Department of Neuromuscular Research, National Center of Neurology and Psychiatry (NCNP), National Institute of Neuroscience, 4-1-1 Ogawahigashi, Tokyo 187-8502, Japan; Medical Genome Center, NCNP, Tokyo, Kodaira, Japan. Electronic address: nishino@ncnp.go.jp.
INSERM, GIN-U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, University Grenoble Alpes, Bat EJ Safra, Chemin Fortuné Ferrini, La Tronche, Grenoble, France.
INSERM, GIN-U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, University Grenoble Alpes, Bat EJ Safra, Chemin Fortuné Ferrini, La Tronche, Grenoble, France.
Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 187-8502 Tokyo, Japan; Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, 187-8551 Tokyo, Japan.
From the Department of Learning, Informatics and Medical Education, Karolinska Institutet; Function Area Occupational Therapy and Physical Therapy, Allied Health Professionals Function, Karolinska University Hospital, Department of Neurobiology, Care Science and Society, Division of Physiotherapy and Department of Medicine, Karolinska Institutet; Division of Rheumatology, Rheumatology Unit, Department of Medicine, Karolinska Institutet, Solna, Sweden; Division of Rheumatology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Division of Rheumatology, Department of Internal Medicine, Medical Research Center, College of Medicine, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul, Korea; Division of Rheumatology, Fiona Stanley Hospital, Institute for Immunology and Infectious Diseases, Murdoch University, Perth; The Notre Dame University Fremantle, Fremantle, Australia; Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam, the Netherlands; Center for Global Health, University of Ottawa, Ottawa, Ontario, Canada.
M. Regardt, PhD, Occupational Therapist, Department of Learning, Informatics and Medical Education, Karolinska Institutet, and Function Area Occupational Therapy and Physical Therapy, Allied Health Professionals Function, Karolinska University Hospital; C.A. Mecoli, MD, Division of Rheumatology, Department of Medicine, Johns Hopkins University; J.K. Park, MD, PhD, Division of Rheumatology, Department of Internal Medicine, Seoul National University Hospital; I. de Groot, Patient Research Partner; C. Sarver, Patient Research Partner; M. Needham, MD, Division of Rheumatology, Fiona Stanley Hospital, Institute for Immunology and Infectious Diseases, Murdoch University, and The Notre Dame University; M. de Visser, MD, PhD, Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience; B. Shea, MSN, Center for Global Health, University of Ottawa; C.O. Bingham III, MD, Division of Rheumatology, Department of Medicine, Johns Hopkins University; I.E. Lundberg, MD, PhD, Division of Rheumatology, Rheumatology Unit, Department of Medicine, Karolinska Institutet; Y.W. Song, MD, PhD, Division of Rheumatology, Department of Internal Medicine, Medical Research Center, College of Medicine, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University; L. Christopher-Stine, MD, Division of Rheumatology, Department of Medicine, Johns Hopkins University; H. Alexanderson, PhD, Physiotherapist, Department of Neurobiology, Care Science and Society, Division of Physiotherapy and Department of Medicine Solna, Karolinska Institutet, and Function Area Occupational Therapy and Physical Therapy, Allied Health Professionals Function, Karolinska University Hospital. M. Regardt and Dr. C. Mecoli are co-first authors.
Department of Neuromuscular Research, National Center of Neurology and Psychiatry (NCNP), National Institute of Neuroscience, 4-1-1 Ogawahigashi, Tokyo 187-8502, Japan; Medical Genome Center, NCNP, Tokyo, Kodaira, Japan; Department of Pediatrics, Showa General Hospital, Tokyo, Kodaira, Japan.
INSERM, GIN-U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, University Grenoble Alpes, Bat EJ Safra, Chemin Fortuné Ferrini, La Tronche, Grenoble, France.
INSERM, GIN-U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, University Grenoble Alpes, Bat EJ Safra, Chemin Fortuné Ferrini, La Tronche, Grenoble, France. isabelle.marty@univ-grenoble-alpes.fr.
Neuromuscular Morphology Unit, Myology Institute, Groupe Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France. matteo.garibaldi@uniroma1.it.
Unit of Neuromuscular Diseases, Neuromuscular Disease Centre, Department of Neurology Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, SAPIENZA University of Rome, Sant'Andrea Hospital, Via di Grottarossa 1035-1039, 00189, Rome, Italy. matteo.garibaldi@uniroma1.it.
Service Neurologie Médicale, Centre de Référence Maladies Neuromusculaire Paris-Est-Ile de France, CHU Raymond-Poincaré Paris Ouest, Garches, France.
U1179 UVSQ-INSERM Handicap Neuromusculaire: Physiologie, Biothérapie et Pharmacologie appliquées, UFR des sciences de la santé Simone Veil, Université Versailles-Saint-Quentin-en-Yvelines, Versailles, France.
Unit of Neuromuscular Diseases, Neuromuscular Disease Centre, Department of Neurology Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, SAPIENZA University of Rome, Sant'Andrea Hospital, Via di Grottarossa 1035-1039, 00189, Rome, Italy.
Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in f...
Total DNA was extracted from the leaves of four species of the Coffeeae tribe (...
All four species have non-nodulated leaf endophytes, which are identified as...
With the development and reduced costs of high-throughput sequencing technology, environmental dark matter, such as novel metagenome-assembled genomes (MAGs) and viruses, is now being discovered easil...
Patients who were infected by the...
The 122 HIV-infected patients were enrolled for the retrospective analysis. All of the patients underwent traditional microbiological tests, mNGS, and (or) mNPS tests. The clinical comprehensive diagn...
Compared with the composite reference standard, the culture showed 42.6% clinical sensitivity and 100% specificity, and the OMT(other microbiological testing) had 38.9% sensitivity and 100% specificit...
Our study indicated that mNPS and mNGS have high sensitivity and specificity for TB diagnosis compared with the traditional methods, and mNPS seems to have better diagnostic performance than mNGS. Mor...
Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availabili...
Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the ...
UMGAP's protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spe...
The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review consi...
Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enable...
Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output fr...
The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun met...
The mining of genomes from non-cultivated microorganisms using metagenomics is a powerful tool to discover novel proteins and other valuable biomolecules. However, function-based metagenome searches a...
Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional a...
The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing ...
Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated...
Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and bi...
Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their ...
