Article
Microbiology
Guan Liu, Xia Yu, Jingjing Luo, Yanjie Hu, Lingling Dong, Guanglu Jiang, Fengmin Huo, Fen Wang, Qian Liang, Hairong Huang
Summary: A novel slow-growing scotochromogenic mycobacterial strain (24(T)) isolated from a Chinese male human's sputum was identified through phylogenetic analysis and genomic comparisons, and proposed to be named as Mycobacterium vicinigordonae sp. nov. based on its distinct phylogenetic, phenotypic, and chemotaxonomic features.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Hanako Fukano, Yuko Kazumi, Nobuya Sakagami, Nagatoshi Fujiwara, Manabu Ato, Satoshi Mitarai, Yoshihiko Hoshino
Summary: In this study, a novel species of slow-growing mycobacteria related to the Mycobacterium gordonae complex was discovered from respiratory samples of patients in Japan. The genomic and phenotypic characteristics of the isolates were analyzed, and it was proposed that they represent a new species named 'Mycobacterium kiyosense sp. nov.'
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Yuko Abe, Kiyoharu Fukushima, Yuki Matsumoto, Takayuki Niitsu, Hiroshi Nabeshima, Yasuharu Nagahama, Eri Akiba, Kako Haduki, Haruko Saito, Tadayoshi Nitta, Akira Kawano, Michio Tanaka, Takanori Matsuki, Daisuke Motooka, Kazuyuki Tsujino, Keisuke Miki, Shota Nakamura, Tetsuya Iida, Hiroshi Kida
Summary: A slowly growing mycobacteria, named Mycobacterium senriense sp. nov., was isolated from a patient with pneumonia, which is a novel species closely related to Mycobacterium avium complex.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Keisuke Kamada, Atsushi Yoshida, Shigekazu Iguchi, Yuko Arai, Yutaka Uzawa, Satoshi Konno, Masahiro Shimojima, Ken Kikuchi
Summary: This study aimed to identify effective treatments against rapidly growing mycobacteria (RGM) infections by investigating the minimum inhibitory concentrations (MIC) of 24 antimicrobial agents and their molecular mechanisms of resistance. The study identified 15 RGM species isolated in Japan and indicated that arbekacin, sitafloxacin, and rifabutin may be possible therapeutic options for RGM infections.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Lingmin Jiang, Yuxin Peng, Jiyoon Seo, Doeun Jeon, Mi Gyeong Jo, Ju Huck Lee, Jae Cheol Jeong, Cha Young Kim, Hyeong Cheol Park, Jiyoung Lee
Summary: A novel strain of bacteria AK-R2A1-2(T) was isolated from the needle leaves of Abies koreana tree and its genome was sequenced. The results showed that this strain can survive at low temperatures and significantly improve the growth of rice seedlings.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Aurelie Morand, Mamadou Lamine Tall, Edmond Kuete Yimagou, Issa Isaac Ngom, Cheikh Ibrahima Lo, Florent Cornu, Michel Tsimaratos, Jean-Christophe Lagier, Anthony Levasseur, Didier Raoult, Pierre-Edouard Fournier
Summary: This study describes a new species Anaerococcus urinomassiliensis, isolated from the urine of a 17-year-old boy with autoimmune hepatitis and membranoproliferative glomerulonephritis. The strain exhibits specific genetic characteristics, is primarily of human origin, and belongs to the genus of anaerobic bacteria.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Chi Young Hwang, Sung Man Seo, Eui-Sang Cho, Young-Do Nam, So-Lim Park, Seong-Il Lim, Myung-Ji Seo
Summary: In this study, a novel bacterial strain MBLB1776(T) was isolated from marine mud in Uljin, the Republic of Korea. The strain was identified as a new species within the genus Paenibacillus, named Paenibacillus aurantius sp. nov. It was found that MBLB1776(T) produced carotenoid pigments, giving the cells an orange color.
