
MICROBES AND ENVIRONMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Kyohei Kuroda, Kengo Kubota, Shuka Kagemasa, Ryosuke Nakai, Yuga Hirakata, Kyosuke Yamamoto, Masaru K. Nobu, Takashi Narihiro
Summary: This study identified a previously unseen symbiosis between Ca. Patescibacteria and Archaea by using fluorescence in situ hybridization and transmission electron microscopy. The 32-520/UBA5633 cells were found to specifically adhere to Methanospirillum, and the metagenome-assembled genomes of these cells encoded unique gene clusters.
MICROBES AND ENVIRONMENTS
(2022)