Article
Multidisciplinary Sciences
Tomoaki Kouya, Yohei Ishiyama, Shota Ohashi, Ryota Kumakubo, Takeshi Yamazaki, Toshiki Otaki
Summary: In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. The bacterium belongs to the fructophilic, acidophilic, and hard-to-grow group, and it is most closely related to Apilactobacillus ozensis based on 16S rRNA gene sequence analysis. Based on the characteristics of strain WR16-4(T), it is proposed to be classified as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.
Article
Environmental Sciences
Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
Summary: Five novel halophilic archaeal strains were isolated from coastal saline sediments and sea salt in China. They demonstrated typical morphology and growth characteristics and showed high similarities with existing species. However, based on genetic and phylogenetic analyses, it is confirmed that these strains represent five new species. This is the first report of a novel haloarchaeon isolated from a marine intertidal zone.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Microbiology
Yoshiaki Kawamura, Yuko Fujimoto, Ryo Kutsuna, Junko Tomida, Kei-ichi Yamamoto, Tohru Miyoshi-Akiyama, Miki Okuno, Yoshitoshi Ogura, Masao Matsuoka, Tatusya Kawaguchi, Hiroyasu Tsutsuki, Tomohiro Sawa
Summary: A novel species of spiral bacterium, Helicobacter kumamotonensis sp. nov., was isolated from the blood of a patient with diffuse large B-cell lymphoma. It is phylogenetically closely related to Helicobacter equorum but forms a distinct lineage. The human isolates can be distinguished from H. equorum by flagella type and biochemical characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Emily Musser, Carol Smith, Tanya A. A. Halse, Donna Kohlerschmidt, Amy Rourke, Alexandra Fiero, Kimberlee A. A. Musser, Vincent Escuyer, Pascal Lapierre
Summary: Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water worldwide. This study identifies a new NTM species isolated from a hand laceration of a patient in New York State. This new NTM has distinct colony morphology and resistance to certain antibiotics, and it is not closely related to any known species in public databases. The authors propose the name Mycobacterium salfingeri sp. nov. for this new NTM representative.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Joo Hyun Han, Sang Eun Lee, Sathiyaraj Srinivasan
Summary: Strain 18JY21-1(T) is a novel species of Paenibacillus, named Paenibacillus albiflavus sp. nov., based on phylogenetic, chemotaxonomic, and phenotypic data analysis.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Shin Ae Lee, Tae-Wan Kim, Mee-Kyung Sang, Jaekyeong Song, Soon-Wo Kwon, Hang-Yeon Weon
Summary: KIS59-12(T) is a novel bacterium isolated from soil in Hodo island, Boryeong, Republic of Korea, belonging to the genus Arachidicoccus and proposed to be named Arachidicoccus soli sp. nov. It shares high sequence similarities with other Arachidicoccus species, while showing differences in genomic and chemotaxonomic characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Mario Hoenemann, Adrian Viehweger, Nadine Dietze, Julia Johnke, Arne C. Rodloff
Summary: This article describes the characterization and naming of a new strain, Leclercia pneumoniae sp. nov., isolated from an infant with pneumonia and septicaemia.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Jihane Kabtani, Muriel Militello, Stephane Ranque
Summary: The genus Coniochaeta belongs to the class Ascomycota and the family Coniochaetaceae. Some species are plant and animal pathogens, while others are involved in human diseases. A new species, Coniochaeta massiliensis, was described and characterised, with genetic and phenotypic analysis showing its uniqueness compared to other species in the genus.
Article
Polymer Science
Farzaneh Firoozeh, Abed Neshan, Azad Khaledi, Mohammad Zibaei, Ala Amiri, Ali Sobhani, Farzad Badmasti, Vajihe Sadat Nikbin
Summary: The synthesized magnetic nanoparticles were used to extract high-quality genomic DNA from Escherichia coli, and the coated nanoparticles showed higher purity and concentration compared to naked nanoparticles.
Article
Veterinary Sciences
Maryam Rahravani, Meysam Moravedji, Ehsan Mostafavi, Mehrdad Mohammadi, Hamid Seyfi, Neda Baseri, Mohammad Mahdi Mozoun, Mina Latifian, Saber Esmaeili
Summary: This study investigated C. burnetii infection in small ruminants and their ticks in western Iran. Results showed the presence of C. burnetii DNA in the samples, indicating a possible role of ticks in the epidemiology of Q fever in Iran.
BMC VETERINARY RESEARCH
(2022)
Article
Parasitology
Saber Esmaeili, Ahmad Ghasemi, Parisa Esmaeili, Farshid Rezaie, Minoo Mohraz, Max Maurin, Ehsan Mostafavi
Summary: This article reports an unusual case of tularemia and highlights the neglect of this disease by the healthcare system in some countries. It emphasizes the need to increase awareness among physicians about tularemia.
Article
Genetics & Heredity
Federica Esposito, Ana Maria Osiceanu, Melissa Sorosina, Linda Ottoboni, Bryan Bollman, Silvia Santoro, Barbara Bettegazzi, Andrea Zauli, Ferdinando Clarelli, Elisabetta Mascia, Andrea Calabria, Daniele Zacchetti, Ruggero Capra, Maurizio Ferrari, Paolo Provero, Dejan Lazarevic, Davide Cittaro, Paola Carrera, Nikolaos Patsopoulos, Daniela Toniolo, A. Dessa Sadovnick, Gianvito Martino, Philip L. De Jager, Giancarlo Comi, Elia Stupka, Carles Vilarino-Guell, Laura Piccio, Filippo Martinelli Boneschi
Summary: A novel variant in the GRAMD1B gene was identified through whole-genome sequencing in a familial MS case, suggesting its potential involvement in disease pathophysiology and modulation of inflammatory response.
Article
Genetics & Heredity
Edoardo Luigi Draetta, Dejan Lazarevic, Paolo Provero, Davide Cittaro
Summary: Through high-throughput sequencing techniques, we discovered that genes with high frequency of somatic mutations in common cancers and ancient evolutionary age are most likely to be involved in abnormal phenotypes and diseases. This provides new insights into the common origin of cancer and genetic diseases and improves the identification of new disease genes.
FRONTIERS IN GENETICS
(2023)
Article
Immunology
Mohammad Hashemzadeh, Aram Asareh Zadegan Dezfuli, Azar Dokht Khosravi, Nazanin Ahmad Khosravi, Abdorazagh Hashemi Shahraki
Summary: This study aimed to identify the drug susceptibility and mutations related to clarithromycin and linezolid resistance in clinical isolates of Mycobacterium fortuitum in Iran. The results showed that 64% of M. fortuitum isolates were resistant to clarithromycin and 18% were resistant to linezolid. DNA sequencing revealed multiple mutations in the erm(39) gene and rrl gene. These findings indicate a high level of antibiotic resistance in M. fortuitum isolates.
ACTA MICROBIOLOGICA ET IMMUNOLOGICA HUNGARICA
(2023)
Article
Biochemistry & Molecular Biology
Giulia Unali, Giovanni Crivicich, Isabel Pagani, Monah Abou-Alezz, Filippo Folchini, Erika Valeri, Vittoria Matafora, Julie A. Reisz, Anna Maria Sole Giordano, Ivan Cuccovillo, Giacomo M. Butta, Lorena Donnici, Angelo D'Alessandro, Raffaele De Francesco, Lara Manganaro, Davide Cittaro, Ivan Merelli, Carolina Petrillo, Angela Bachi, Elisa Vicenzi, Anna Kajaste-Rudnitski
Summary: The interferon-induced transmembrane proteins (IFITM) inhibit endocytic viral entry by binding to phosphatidylinositol 3,4,5-trisphosphate (PIP3), which plays a key role in endosomal antiviral immunity. The level of PIP3 is closely correlated with the potency of endosomal IFITM restriction, and exogenous PIP3 enhances the inhibition of endocytic viruses. These findings elucidate cell-compartment-specific antiviral mechanisms and have potential relevance for the development of broadly acting antiviral strategies.
Article
Microbiology
Federico Di Marco, Andrea Spitaleri, Simone Battaglia, Virginia Batignani, Andrea Maurizio Cabibbe, Daniela Maria Cirillo
Summary: This study compared the performances of short-reads (SRS), long-reads (LRS), and hybrid-reads (HYBR) in various investigative tasks in Mycobacterium tuberculosis (MTB) genome analysis. The results showed that HYBR exhibited the best performance in genome coverage estimation and variant calling, and also had better assembly quality compared to SRS and LRS. Therefore, the use of HYBR technology can provide a comprehensive resolution of the MTB genome and achieve more accurate analysis results.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Roshan Dinparastisaleh, Mehdi Mirsaeidi
Summary: In this study, we introduce UF_RH5, a novel lytic phage that targets clinically isolated Pseudomonas aeruginosa. It belongs to the Siphovirus morphology family, Septimatrevirus genus, with a 42,566-bp genome and a GC content of 53.60%, encoding 58 proteins. Under electron microscopy, UF_RH5 is observed to have a length of 121 nm and a capsid size of 45 nm.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Mehdi Mirsaeidi
Summary: Here, the genome sequence of a new Pseudomonas aeruginosa bacteriophage, UF_RH1, is presented. This lytic phage has a genome size of 42,567 bp and belongs to the Siphoviridae family and Septimatrevirus genus. UF_RH1 shows genetic similarities with Stenotrophomonas phage vB_SmaS-DLP_2.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Abdolrazagh Hashemi Shahraki, Majid Vahed, Shahla Masood, Mehdi Mirsaeidi
Summary: We present the genome sequence of a lytic phage, UF_RH6, that infects Pseudomonas aeruginosa. This phage was isolated from a respiratory secretion sample obtained from a patient with pulmonary P. aeruginosa. UF_RH6 belongs to the Caudoviricetes family and the Samunavirus genus. The genome of UF_RH6 is 94,715 bp long and encodes 130 proteins.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biochemical Research Methods
Davide Cittaro, Dejan Lazarevic, Giovanni Tonon, Francesca Giannese
Summary: scGET-seq is a method that profiles both euchromatin and heterochromatin simultaneously. It utilizes the combined action of transposase Tn5 and its hybrid form TnH, which specifically targets H3K9me3 domains. This article provides a step-by-step protocol for performing scGET-seq on single cells using a 103 Chromium Controller, including transposome preparation and validation, nuclei preparation and transposition, encapsulation, library preparation, sequencing, and data analysis.
Article
Environmental Sciences
Javad Sadeghi, Abdolrazagh Hashemi Shahraki, Subba Rao Chaganti, Daniel Heath
Summary: This study used metatranscriptomics to investigate the gene transcription variation of freshwater bacterial communities across three seasons in Ontario, Canada. The results showed high transcriptional activity in summer and fall, and surprisingly, a significant portion of genes associated with physiological and ecological activity remained active in freezing temperatures during winter. The study provides a baseline for further research on freshwater bacterial communities, health-related microbial activity/dormancy, and the factors driving their functional variation.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Sana Eybpoosh, Alireza Biglari, Rahim Sorouri, Fatemeh Ashrafian, Mona Sadat Larijani, Vicente Verez-Bencomo, Maria Eugenia Toledo-Romani, Carmen Valenzuela Silva, Mostafa Salehi-Vaziri, Sarah Dahmardeh, Delaram Doroud, Mohammad Banifazl, Ehsan Mostafavi, Anahita Bavand, Amitis Ramezani
Summary: This study evaluated and compared the efficacy of PastoCovac Plus protein-subunit vaccine with ChAdOx1-S and BBIBP-CorV in volunteers who had been primed with two doses of ChAdOx1-S or BBIBP-CorV vaccines. The results showed that PastoCovac Plus effectively increased specific antibody levels and could be used in heterologous regimens to boost humoral immune responses.
Article
Biology
Tommaso Lanciano, Aurora Savino, Francesca Porcu, Davide Cittaro, Francesco Bonchi, Paolo Provero
Summary: Biological networks are widely used in functional genomics to describe relationships between genes and proteins. Contrast subgraphs are an effective technique for comparing networks from different conditions or techniques. This study demonstrates the utility of contrast subgraphs in comparing gene and protein networks in breast cancer subtypes, transcriptomic and proteomic data, and protein-protein interaction networks in different cell lines.